[outreach] Help trying to create R package

[outreach] Help trying to create R package

[Laura Lazzati]

 Hi!
I'm creating a new thread so that it does not end up messy.
I am reading about defining new packages, and since I have always
installed R with apt, I am trying to do so with ./configure make make
install to have it running on my VM, and then try to create the
package and check if both works

I am having trouble with the ./configure part. I find missing
dependencies, that I try to solve using guix package -i PACKAGE

I am running

 ./configure --with-readline=no --with-x=no

First I faced not having gfortran, so I run
guix install -i fortran
ran ./configure again, and ended up installing
zlib and bzlip2 (both with guix package)
Now, after running ./configure, I get the error:
configure: error: "liblzma library and headers are required"
but I cannot find that with guix package.
Any Ideas about what I should do?

besides, I don't  know why I still get every time I run guix package
-i, for instance:
The following package will be installed:
   bzip2    1.0.6    /gnu/store/rw1ilvs76rf2p4p0bi1fx3bffprwwb7g-bzip2-1.0.6

substitute: guile: warning: failed to install locale
substitute: hint: Consider installing the `glibc-utf8-locales' or
`glibc-locales' package and
substitute: defining `GUIX_LOCPATH', along these lines:
substitute:
substitute:      guix package -i glibc-utf8-locales
substitute:      export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
substitute:
substitute: See the "Application Setup" section in the manual, for more info.

When I run guix package -I I get:
hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
recutils    1.7    out
/gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
glibc-locales    2.27    out
/gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
glibc-utf8-locales    2.27    out
/gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
gfortran    7.3.0    out
/gnu/store/mw65pcca7x7mmq8v2r427f3plrahhyxl-gfortran-7.3.0
zlib    1.2.11    out    /gnu/store/fxiwj2wpp11sif613axdax7gmwzsg6kp-zlib-1.2.11
bzip2    1.0.6    out    /gnu/store/rw1ilvs76rf2p4p0bi1fx3bffprwwb7g-bzip2-1.0.6

And even at the bottom of my .bashrc I have:

  export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
    export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
    export CPATH="/home/laura/.guix-profile/include${CPATH:+:}$CPATH"
    export LIBRARY_PATH="/home/laura/.guix-profile/lib${LIBRARY_PATH:+:}$LIBRARY_PATH"

Could you help me clarify this?

-Recall I am running everything under an Ubuntu distro -
Regards,
Laura

Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Hello Laura,

Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
okt. 13., Szo, 15:37):
>
>  Hi!
> I'm creating a new thread so that it does not end up messy.
> I am reading about defining new packages, and since I have always
> installed R with apt, I am trying to do so with ./configure make make
> install to have it running on my VM, and then try to create the
> package and check if both works
>

It seems to me that there is some misunderstanding. R, the language itself is
packaged:
(see the variable r-with-test near the top of
gnu/packages/statistics.scm, if you are interested, but I would leave
that for later).
You should try packaging some R package, for example from CRAN.
See https://cran.r-project.org/web/packages/available_packages_by_name.html for
a package list. Please select something that is not already packaged. R packages
in guix are named like r-*. Once you have a candidate, you can use the
cran importer
to generate the package definition.

See it here: https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-import.html

> I am having trouble with the ./configure part. I find missing
> dependencies, that I try to solve using guix package -i PACKAGE
>
> I am running
>
>  ./configure --with-readline=no --with-x=no
>
> First I faced not having gfortran, so I run
> guix install -i fortran
> ran ./configure again, and ended up installing
> zlib and bzlip2 (both with guix package)
> Now, after running ./configure, I get the error:
> configure: error: "liblzma library and headers are required"
> but I cannot find that with guix package.
> Any Ideas about what I should do?
>

Most probably what you are looking for is provided by package xz, but
as I said, you don't need this.

> besides, I don't  know why I still get every time I run guix package
> -i, for instance:
> The following package will be installed:
>    bzip2    1.0.6    /gnu/store/rw1ilvs76rf2p4p0bi1fx3bffprwwb7g-bzip2-1.0.6
>
> substitute: guile: warning: failed to install locale
> substitute: hint: Consider installing the `glibc-utf8-locales' or
> `glibc-locales' package and
> substitute: defining `GUIX_LOCPATH', along these lines:
> substitute:
> substitute:      guix package -i glibc-utf8-locales
> substitute:      export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
> substitute:
> substitute: See the "Application Setup" section in the manual, for more info.
>
> When I run guix package -I I get:
> hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> recutils    1.7    out
> /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> glibc-locales    2.27    out
> /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> glibc-utf8-locales    2.27    out
> /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> gfortran    7.3.0    out
> /gnu/store/mw65pcca7x7mmq8v2r427f3plrahhyxl-gfortran-7.3.0
> zlib    1.2.11    out    /gnu/store/fxiwj2wpp11sif613axdax7gmwzsg6kp-zlib-1.2.11
> bzip2    1.0.6    out    /gnu/store/rw1ilvs76rf2p4p0bi1fx3bffprwwb7g-bzip2-1.0.6
>
> And even at the bottom of my .bashrc I have:
>
>   export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
>     export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
>     export CPATH="/home/laura/.guix-profile/include${CPATH:+:}$CPATH"
>     export LIBRARY_PATH="/home/laura/.guix-profile/lib${LIBRARY_PATH:+:}$LIBRARY_PATH"
>
> Could you help me clarify this?
>

I will have a look at this, and get back to you, but this is not
critical ,you can go on with packaging.

> -Recall I am running everything under an Ubuntu distro -
> Regards,
> Laura

Re: [outreach] Help trying to create R package

[Catonano]

[-- Attachment #1: Type: text/plain, Size: 3395 bytes --]

Hi Laura !

Il giorno sab 13 ott 2018 alle ore 15:37 Laura Lazzati <
laura.lazzati.15@gmail.com> ha scritto:
>
>  Hi!
> I'm creating a new thread so that it does not end up messy.
> I am reading about defining new packages, and since I have always
> installed R with apt, I am trying to do so with ./configure make make
> install to have it running on my VM, and then try to create the
> package and check if both works

you don't need to package R yourself, R is already packaged and available
in Guix, i believe.

If you want to package a R based package for Guix you can use the so called
Cran importer

Try this line at the prompt

guix import cran your-R-package

This line invokes a so called importer and the importer should return you
the recipe of your R package written in scheme

You could append such definition to an existing Guix file (probably with
some minor tweaks) and that should allow you to build the package and all
the dependencies will be taken care of automatically

I did this myself some time ago

In order to append the definition of your package to an existing Guix file
you will probably need some more guidance, but for now you could just run
the importer and let us now what you obtained

Probably you'll need to build the package, then modify the recipe a bit,
build it again... for a few times; that's ok

You can read about the importers here

https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-import.html#Invoking-guix-import


> substitute: guile: warning: failed to install locale
> substitute: hint: Consider installing the `glibc-utf8-locales' or
> `glibc-locales' package and
> substitute: defining `GUIX_LOCPATH', along these lines:
> substitute:
> substitute:      guix package -i glibc-utf8-locales
> substitute:      export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
> substitute:
> substitute: See the "Application Setup" section in the manual, for more
info.
>
> When I run guix package -I I get:
> hello    2.10    out
 /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> recutils    1.7    out
> /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> glibc-locales    2.27    out
> /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> glibc-utf8-locales    2.27    out
> /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> gfortran    7.3.0    out
> /gnu/store/mw65pcca7x7mmq8v2r427f3plrahhyxl-gfortran-7.3.0
> zlib    1.2.11    out
 /gnu/store/fxiwj2wpp11sif613axdax7gmwzsg6kp-zlib-1.2.11
> bzip2    1.0.6    out
 /gnu/store/rw1ilvs76rf2p4p0bi1fx3bffprwwb7g-bzip2-1.0.6
>
> And even at the bottom of my .bashrc I have:
>
>   export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
>     export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
>     export CPATH="/home/laura/.guix-profile/include${CPATH:+:}$CPATH"
>     export
LIBRARY_PATH="/home/laura/.guix-profile/lib${LIBRARY_PATH:+:}$LIBRARY_PATH"

when running Guix on top of a foreign distribution, this problem is very
common.
I lived with this for several months myself

Reaching a solution to this can be tedious and often the solutions are
short lived

Because this has to do with how the basic C libraries provided by Guix and
those provided by the foreign distro relate with each other (usually not so
well)

But this is not critical, you can successfully package some R based
packages for Guix anyway

Hope this helps !

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Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Sat, Oct 13, 2018 at 3:25 PM Catonano <catonano@gmail.com> wrote:
>
> Hi Laura !
>
> Il giorno sab 13 ott 2018 alle ore 15:37 Laura Lazzati <laura.lazzati.15@gmail.com> ha scritto:
> >
> >  Hi!
> > I'm creating a new thread so that it does not end up messy.
> > I am reading about defining new packages, and since I have always
> > installed R with apt, I am trying to do so with ./configure make make
> > install to have it running on my VM, and then try to create the
> > package and check if both works
>
> you don't need to package R yourself, R is already packaged and available in Guix, i believe.
>
> If you want to package a R based package for Guix you can use the so called Cran importer
>
> Try this line at the prompt
>
> guix import cran your-R-package
>
> This line invokes a so called importer and the importer should return you the recipe of your R package written in scheme
>
> You could append such definition to an existing Guix file (probably with some minor tweaks) and that should allow you to build the package and all the dependencies will be taken care of automatically
>
> I did this myself some time ago
>
> In order to append the definition of your package to an existing Guix file you will probably need some more guidance, but for now you could just run the importer and let us now what you obtained
>
> Probably you'll need to build the package, then modify the recipe a bit, build it again... for a few times; that's ok
>
> You can read about the importers here
>
> https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-import.html#Invoking-guix-import
>
Thanks both of you for helping with this, since I was reading all the
reference guide  to see how to create a package for whole R while
thinking that there is no time for that.
>
> > substitute: guile: warning: failed to install locale
> > substitute: hint: Consider installing the `glibc-utf8-locales' or
> > `glibc-locales' package and
> > substitute: defining `GUIX_LOCPATH', along these lines:
> > substitute:
> > substitute:      guix package -i glibc-utf8-locales
> > substitute:      export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
> > substitute:
> > substitute: See the "Application Setup" section in the manual, for more info.
> >
> > When I run guix package -I I get:
> > hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> > recutils    1.7    out
> > /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> > glibc-locales    2.27    out
> > /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> > glibc-utf8-locales    2.27    out
> > /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> > gfortran    7.3.0    out
> > /gnu/store/mw65pcca7x7mmq8v2r427f3plrahhyxl-gfortran-7.3.0
> > zlib    1.2.11    out    /gnu/store/fxiwj2wpp11sif613axdax7gmwzsg6kp-zlib-1.2.11
> > bzip2    1.0.6    out    /gnu/store/rw1ilvs76rf2p4p0bi1fx3bffprwwb7g-bzip2-1.0.6
> >
> > And even at the bottom of my .bashrc I have:
> >
> >   export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
> >     export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> >     export CPATH="/home/laura/.guix-profile/include${CPATH:+:}$CPATH"
> >     export LIBRARY_PATH="/home/laura/.guix-profile/lib${LIBRARY_PATH:+:}$LIBRARY_PATH"
>
> when running Guix on top of a foreign distribution, this problem is very common.
> I lived with this for several months myself
>
> Reaching a solution to this can be tedious and often the solutions are short lived
>
> Because this has to do with how the basic C libraries provided by Guix and those provided by the foreign distro relate with each other (usually not so well)
>
> But this is not critical, you can successfully package some R based packages for Guix anyway
Thank you for this too , I have been stuck with it without knowing
"why is this happening if I have already exported, sourced just in
case" and so on. It is a warning and things end up installed but you
never know if it can affect something else.
>
> Hope this helps !

Re: [outreach] Help trying to create R package

[Laura Lazzati]

Hi!
I don't know why when I reppied to all in my last mail some of you
were not included

On Sat, Oct 13, 2018 at 9:40 PM Laura Lazzati
<laura.lazzati.15@gmail.com> wrote:
>
> On Sat, Oct 13, 2018 at 3:25 PM Catonano <catonano@gmail.com> wrote:
> >
> > Hi Laura !
> >
> > Il giorno sab 13 ott 2018 alle ore 15:37 Laura Lazzati <laura.lazzati.15@gmail.com> ha scritto:
> > >
> > >  Hi!
> > > I'm creating a new thread so that it does not end up messy.
> > > I am reading about defining new packages, and since I have always
> > > installed R with apt, I am trying to do so with ./configure make make
> > > install to have it running on my VM, and then try to create the
> > > package and check if both works
> >
> > you don't need to package R yourself, R is already packaged and available in Guix, i believe.
> >
> > If you want to package a R based package for Guix you can use the so called Cran importer
> >
> > Try this line at the prompt
> >
> > guix import cran your-R-package
> >
> > This line invokes a so called importer and the importer should return you the recipe of your R package written in scheme
> >
> > You could append such definition to an existing Guix file (probably with some minor tweaks) and that should allow you to build the package and all the dependencies will be taken care of automatically
> >
> > I did this myself some time ago

I've reading the documentation as well as trying some commands,and
there are some problems I am facing. I don't know what I am doing
wrong.

First, I ran:
$ guix package -s r-* | recsel -p name >> resultOfSearchingRpackages.txt
And reading the output file, I found that the packages belonging to R
that are available are:
name: r-rtracklayer
name: r-rcas
name: r-qtl
name: r-ggridges
name: r-feather
I also took a look at each of them with
$guix package --show=PACKAGENAME
Then, I tried:
$ guix import cran --archive=bioconductor tracklayer

But got this output:
acktrace:
          17 (apply-smob/1 #<catch-closure 223b160>)
In ice-9/boot-9.scm:
    705:2 16 (call-with-prompt _ _ #<procedure default-prompt-handle…>)
In ice-9/eval.scm:
    619:8 15 (_ #(#(#<directory (guile-user) 22f6140>)))
In guix/ui.scm:
  1578:12 14 (run-guix-command _ . _)
In guix/scripts/import.scm:
   114:11 13 (guix-import . _)
In guix/scripts/import/cran.scm:
   107:23 12 (guix-import-cran . _)
In guix/memoization.scm:
     98:0 11 (_ #<hash-table 28ce000 0/31> ("tracklayer" #) _)
In unknown file:
          10 (_ #<procedure 28d8d60 at guix/memoization.scm:179:32 …> …)
In guix/import/cran.scm:
   349:12  9 (_ _ _)
   183:21  8 (fetch-description _ "tracklayer")
   160:15  7 (latest-bioconductor-package-version _)
In ice-9/boot-9.scm:
    829:9  6 (catch _ _ #<procedure 7fa48a6a8218 at guix/import/cra…> …)
In guix/import/cran.scm:
   153:36  5 (_)
In ice-9/boot-9.scm:
    829:9  4 (catch _ _ #<procedure 28e0b40 at guix/http-client.scm…> …)
In guix/http-client.scm:
   182:20  3 (_)
    88:25  2 (http-fetch _ #:port _ #:text? _ #:buffered? _ # _ # _ # …)
In guix/build/download.scm:
    398:4  1 (open-connection-for-uri _ #:timeout _ # _)
    296:6  0 (tls-wrap #<closed: file 27f1690> _ # _)

guix/build/download.scm:296:6: In procedure tls-wrap:
X.509 certificate of 'bioconductor.org' could not be verified:
  signer-not-found
  invalid

I don't know what's wrong, could you give me a hand?


> > In order to append the definition of your package to an existing Guix file you will probably need some more guidance, but for now you could just run the importer and let us now what you obtained
> >
> > Probably you'll need to build the package, then modify the recipe a bit, build it again... for a few times; that's ok
> >
> > You can read about the importers here
> >
> > https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-import.html#Invoking-guix-import
> >
> Thanks both of you for helping with this, since I was reading all the
> reference guide  to see how to create a package for whole R while
> thinking that there is no time for that.
> >
> > > substitute: guile: warning: failed to install locale
> > > substitute: hint: Consider installing the `glibc-utf8-locales' or
> > > `glibc-locales' package and
> > > substitute: defining `GUIX_LOCPATH', along these lines:
> > > substitute:
> > > substitute:      guix package -i glibc-utf8-locales
> > > substitute:      export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
> > > substitute:
> > > substitute: See the "Application Setup" section in the manual, for more info.
> > >
> > > When I run guix package -I I get:
> > > hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> > > recutils    1.7    out
> > > /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> > > glibc-locales    2.27    out
> > > /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> > > glibc-utf8-locales    2.27    out
> > > /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> > > gfortran    7.3.0    out
> > > /gnu/store/mw65pcca7x7mmq8v2r427f3plrahhyxl-gfortran-7.3.0
> > > zlib    1.2.11    out    /gnu/store/fxiwj2wpp11sif613axdax7gmwzsg6kp-zlib-1.2.11
> > > bzip2    1.0.6    out    /gnu/store/rw1ilvs76rf2p4p0bi1fx3bffprwwb7g-bzip2-1.0.6
> > >
> > > And even at the bottom of my .bashrc I have:
> > >
> > >   export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
> > >     export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> > >     export CPATH="/home/laura/.guix-profile/include${CPATH:+:}$CPATH"
> > >     export LIBRARY_PATH="/home/laura/.guix-profile/lib${LIBRARY_PATH:+:}$LIBRARY_PATH"
> >
> > when running Guix on top of a foreign distribution, this problem is very common.
> > I lived with this for several months myself
> >
> > Reaching a solution to this can be tedious and often the solutions are short lived
> >
> > Because this has to do with how the basic C libraries provided by Guix and those provided by the foreign distro relate with each other (usually not so well)
> >
> > But this is not critical, you can successfully package some R based packages for Guix anyway
> Thank you for this too , I have been stuck with it without knowing
> "why is this happening if I have already exported, sourced just in
> case" and so on. It is a warning and things end up installed but you
> never know if it can affect something else.
> >
> > Hope this helps !

Regards!

Laura

Re: [outreach] Help trying to create R package

[Björn Höfling]

[-- Attachment #1: Type: text/plain, Size: 3685 bytes --]

Hi Laura,

On Mon, 15 Oct 2018 19:47:38 -0300
Laura Lazzati <laura.lazzati.15@gmail.com> wrote:

> I've reading the documentation as well as trying some commands,and
> there are some problems I am facing. I don't know what I am doing
> wrong.
> 
> First, I ran:
> $ guix package -s r-* | recsel -p name >>
> resultOfSearchingRpackages.txt And reading the output file, I found
> that the packages belonging to R that are available are:
> name: r-rtracklayer
> name: r-rcas
> name: r-qtl
> name: r-ggridges
> name: r-feather
> I also took a look at each of them with
> $guix package --show=PACKAGENAME
> Then, I tried:
> $ guix import cran --archive=bioconductor tracklayer
> 
> But got this output:
> acktrace:
>           17 (apply-smob/1 #<catch-closure 223b160>)
> In ice-9/boot-9.scm:
>     705:2 16 (call-with-prompt _ _ #<procedure
> default-prompt-handle…>) In ice-9/eval.scm:
>     619:8 15 (_ #(#(#<directory (guile-user) 22f6140>)))
> In guix/ui.scm:
>   1578:12 14 (run-guix-command _ . _)
> In guix/scripts/import.scm:
>    114:11 13 (guix-import . _)
> In guix/scripts/import/cran.scm:
>    107:23 12 (guix-import-cran . _)
> In guix/memoization.scm:
>      98:0 11 (_ #<hash-table 28ce000 0/31> ("tracklayer" #) _)
> In unknown file:
>           10 (_ #<procedure 28d8d60 at guix/memoization.scm:179:32 …>
> …) In guix/import/cran.scm:
>    349:12  9 (_ _ _)
>    183:21  8 (fetch-description _ "tracklayer")
>    160:15  7 (latest-bioconductor-package-version _)
> In ice-9/boot-9.scm:
>     829:9  6 (catch _ _ #<procedure 7fa48a6a8218 at guix/import/cra…>
> …) In guix/import/cran.scm:
>    153:36  5 (_)
> In ice-9/boot-9.scm:
>     829:9  4 (catch _ _ #<procedure 28e0b40 at guix/http-client.scm…>
> …) In guix/http-client.scm:
>    182:20  3 (_)
>     88:25  2 (http-fetch _ #:port _ #:text? _ #:buffered? _ # _ # _ #
> …) In guix/build/download.scm:
>     398:4  1 (open-connection-for-uri _ #:timeout _ # _)
>     296:6  0 (tls-wrap #<closed: file 27f1690> _ # _)
> 
> guix/build/download.scm:296:6: In procedure tls-wrap:
> X.509 certificate of 'bioconductor.org' could not be verified:
>   signer-not-found
>   invalid
> 
> I don't know what's wrong, could you give me a hand?

See the last message: "certificate could not be verified".

You need to install certificates first and setup some environment
variables.

That is described here:

https://www.gnu.org/software/guix/manual/en/guix.html#X_002e509-Certificates

Can you get over that problem then?

Unfortunately, I'm getting then to another error:

guix import cran --archive=bioconductor tracklayer
Backtrace:
           9 (primitive-load "/home/bjoern/.config/guix/current/bin/…")
In guix/ui.scm:
  1583:12  8 (run-guix-command _ . _)
In guix/scripts/import.scm:
   115:11  7 (guix-import . _)
In guix/scripts/import/cran.scm:
   107:23  6 (guix-import-cran . _)
In guix/memoization.scm:
     98:0  5 (_ #<hash-table 262ebc0 0/31> ("tracklayer" #) _)
In unknown file:
           4 (_ #<procedure 26e9760 at guix/memoization.scm:179:32 …> …)
In guix/import/cran.scm:
   349:12  3 (_ _ _)
   184:26  2 (fetch-description _ _)
In guix/build-system/r.scm:
     53:8  1 (bioconductor-uri "tracklayer" #f)
In unknown file:
           0 (string-append "https://bioconductor.org/packages/rele…" …)

ERROR: In procedure string-append:
In procedure string-append: Wrong type (expecting string): #f


Currently, I don't have time to track that down further.

Either you don't have that second problem, someone else has a solution,
or I will come back to this back later.

Björn

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Re: [outreach] Help trying to create R package

[Björn Höfling]

[-- Attachment #1: Type: text/plain, Size: 4870 bytes --]

On Tue, 16 Oct 2018 07:44:12 +0200
Björn Höfling <bjoern.hoefling@bjoernhoefling.de> wrote:

> Hi Laura,
> 
> On Mon, 15 Oct 2018 19:47:38 -0300
> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> 
> > I've reading the documentation as well as trying some commands,and
> > there are some problems I am facing. I don't know what I am doing
> > wrong.
> > 
> > First, I ran:
> > $ guix package -s r-* | recsel -p name >>
> > resultOfSearchingRpackages.txt And reading the output file, I found
> > that the packages belonging to R that are available are:
> > name: r-rtracklayer
> > name: r-rcas
> > name: r-qtl
> > name: r-ggridges
> > name: r-feather
> > I also took a look at each of them with
> > $guix package --show=PACKAGENAME
> > Then, I tried:
> > $ guix import cran --archive=bioconductor tracklayer
> > 
> > But got this output:
> > acktrace:
> >           17 (apply-smob/1 #<catch-closure 223b160>)
> > In ice-9/boot-9.scm:
> >     705:2 16 (call-with-prompt _ _ #<procedure
> > default-prompt-handle…>) In ice-9/eval.scm:
> >     619:8 15 (_ #(#(#<directory (guile-user) 22f6140>)))
> > In guix/ui.scm:
> >   1578:12 14 (run-guix-command _ . _)
> > In guix/scripts/import.scm:
> >    114:11 13 (guix-import . _)
> > In guix/scripts/import/cran.scm:
> >    107:23 12 (guix-import-cran . _)
> > In guix/memoization.scm:
> >      98:0 11 (_ #<hash-table 28ce000 0/31> ("tracklayer" #) _)
> > In unknown file:
> >           10 (_ #<procedure 28d8d60 at guix/memoization.scm:179:32
> > …> …) In guix/import/cran.scm:
> >    349:12  9 (_ _ _)
> >    183:21  8 (fetch-description _ "tracklayer")
> >    160:15  7 (latest-bioconductor-package-version _)
> > In ice-9/boot-9.scm:
> >     829:9  6 (catch _ _ #<procedure 7fa48a6a8218 at
> > guix/import/cra…> …) In guix/import/cran.scm:
> >    153:36  5 (_)
> > In ice-9/boot-9.scm:
> >     829:9  4 (catch _ _ #<procedure 28e0b40 at
> > guix/http-client.scm…> …) In guix/http-client.scm:
> >    182:20  3 (_)
> >     88:25  2 (http-fetch _ #:port _ #:text? _ #:buffered? _ # _ # _
> > # …) In guix/build/download.scm:
> >     398:4  1 (open-connection-for-uri _ #:timeout _ # _)
> >     296:6  0 (tls-wrap #<closed: file 27f1690> _ # _)
> > 
> > guix/build/download.scm:296:6: In procedure tls-wrap:
> > X.509 certificate of 'bioconductor.org' could not be verified:
> >   signer-not-found
> >   invalid
> > 
> > I don't know what's wrong, could you give me a hand?  
> 
> See the last message: "certificate could not be verified".
> 
> You need to install certificates first and setup some environment
> variables.
> 
> That is described here:
> 
> https://www.gnu.org/software/guix/manual/en/guix.html#X_002e509-Certificates
> 
> Can you get over that problem then?
> 
> Unfortunately, I'm getting then to another error:
> 
> guix import cran --archive=bioconductor tracklayer
> Backtrace:
>            9 (primitive-load
> "/home/bjoern/.config/guix/current/bin/…") In guix/ui.scm:
>   1583:12  8 (run-guix-command _ . _)
> In guix/scripts/import.scm:
>    115:11  7 (guix-import . _)
> In guix/scripts/import/cran.scm:
>    107:23  6 (guix-import-cran . _)
> In guix/memoization.scm:
>      98:0  5 (_ #<hash-table 262ebc0 0/31> ("tracklayer" #) _)
> In unknown file:
>            4 (_ #<procedure 26e9760 at guix/memoization.scm:179:32 …>
> …) In guix/import/cran.scm:
>    349:12  3 (_ _ _)
>    184:26  2 (fetch-description _ _)
> In guix/build-system/r.scm:
>      53:8  1 (bioconductor-uri "tracklayer" #f)
> In unknown file:
>            0 (string-append "https://bioconductor.org/packages/rele…"
> …)
> 
> ERROR: In procedure string-append:
> In procedure string-append: Wrong type (expecting string): #f
> 
> 
> Currently, I don't have time to track that down further.
> 
> Either you don't have that second problem, someone else has a
> solution, or I will come back to this back later.


I tracked it down:

The cause is that:

guix/import/cran.scm:

(define (latest-bioconductor-package-version name)
  "Return the version string corresponding to the latest release of the
bioconductor package NAME, or #F if the package is unknown."

actually returns #f. It's a bit said that this #f is not checked
further down. The problem is the package name. If you add an "r" before
the package name, it should work (suppose you fixed the first problem):

guix import cran --archive=bioconductor rtracklayer 

Björn

PS: I personally think the Scheme backtraces are a bit hard to read
(I'm more used to Java), especially with the "In unknown file" parts,
but anyway you can get your information out of it. Try to look at them,
read the error message carefully. Find the lines in source code. Get
your way up, where is that abnormal #f coming from?


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Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Hello Björn,

Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
2018. okt. 16., K, 8:24):
>
> On Tue, 16 Oct 2018 07:44:12 +0200
> Björn Höfling <bjoern.hoefling@bjoernhoefling.de> wrote:
>
> > Hi Laura,
> >
> > On Mon, 15 Oct 2018 19:47:38 -0300
> > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> >
> > > I've reading the documentation as well as trying some commands,and
> > > there are some problems I am facing. I don't know what I am doing
> > > wrong.
> > >
> > > First, I ran:
> > > $ guix package -s r-* | recsel -p name >>
> > > resultOfSearchingRpackages.txt And reading the output file, I found
> > > that the packages belonging to R that are available are:
> > > name: r-rtracklayer
> > > name: r-rcas
> > > name: r-qtl
> > > name: r-ggridges
> > > name: r-feather
> > > I also took a look at each of them with
> > > $guix package --show=PACKAGENAME
> > > Then, I tried:
> > > $ guix import cran --archive=bioconductor tracklayer
> > >
> > > But got this output:
> > > acktrace:
> > >           17 (apply-smob/1 #<catch-closure 223b160>)
> > > In ice-9/boot-9.scm:
> > >     705:2 16 (call-with-prompt _ _ #<procedure
> > > default-prompt-handle…>) In ice-9/eval.scm:
> > >     619:8 15 (_ #(#(#<directory (guile-user) 22f6140>)))
> > > In guix/ui.scm:
> > >   1578:12 14 (run-guix-command _ . _)
> > > In guix/scripts/import.scm:
> > >    114:11 13 (guix-import . _)
> > > In guix/scripts/import/cran.scm:
> > >    107:23 12 (guix-import-cran . _)
> > > In guix/memoization.scm:
> > >      98:0 11 (_ #<hash-table 28ce000 0/31> ("tracklayer" #) _)
> > > In unknown file:
> > >           10 (_ #<procedure 28d8d60 at guix/memoization.scm:179:32
> > > …> …) In guix/import/cran.scm:
> > >    349:12  9 (_ _ _)
> > >    183:21  8 (fetch-description _ "tracklayer")
> > >    160:15  7 (latest-bioconductor-package-version _)
> > > In ice-9/boot-9.scm:
> > >     829:9  6 (catch _ _ #<procedure 7fa48a6a8218 at
> > > guix/import/cra…> …) In guix/import/cran.scm:
> > >    153:36  5 (_)
> > > In ice-9/boot-9.scm:
> > >     829:9  4 (catch _ _ #<procedure 28e0b40 at
> > > guix/http-client.scm…> …) In guix/http-client.scm:
> > >    182:20  3 (_)
> > >     88:25  2 (http-fetch _ #:port _ #:text? _ #:buffered? _ # _ # _
> > > # …) In guix/build/download.scm:
> > >     398:4  1 (open-connection-for-uri _ #:timeout _ # _)
> > >     296:6  0 (tls-wrap #<closed: file 27f1690> _ # _)
> > >
> > > guix/build/download.scm:296:6: In procedure tls-wrap:
> > > X.509 certificate of 'bioconductor.org' could not be verified:
> > >   signer-not-found
> > >   invalid
> > >
> > > I don't know what's wrong, could you give me a hand?
> >
> > See the last message: "certificate could not be verified".
> >
> > You need to install certificates first and setup some environment
> > variables.
> >
> > That is described here:
> >
> > https://www.gnu.org/software/guix/manual/en/guix.html#X_002e509-Certificates
> >
> > Can you get over that problem then?
> >
> > Unfortunately, I'm getting then to another error:
> >
> > guix import cran --archive=bioconductor tracklayer
> > Backtrace:
> >            9 (primitive-load
> > "/home/bjoern/.config/guix/current/bin/…") In guix/ui.scm:
> >   1583:12  8 (run-guix-command _ . _)
> > In guix/scripts/import.scm:
> >    115:11  7 (guix-import . _)
> > In guix/scripts/import/cran.scm:
> >    107:23  6 (guix-import-cran . _)
> > In guix/memoization.scm:
> >      98:0  5 (_ #<hash-table 262ebc0 0/31> ("tracklayer" #) _)
> > In unknown file:
> >            4 (_ #<procedure 26e9760 at guix/memoization.scm:179:32 …>
> > …) In guix/import/cran.scm:
> >    349:12  3 (_ _ _)
> >    184:26  2 (fetch-description _ _)
> > In guix/build-system/r.scm:
> >      53:8  1 (bioconductor-uri "tracklayer" #f)
> > In unknown file:
> >            0 (string-append "https://bioconductor.org/packages/rele…"
> > …)
> >
> > ERROR: In procedure string-append:
> > In procedure string-append: Wrong type (expecting string): #f
> >
> >
> > Currently, I don't have time to track that down further.
> >
> > Either you don't have that second problem, someone else has a
> > solution, or I will come back to this back later.
>
>
> I tracked it down:
>
> The cause is that:
>
> guix/import/cran.scm:
>
> (define (latest-bioconductor-package-version name)
>   "Return the version string corresponding to the latest release of the
> bioconductor package NAME, or #F if the package is unknown."
>
> actually returns #f. It's a bit said that this #f is not checked
> further down. The problem is the package name. If you add an "r" before
> the package name, it should work (suppose you fixed the first problem):
>
> guix import cran --archive=bioconductor rtracklayer
>
> Björn
>

Thanks for having a look at this.

> PS: I personally think the Scheme backtraces are a bit hard to read
> (I'm more used to Java), especially with the "In unknown file" parts,
> but anyway you can get your information out of it. Try to look at them,
> read the error message carefully. Find the lines in source code. Get
> your way up, where is that abnormal #f coming from?
>

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Tue, Oct 16, 2018 at 5:29 AM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> Hello Björn,
>
> Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
> 2018. okt. 16., K, 8:24):
> >
> > On Tue, 16 Oct 2018 07:44:12 +0200
> > Björn Höfling <bjoern.hoefling@bjoernhoefling.de> wrote:
> >
> > > Hi Laura,
> > >
> > > On Mon, 15 Oct 2018 19:47:38 -0300
> > > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> > >
> > > > I've reading the documentation as well as trying some commands,and
> > > > there are some problems I am facing. I don't know what I am doing
> > > > wrong.
> > > >
> > > > First, I ran:
> > > > $ guix package -s r-* | recsel -p name >>
> > > > resultOfSearchingRpackages.txt And reading the output file, I found
> > > > that the packages belonging to R that are available are:
> > > > name: r-rtracklayer
> > > > name: r-rcas
> > > > name: r-qtl
> > > > name: r-ggridges
> > > > name: r-feather
> > > > I also took a look at each of them with
> > > > $guix package --show=PACKAGENAME
> > > > Then, I tried:
> > > > $ guix import cran --archive=bioconductor tracklayer
> > > >
> > > > But got this output:
> > > > acktrace:
> > > >           17 (apply-smob/1 #<catch-closure 223b160>)
> > > > In ice-9/boot-9.scm:
> > > >     705:2 16 (call-with-prompt _ _ #<procedure
> > > > default-prompt-handle…>) In ice-9/eval.scm:
> > > >     619:8 15 (_ #(#(#<directory (guile-user) 22f6140>)))
> > > > In guix/ui.scm:
> > > >   1578:12 14 (run-guix-command _ . _)
> > > > In guix/scripts/import.scm:
> > > >    114:11 13 (guix-import . _)
> > > > In guix/scripts/import/cran.scm:
> > > >    107:23 12 (guix-import-cran . _)
> > > > In guix/memoization.scm:
> > > >      98:0 11 (_ #<hash-table 28ce000 0/31> ("tracklayer" #) _)
> > > > In unknown file:
> > > >           10 (_ #<procedure 28d8d60 at guix/memoization.scm:179:32
> > > > …> …) In guix/import/cran.scm:
> > > >    349:12  9 (_ _ _)
> > > >    183:21  8 (fetch-description _ "tracklayer")
> > > >    160:15  7 (latest-bioconductor-package-version _)
> > > > In ice-9/boot-9.scm:
> > > >     829:9  6 (catch _ _ #<procedure 7fa48a6a8218 at
> > > > guix/import/cra…> …) In guix/import/cran.scm:
> > > >    153:36  5 (_)
> > > > In ice-9/boot-9.scm:
> > > >     829:9  4 (catch _ _ #<procedure 28e0b40 at
> > > > guix/http-client.scm…> …) In guix/http-client.scm:
> > > >    182:20  3 (_)
> > > >     88:25  2 (http-fetch _ #:port _ #:text? _ #:buffered? _ # _ # _
> > > > # …) In guix/build/download.scm:
> > > >     398:4  1 (open-connection-for-uri _ #:timeout _ # _)
> > > >     296:6  0 (tls-wrap #<closed: file 27f1690> _ # _)
> > > >
> > > > guix/build/download.scm:296:6: In procedure tls-wrap:
> > > > X.509 certificate of 'bioconductor.org' could not be verified:
> > > >   signer-not-found
> > > >   invalid
> > > >
> > > > I don't know what's wrong, could you give me a hand?
> > >
> > > See the last message: "certificate could not be verified".
> > >
> > > You need to install certificates first and setup some environment
> > > variables.
> > >
> > > That is described here:
> > >
> > > https://www.gnu.org/software/guix/manual/en/guix.html#X_002e509-Certificates
> > >
> > > Can you get over that problem then?
> > >
> > > Unfortunately, I'm getting then to another error:
> > >
> > > guix import cran --archive=bioconductor tracklayer
> > > Backtrace:
> > >            9 (primitive-load
> > > "/home/bjoern/.config/guix/current/bin/…") In guix/ui.scm:
> > >   1583:12  8 (run-guix-command _ . _)
> > > In guix/scripts/import.scm:
> > >    115:11  7 (guix-import . _)
> > > In guix/scripts/import/cran.scm:
> > >    107:23  6 (guix-import-cran . _)
> > > In guix/memoization.scm:
> > >      98:0  5 (_ #<hash-table 262ebc0 0/31> ("tracklayer" #) _)
> > > In unknown file:
> > >            4 (_ #<procedure 26e9760 at guix/memoization.scm:179:32 …>
> > > …) In guix/import/cran.scm:
> > >    349:12  3 (_ _ _)
> > >    184:26  2 (fetch-description _ _)
> > > In guix/build-system/r.scm:
> > >      53:8  1 (bioconductor-uri "tracklayer" #f)
> > > In unknown file:
> > >            0 (string-append "https://bioconductor.org/packages/rele…"
> > > …)
> > >
> > > ERROR: In procedure string-append:
> > > In procedure string-append: Wrong type (expecting string): #f
> > >
> > >
> > > Currently, I don't have time to track that down further.
> > >
> > > Either you don't have that second problem, someone else has a
> > > solution, or I will come back to this back later.
> >
> >
> > I tracked it down:
> >
> > The cause is that:
> >
> > guix/import/cran.scm:
> >
> > (define (latest-bioconductor-package-version name)
> >   "Return the version string corresponding to the latest release of the
> > bioconductor package NAME, or #F if the package is unknown."
> >
> > actually returns #f. It's a bit said that this #f is not checked
> > further down. The problem is the package name. If you add an "r" before
> > the package name, it should work (suppose you fixed the first problem):
> >
> > guix import cran --archive=bioconductor rtracklayer
> >
> > Björn
> >
>
> Thanks for having a look at this.

Thank you again!
I am trying to do my best. I am reading the documentation carefully, I
recall mentioning that I am that kind of person,  but I also know that
time counts for the contributions. And if I figure out how to package
R packages, then I can also package more packages and, whatever the
result of outreachy might be, well, there are more useful packages in
guix.
For instance, I tried, before of asking for help with  the example
shown with cairo and it worked fine, so I was  not understanding very
well what was happening,
In addition, I have just run
$ guix package -s "\<R\>" | recsel -p name,synopsis >>
outputRwithNameAndSynopsis.txt
and found even more R packages already installed.
Well, time to work!
> > PS: I personally think the Scheme backtraces are a bit hard to read
> > (I'm more used to Java), especially with the "In unknown file" parts,
> > but anyway you can get your information out of it. Try to look at them,
> > read the error message carefully. Find the lines in source code. Get
> > your way up, where is that abnormal #f coming from?
> >
Regards!
Laura

Re: [outreach] Help trying to create R package

[Björn Höfling]

[-- Attachment #1: Type: text/plain, Size: 2569 bytes --]

Hi Laura,

On Tue, 16 Oct 2018 10:13:23 -0300
Laura Lazzati <laura.lazzati.15@gmail.com> wrote:

[importing problems ...]

Could you solve your certificate-problem? Have you been successfully in
importing a package?

Unfortunately the package of your choice is already part of guix:


$ guix package -s "rtracklayer$"
name: r-rtracklayer
version: 1.40.6
outputs: out
systems: x86_64-linux i686-linux armhf-linux aarch64-linux mips64el-linux
dependencies: pkg-config@0.29.2 r-biocgenerics@0.26.0 r-biostrings@2.48.0
+ r-genomeinfodb@1.16.0 r-genomicalignments@1.16.0 r-genomicranges@1.32.6
+ r-iranges@2.14.11 r-rcurl@1.95-0.1.2 r-rsamtools@1.32.3 r-s4vectors@0.18.3
+ r-xml@3.98-1.16 r-xvector@0.20.0 zlib@1.2.11
location: gnu/packages/bioinformatics.scm:7696:2
homepage: https://bioconductor.org/packages/rtracklayer
license: Artistic License 2.0
synopsis: R interface to genome browsers and their annotation tracks  
description: rtracklayer is an extensible framework for interacting with
+ multiple genome browsers (currently UCSC built-in) and manipulating annotation
+ tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig
+ and 2bit built-in).  The user may export/import tracks to/from the supported
+ browsers, as well as query and modify the browser state, such as the current
+ viewport.
relevance: 4

Can you find another one?


> I am trying to do my best. I am reading the documentation carefully, I
> recall mentioning that I am that kind of person,  but I also know that
> time counts for the contributions. 

Yes, you mentioned that :-) The documentation is huge, with lots of
special concepts. I would recommend reading it only partially, whenever
you need more information.


> And if I figure out how to package
> R packages, then I can also package more packages and, whatever the
> result of outreachy might be, well, there are more useful packages in
> guix.
> For instance, I tried, before of asking for help with  the example
> shown with cairo and it worked fine, so I was  not understanding very
> well what was happening,
> In addition, I have just run
> $ guix package -s "\<R\>" | recsel -p name,synopsis >>
> outputRwithNameAndSynopsis.txt
> and found even more R packages already installed.

Here is another one:

guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt

the carret-symbol "^" matches the beginning of the line.
There are some empty lines, which get sorted out with the grep.


> Well, time to work!

Good luck!

Björn

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Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
<bjoern.hoefling@bjoernhoefling.de> wrote:
>
> Hi Laura,
Hi! I had not answered yet because I thought I would be too verbose.
If so, please do a Laura -v instead of Laura -vvvvvvv.
Thanks for writing :) it encourages me a lot.
>
> On Tue, 16 Oct 2018 10:13:23 -0300
> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
>
> [importing problems ...]
>
> Could you solve your certificate-problem? Have you been successfully in
> importing a package?
Yes! I love reading ALL the documentation, but I focused mainly in
chapters 3 to 5, and the part about the certificate stuff is 6. That
is why I did not know about it.
>
> Unfortunately the package of your choice is already part of guix:
>
>
> $ guix package -s "rtracklayer$"
> name: r-rtracklayer
> version: 1.40.6
> outputs: out
> systems: x86_64-linux i686-linux armhf-linux aarch64-linux mips64el-linux
> dependencies: pkg-config@0.29.2 r-biocgenerics@0.26.0 r-biostrings@2.48.0
> + r-genomeinfodb@1.16.0 r-genomicalignments@1.16.0 r-genomicranges@1.32.6
> + r-iranges@2.14.11 r-rcurl@1.95-0.1.2 r-rsamtools@1.32.3 r-s4vectors@0.18.3
> + r-xml@3.98-1.16 r-xvector@0.20.0 zlib@1.2.11
> location: gnu/packages/bioinformatics.scm:7696:2
> homepage: https://bioconductor.org/packages/rtracklayer
> license: Artistic License 2.0
> synopsis: R interface to genome browsers and their annotation tracks
> description: rtracklayer is an extensible framework for interacting with
> + multiple genome browsers (currently UCSC built-in) and manipulating annotation
> + tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig
> + and 2bit built-in).  The user may export/import tracks to/from the supported
> + browsers, as well as query and modify the browser state, such as the current
> + viewport.
> relevance: 4
>
> Can you find another one?
Yes! I knew that the package was already available for guix, but I
just wanted to see the template, with guix import, to use it for
others.
>
>
> > I am trying to do my best. I am reading the documentation carefully, I
> > recall mentioning that I am that kind of person,  but I also know that
> > time counts for the contributions.
>
> Yes, you mentioned that :-) The documentation is huge, with lots of
> special concepts. I would recommend reading it only partially, whenever
> you need more information.
I have already answered this :( I know I don't have time to do things
this way, at least for the contribution(s)
>
>
> > And if I figure out how to package
> > R packages, then I can also package more packages and, whatever the
> > result of outreachy might be, well, there are more useful packages in
> > guix.
> > For instance, I tried, before of asking for help with  the example
> > shown with cairo and it worked fine, so I was  not understanding very
> > well what was happening,
> > In addition, I have just run
> > $ guix package -s "\<R\>" | recsel -p name,synopsis >>
> > outputRwithNameAndSynopsis.txt
> > and found even more R packages already installed.
>
> Here is another one:
>
> guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt

Something I faced after writing, was that in the link one of you provided:
[1]https://guix.mdc-berlin.de/
I have all the packages that are already available in guix. I like
using the guix package command to practice that too, but i found it
practical to see packages easier. I found out that package aspi
(https://CRAN.R-project.org/package=aspi) is not available, and I
would like to ask you if you believe it is a good candidate.
One available package, according to [1] is r-abe
(https://cran.r-project.org/web/packages/abe/index.html)
I wanted to see the template, so I ran:
$ guix import cran abe
And got the template, that matches even the version, and everything
stated in the site.
But then I tried:
$ guix package -i r-abe and got no results.
In fact, after running the command you have just provided, r-abe is
not appearing in the r.txt file.
I can't understand why that is happening. Am I missing something, or
is there maybe an inconsistency between [1] and the guix installed in
my foreign distro?
Just wanted to install it to run guix edit to check if the suggested
packages were already available or if I needed to package them too,
but I have installed r-ade4, which has both imports and suggests, and
I have just run:
$guix import cran ade4
And noticed that it only states in the template the Import package (MASS)

Here is my template for aspi (I named it for myself r-aspi.scm). I ran
guix download from its site, and also guix hash to convert it to
base32:

(define-public r-aspi
(package
  (name "r-aspi")
  (version "0.2.0")
  (source
    (origin
      (method url-fetch)
      (uri (cran-uri "aspi" version))
      (sha256
        (base32
          "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"))))
  (build-system r-build-system)
   (home-page
    "https://cran.r-project.org/web/packages/aspi/")
  (synopsis
    "Analysis of Symmetry of Parasitic Infections")
  (description
    "Tools for the analysis and visualization of bilateral asymmetry
in parasitic infections.")
  (license gpl3+)))
And that's were I ended up today (it is still Tuesday, almost 10pm)
>
> the carret-symbol "^" matches the beginning of the line.
> There are some empty lines, which get sorted out with the grep.
Thanks :) I knew about the regex, but everything  is always welcome :)
sometimes it is true that after reading too much info you end up
messed up if you do not have enough time to practice and try
everything.

>
>
> > Well, time to work!
>
> Good luck!
Thanks!
>
> Björn
Regards,

Laura

Re: [outreach] Help trying to create R package

[Björn Höfling]

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Hi Laura,

On Tue, 16 Oct 2018 22:01:58 -0300
Laura Lazzati <laura.lazzati.15@gmail.com> wrote:

> On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
> <bjoern.hoefling@bjoernhoefling.de> wrote:
> >
> > Hi Laura,  
> Hi! I had not answered yet because I thought I would be too verbose.
> If so, please do a Laura -v instead of Laura -vvvvvvv.
> Thanks for writing :) it encourages me a lot.

You're welcome. It's nice to hear from your progress. Verbosity-level
is fine :-)

[..]

> > Here is another one:
> >
> > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt  
> 
> Something I faced after writing, was that in the link one of you
> provided: [1]https://guix.mdc-berlin.de/
> I have all the packages that are already available in guix. I like
> using the guix package command to practice that too, but i found it
> practical to see packages easier. I found out that package aspi
> (https://CRAN.R-project.org/package=aspi) is not available, and I
> would like to ask you if you believe it is a good candidate.
> One available package, according to [1] is r-abe
> (https://cran.r-project.org/web/packages/abe/index.html)

Sorry I have no clue of R at all. Could someone else please answer that
question, is r-aspi a good candidate?

https://cran.r-project.org/web/packages/aspi/index.html


> I wanted to see the template, so I ran:
> $ guix import cran abe
> And got the template, that matches even the version, and everything
> stated in the site.
> But then I tried:
> $ guix package -i r-abe and got no results.
> In fact, after running the command you have just provided, r-abe is
> not appearing in the r.txt file.
> I can't understand why that is happening. Am I missing something, or
> is there maybe an inconsistency between [1] and the guix installed in
> my foreign distro?

Concerning r-abe: I don't know how the list at guix-hpc is created
, how often it is updated or if there are extra packages in there. In
your case, I suppose you lack behind:

There is a commit for r-abe from 2019-09-13, so it is only a month old.
I think you are lacking behind. Have you done a `guix pull`? That's the
command used to update the package definitions.

In case you already did a guix pull recently, and you still don't see
it, there could be a problem with your $PATH, that the wrong guix is
coming first. Do a `which guix`.
Guix should be the one in ~/.config/guix/current/bin/guix


> Just wanted to install it to run guix edit to check if the suggested
> packages were already available or if I needed to package them too,
> but I have installed r-ade4, which has both imports and suggests, and
> I have just run:
> $guix import cran ade4
> And noticed that it only states in the template the Import package
> (MASS)

If I see that right, for R we only add the "Imports" packages, as they
are absolutely needed for compiling/running. All "Suggests" can be
installed/used just at runtime. Please correct me anyone if I'm wrong,
I'm not into R.

 
> Here is my template for aspi (I named it for myself r-aspi.scm). I ran
> guix download from its site, and also guix hash to convert it to
> base32:
> 
> (define-public r-aspi
> (package
>   (name "r-aspi")
>   (version "0.2.0")
>   (source
>     (origin
>       (method url-fetch)
>       (uri (cran-uri "aspi" version))
>       (sha256
>         (base32
>           "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"))))
>   (build-system r-build-system)
>    (home-page
>     "https://cran.r-project.org/web/packages/aspi/")
>   (synopsis
>     "Analysis of Symmetry of Parasitic Infections")
>   (description
>     "Tools for the analysis and visualization of bilateral asymmetry
> in parasitic infections.")
>   (license gpl3+)))
> And that's were I ended up today (it is still Tuesday, almost 10pm)

I haven't done a full review, but that looks good. Next you need to get
the guix sources and prepare a patch.

That's described here:

https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing


Björn

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Re: [outreach] Help trying to create R package

[Gábor Boskovits]

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ÜHi Laura,



Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont: 2018.
okt. 17., Sze 9:17):

> Hi Laura,
>
> On Tue, 16 Oct 2018 22:01:58 -0300
> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
>
> > On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
> > <bjoern.hoefling@bjoernhoefling.de> wrote:
> > >
> > > Hi Laura,
> > Hi! I had not answered yet because I thought I would be too verbose.
> > If so, please do a Laura -v instead of Laura -vvvvvvv.
> > Thanks for writing :) it encourages me a lot.
>
> You're welcome. It's nice to hear from your progress. Verbosity-level
> is fine :-)
>
> [..]
>
> > > Here is another one:
> > >
> > > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt
> >
> > Something I faced after writing, was that in the link one of you
> > provided: [1]https://guix.mdc-berlin.de/
> > I have all the packages that are already available in guix. I like
> > using the guix package command to practice that too, but i found it
> > practical to see packages easier. I found out that package aspi
> > (https://CRAN.R-project.org/package=aspi) is not available, and I
> > would like to ask you if you believe it is a good candidate.
> > One available package, according to [1] is r-abe
> > (https://cran.r-project.org/web/packages/abe/index.html)
>
> Sorry I have no clue of R at all. Could someone else please answer that
> question, is r-aspi a good candidate?
>
> https://cran.r-project.org/web/packages/aspi/index.html
>
>
> > I wanted to see the template, so I ran:
> > $ guix import cran abe
> > And got the template, that matches even the version, and everything
> > stated in the site.
> > But then I tried:
> > $ guix package -i r-abe and got no results.
>
This happens, as the installed guix doesn't know where to find the package
definition. There are several ways around that, for example see the -f flag
of guix package, in the invoking guix package section of the manual.

> > In fact, after running the command you have just provided, r-abe is
> > not appearing in the r.txt file.
> > I can't understand why that is happening. Am I missing something, or
> > is there maybe an inconsistency between [1] and the guix installed in
> > my foreign distro?
>
> Concerning r-abe: I don't know how the list at guix-hpc is created
> , how often it is updated or if there are extra packages in there. In
> your case, I suppose you lack behind:
>
> There is a commit for r-abe from 2019-09-13, so it is only a month old.
> I think you are lacking behind. Have you done a `guix pull`? That's the
> command used to update the package definitions.
>
> In case you already did a guix pull recently, and you still don't see
> it, there could be a problem with your $PATH, that the wrong guix is
> coming first. Do a `which guix`.
> Guix should be the one in ~/.config/guix/current/bin/guix
>

Yes, please run guix pull, and check which guix output.


>
> > Just wanted to install it to run guix edit to check if the suggested
> > packages were already available or if I needed to package them too,
> > but I have installed r-ade4, which has both imports and suggests, and
> > I have just run:
> > $guix import cran ade4
> > And noticed that it only states in the template the Import package
> > (MASS)
>
> If I see that right, for R we only add the "Imports" packages, as they
> are absolutely needed for compiling/running. All "Suggests" can be
> installed/used just at runtime. Please correct me anyone if I'm wrong,
> I'm not into R.
>
>
> > Here is my template for aspi (I named it for myself r-aspi.scm). I ran
> > guix download from its site, and also guix hash to convert it to
> > base32:
> >
> > (define-public r-aspi
> > (package
> >   (name "r-aspi")
> >   (version "0.2.0")
> >   (source
> >     (origin
> >       (method url-fetch)
> >       (uri (cran-uri "aspi" version))
> >       (sha256
> >         (base32
> >           "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"))))
> >   (build-system r-build-system)
> >    (home-page
> >     "https://cran.r-project.org/web/packages/aspi/")
> >   (synopsis
> >     "Analysis of Symmetry of Parasitic Infections")
> >   (description
> >     "Tools for the analysis and visualization of bilateral asymmetry
> > in parasitic infections.")
> >   (license gpl3+)))
> > And that's were I ended up today (it is still Tuesday, almost 10pm)
>
> I haven't done a full review, but that looks good. Next you need to get
> the guix sources and prepare a patch.
>
> That's described here:
>
>
> https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
>
>
> Björn
>

Best regards,
g_bor

>

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Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Wed, Oct 17, 2018 at 5:21 AM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> ÜHi Laura,
>
>
>
> Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont: 2018. okt. 17., Sze 9:17):
>>
>> Hi Laura,
>>
>> On Tue, 16 Oct 2018 22:01:58 -0300
>> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
>>
>> > On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
>> > <bjoern.hoefling@bjoernhoefling.de> wrote:
>> > >
>> > > Hi Laura,
>> > Hi! I had not answered yet because I thought I would be too verbose.
>> > If so, please do a Laura -v instead of Laura -vvvvvvv.
>> > Thanks for writing :) it encourages me a lot.
>>
>> You're welcome. It's nice to hear from your progress. Verbosity-level
>> is fine :-)
Thanks :) Hope you enjoy my nerd jokes

>> [..]
>>
>> > > Here is another one:
>> > >
>> > > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt
>> >
>> > Something I faced after writing, was that in the link one of you
>> > provided: [1]https://guix.mdc-berlin.de/
>> > I have all the packages that are already available in guix. I like
>> > using the guix package command to practice that too, but i found it
>> > practical to see packages easier. I found out that package aspi
>> > (https://CRAN.R-project.org/package=aspi) is not available, and I
>> > would like to ask you if you believe it is a good candidate.
>> > One available package, according to [1] is r-abe
>> > (https://cran.r-project.org/web/packages/abe/index.html)
>>
>> Sorry I have no clue of R at all. Could someone else please answer that
>> question, is r-aspi a good candidate?
>>
>> https://cran.r-project.org/web/packages/aspi/index.html
>>
>>
>> > I wanted to see the template, so I ran:
>> > $ guix import cran abe
>> > And got the template, that matches even the version, and everything
>> > stated in the site.
>> > But then I tried:
>> > $ guix package -i r-abe and got no results.
>
> This happens, as the installed guix doesn't know where to find the package definition. There are several ways around that, for example see the -f flag of guix package, in the invoking guix package section of the manual.
>>
>> > In fact, after running the command you have just provided, r-abe is
>> > not appearing in the r.txt file.
>> > I can't understand why that is happening. Am I missing something, or
>> > is there maybe an inconsistency between [1] and the guix installed in
>> > my foreign distro?
>>
>> Concerning r-abe: I don't know how the list at guix-hpc is created
>> , how often it is updated or if there are extra packages in there. In
>> your case, I suppose you lack behind:
>>
>> There is a commit for r-abe from 2019-09-13, so it is only a month old.
>> I think you are lacking behind. Have you done a `guix pull`? That's the
>> command used to update the package definitions.
>>
>> In case you already did a guix pull recently, and you still don't see
>> it, there could be a problem with your $PATH, that the wrong guix is
>> coming first. Do a `which guix`.
>> Guix should be the one in ~/.config/guix/current/bin/guix
>
>
> Yes, please run guix pull, and check which guix output.
I have to take a look at my .bash_history, but I guess somewhere I ran
guix pull because I recall seing something about the $PATH stuff. I
did not run guix output. It doesn'matter, I save my machine state and
run all that now.
>
>>
>>
>> > Just wanted to install it to run guix edit to check if the suggested
>> > packages were already available or if I needed to package them too,
>> > but I have installed r-ade4, which has both imports and suggests, and
>> > I have just run:
>> > $guix import cran ade4
>> > And noticed that it only states in the template the Import package
>> > (MASS)
>>
>> If I see that right, for R we only add the "Imports" packages, as they
>> are absolutely needed for compiling/running. All "Suggests" can be
>> installed/used just at runtime. Please correct me anyone if I'm wrong,
>> I'm not into R.
>>
>>
>> > Here is my template for aspi (I named it for myself r-aspi.scm). I ran
>> > guix download from its site, and also guix hash to convert it to
>> > base32:
>> >
>> > (define-public r-aspi
>> > (package
>> >   (name "r-aspi")
>> >   (version "0.2.0")
>> >   (source
>> >     (origin
>> >       (method url-fetch)
>> >       (uri (cran-uri "aspi" version))
>> >       (sha256
>> >         (base32
>> >           "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"))))
>> >   (build-system r-build-system)
>> >    (home-page
>> >     "https://cran.r-project.org/web/packages/aspi/")
>> >   (synopsis
>> >     "Analysis of Symmetry of Parasitic Infections")
>> >   (description
>> >     "Tools for the analysis and visualization of bilateral asymmetry
>> > in parasitic infections.")
>> >   (license gpl3+)))
>> > And that's were I ended up today (it is still Tuesday, almost 10pm)
>>
>> I haven't done a full review, but that looks good. Next you need to get
>> the guix sources and prepare a patch.
Thanks, I took a look at most of the R packages in cran site, and
chose it because of two reasons: it has to do with bioinformatics due
to its description, and as it does not mention imports so I found it
easy for a first R package contribution. If it works fine, then I can
go on packaging more complicated R packages.

>> That's described here:
>>
>> https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
>>
>>
>> Björn
>
>
> Best regards,
> g_bor

Thanks both!
Regards,
Laura

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Wed, Oct 17, 2018 at 11:27 AM Laura Lazzati
<laura.lazzati.15@gmail.com> wrote:
>
> On Wed, Oct 17, 2018 at 5:21 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> >
> > ÜHi Laura,
> >
> >
> >
> > Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont: 2018. okt. 17., Sze 9:17):
> >>
> >> Hi Laura,
> >>
> >> On Tue, 16 Oct 2018 22:01:58 -0300
> >> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> >>
> >> > On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
> >> > <bjoern.hoefling@bjoernhoefling.de> wrote:
> >> > >
> >> > > Hi Laura,
> >> > Hi! I had not answered yet because I thought I would be too verbose.
> >> > If so, please do a Laura -v instead of Laura -vvvvvvv.
> >> > Thanks for writing :) it encourages me a lot.
> >>
> >> You're welcome. It's nice to hear from your progress. Verbosity-level
> >> is fine :-)
> Thanks :) Hope you enjoy my nerd jokes
>
> >> [..]
> >>
> >> > > Here is another one:
> >> > >
> >> > > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt
> >> >
> >> > Something I faced after writing, was that in the link one of you
> >> > provided: [1]https://guix.mdc-berlin.de/
> >> > I have all the packages that are already available in guix. I like
> >> > using the guix package command to practice that too, but i found it
> >> > practical to see packages easier. I found out that package aspi
> >> > (https://CRAN.R-project.org/package=aspi) is not available, and I
> >> > would like to ask you if you believe it is a good candidate.
> >> > One available package, according to [1] is r-abe
> >> > (https://cran.r-project.org/web/packages/abe/index.html)
> >>
> >> Sorry I have no clue of R at all. Could someone else please answer that
> >> question, is r-aspi a good candidate?
> >>
> >> https://cran.r-project.org/web/packages/aspi/index.html
> >>
> >>
> >> > I wanted to see the template, so I ran:
> >> > $ guix import cran abe
> >> > And got the template, that matches even the version, and everything
> >> > stated in the site.
> >> > But then I tried:
> >> > $ guix package -i r-abe and got no results.
> >
> > This happens, as the installed guix doesn't know where to find the package definition. There are several ways around that, for example see the -f flag of guix package, in the invoking guix package section of the manual.
> >>
> >> > In fact, after running the command you have just provided, r-abe is
> >> > not appearing in the r.txt file.
> >> > I can't understand why that is happening. Am I missing something, or
> >> > is there maybe an inconsistency between [1] and the guix installed in
> >> > my foreign distro?
> >>
> >> Concerning r-abe: I don't know how the list at guix-hpc is created
> >> , how often it is updated or if there are extra packages in there. In
> >> your case, I suppose you lack behind:
> >>
> >> There is a commit for r-abe from 2019-09-13, so it is only a month old.
> >> I think you are lacking behind. Have you done a `guix pull`? That's the
> >> command used to update the package definitions.
> >>
> >> In case you already did a guix pull recently, and you still don't see
> >> it, there could be a problem with your $PATH, that the wrong guix is
> >> coming first. Do a `which guix`.
> >> Guix should be the one in ~/.config/guix/current/bin/guix
> >
> >
> > Yes, please run guix pull, and check which guix output.
> I have to take a look at my .bash_history, but I guess somewhere I ran
> guix pull because I recall seing something about the $PATH stuff. I
> did not run guix output. It doesn'matter, I save my machine state and
> run all that now.
You were right. I took a look at my .bashrc file, and I had an:
export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
I ran $guix pull, did the PATH export in my CLI, then checked the output of
$which guix, that was the same that was mentioned by you,
commented that previous line in .bashrc,
added  export PATH="/home/laura/.config/guix/current/bin${PATH:+:}$PATH"
and ran again the command to check the available R packages, made a
diff with the previous one, and now at least r-bae appears.
> >
> >>
> >>
> >> > Just wanted to install it to run guix edit to check if the suggested
> >> > packages were already available or if I needed to package them too,
> >> > but I have installed r-ade4, which has both imports and suggests, and
> >> > I have just run:
> >> > $guix import cran ade4
> >> > And noticed that it only states in the template the Import package
> >> > (MASS)
> >>
> >> If I see that right, for R we only add the "Imports" packages, as they
> >> are absolutely needed for compiling/running. All "Suggests" can be
> >> installed/used just at runtime. Please correct me anyone if I'm wrong,
> >> I'm not into R.
> >>
> >>
> >> > Here is my template for aspi (I named it for myself r-aspi.scm). I ran
> >> > guix download from its site, and also guix hash to convert it to
> >> > base32:
> >> >
> >> > (define-public r-aspi
> >> > (package
> >> >   (name "r-aspi")
> >> >   (version "0.2.0")
> >> >   (source
> >> >     (origin
> >> >       (method url-fetch)
> >> >       (uri (cran-uri "aspi" version))
> >> >       (sha256
> >> >         (base32
> >> >           "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"))))
> >> >   (build-system r-build-system)
> >> >    (home-page
> >> >     "https://cran.r-project.org/web/packages/aspi/")
> >> >   (synopsis
> >> >     "Analysis of Symmetry of Parasitic Infections")
> >> >   (description
> >> >     "Tools for the analysis and visualization of bilateral asymmetry
> >> > in parasitic infections.")
> >> >   (license gpl3+)))
> >> > And that's were I ended up today (it is still Tuesday, almost 10pm)
> >>
> >> I haven't done a full review, but that looks good. Next you need to get
> >> the guix sources and prepare a patch.
> Thanks, I took a look at most of the R packages in cran site, and
> chose it because of two reasons: it has to do with bioinformatics due
> to its description, and as it does not mention imports so I found it
> easy for a first R package contribution. If it works fine, then I can
> go on packaging more complicated R packages.
>
> >> That's described here:
> >>
> >> https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> >>
> >>
> >> Björn
> >
> >
> > Best regards,
> > g_bor
>
> Thanks both!
> Regards,
> Laura
Thanks again, time to read how to go on with my contribution :)
Laura

Re: [outreach] Help trying to create R package

[Clément Lassieur]

Hi Laura,

Laura Lazzati <laura.lazzati.15@gmail.com> writes:

> You were right. I took a look at my .bashrc file, and I had an:
> export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> I ran $guix pull, did the PATH export in my CLI, then checked the output of
> $which guix, that was the same that was mentioned by you,
> commented that previous line in .bashrc,
> added  export PATH="/home/laura/.config/guix/current/bin${PATH:+:}$PATH"
> and ran again the command to check the available R packages, made a
> diff with the previous one, and now at least r-bae appears.

You should export environment variables such as PATH in
‘~/.bash_profile’ instead of ‘~/.bashrc’.  :-)

Quoting the documentation[1]:

    Users sometimes wrongfully augment environment variables such as
    ‘PATH’ in their ‘~/.bashrc’ file.  As a consequence, when ‘guix
    environment’ launches it, Bash may read ‘~/.bashrc’, thereby
    introducing “impurities” in these environment variables.  It is an
    error to define such environment variables in ‘.bashrc’; instead,
    they should be defined in ‘.bash_profile’, which is sourced only by
    log-in shells.  See ‘Bash Startup Files[2]’, for details on Bash
    start-up files.

Cheers,
Clément

[1]: https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-environment.html#FOOT15
[2]: https://www.gnu.org/software/bash/manual/html_node/Bash-Startup-Files.html#Bash-Startup-Files

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Wed, Oct 17, 2018 at 2:13 PM Clément Lassieur <clement@lassieur.org> wrote:
>
> Hi Laura,
>
> Laura Lazzati <laura.lazzati.15@gmail.com> writes:
>
> > You were right. I took a look at my .bashrc file, and I had an:
> > export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> > I ran $guix pull, did the PATH export in my CLI, then checked the output of
> > $which guix, that was the same that was mentioned by you,
> > commented that previous line in .bashrc,
> > added  export PATH="/home/laura/.config/guix/current/bin${PATH:+:}$PATH"
> > and ran again the command to check the available R packages, made a
> > diff with the previous one, and now at least r-bae appears.
>
> You should export environment variables such as PATH in
> ‘~/.bash_profile’ instead of ‘~/.bashrc’.  :-)
>
> Quoting the documentation[1]:
>
>     Users sometimes wrongfully augment environment variables such as
>     ‘PATH’ in their ‘~/.bashrc’ file.  As a consequence, when ‘guix
>     environment’ launches it, Bash may read ‘~/.bashrc’, thereby
>     introducing “impurities” in these environment variables.  It is an
>     error to define such environment variables in ‘.bashrc’; instead,
>     they should be defined in ‘.bash_profile’, which is sourced only by
>     log-in shells.  See ‘Bash Startup Files[2]’, for details on Bash
>     start-up files.
Thanks! I am reading that part now, specially [2].
I have deleted the env variables from .bashrc and have just set them
in .profile, since my distro is Ubuntu, and I am reading that Ubuntu
does not use .bash_profile. Everything seems to be working fine. Thank
you again :)

> Cheers,
> Clément
>
> [1]: https://www.gnu.org/software/guix/manual/en/html_node/Invoking-guix-environment.html#FOOT15
> [2]: https://www.gnu.org/software/bash/manual/html_node/Bash-Startup-Files.html#Bash-Startup-Files

Re: [outreach] Help trying to create R package

[Laura Lazzati]

Hi! I'm stuck :/
On Wed, Oct 17, 2018 at 4:17 AM Björn Höfling
<bjoern.hoefling@bjoernhoefling.de> wrote:
>
> Hi Laura,
>
> On Tue, 16 Oct 2018 22:01:58 -0300
> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
>
> > On Tue, Oct 16, 2018 at 7:19 PM Björn Höfling
> > <bjoern.hoefling@bjoernhoefling.de> wrote:
> > >
> > > Hi Laura,
> > Hi! I had not answered yet because I thought I would be too verbose.
> > If so, please do a Laura -v instead of Laura -vvvvvvv.
> > Thanks for writing :) it encourages me a lot.
>
> You're welcome. It's nice to hear from your progress. Verbosity-level
> is fine :-)
>
> [..]
>
> > > Here is another one:
> > >
> > > guix package -s "^r-" | recsel -p name| grep '\S' | sort >r.txt
> >
> > Something I faced after writing, was that in the link one of you
> > provided: [1]https://guix.mdc-berlin.de/
> > I have all the packages that are already available in guix. I like
> > using the guix package command to practice that too, but i found it
> > practical to see packages easier. I found out that package aspi
> > (https://CRAN.R-project.org/package=aspi) is not available, and I
> > would like to ask you if you believe it is a good candidate.
> > One available package, according to [1] is r-abe
> > (https://cran.r-project.org/web/packages/abe/index.html)
>
> Sorry I have no clue of R at all. Could someone else please answer that
> question, is r-aspi a good candidate?
>
> https://cran.r-project.org/web/packages/aspi/index.html
>
>
> > I wanted to see the template, so I ran:
> > $ guix import cran abe
> > And got the template, that matches even the version, and everything
> > stated in the site.
> > But then I tried:
> > $ guix package -i r-abe and got no results.
> > In fact, after running the command you have just provided, r-abe is
> > not appearing in the r.txt file.
> > I can't understand why that is happening. Am I missing something, or
> > is there maybe an inconsistency between [1] and the guix installed in
> > my foreign distro?
>
> Concerning r-abe: I don't know how the list at guix-hpc is created
> , how often it is updated or if there are extra packages in there. In
> your case, I suppose you lack behind:
>
> There is a commit for r-abe from 2019-09-13, so it is only a month old.
> I think you are lacking behind. Have you done a `guix pull`? That's the
> command used to update the package definitions.
>
> In case you already did a guix pull recently, and you still don't see
> it, there could be a problem with your $PATH, that the wrong guix is
> coming first. Do a `which guix`.
> Guix should be the one in ~/.config/guix/current/bin/guix
>
>
> > Just wanted to install it to run guix edit to check if the suggested
> > packages were already available or if I needed to package them too,
> > but I have installed r-ade4, which has both imports and suggests, and
> > I have just run:
> > $guix import cran ade4
> > And noticed that it only states in the template the Import package
> > (MASS)
>
> If I see that right, for R we only add the "Imports" packages, as they
> are absolutely needed for compiling/running. All "Suggests" can be
> installed/used just at runtime. Please correct me anyone if I'm wrong,
> I'm not into R.
>
>
> > Here is my template for aspi (I named it for myself r-aspi.scm). I ran
> > guix download from its site, and also guix hash to convert it to
> > base32:
> >
> > (define-public r-aspi
> > (package
> >   (name "r-aspi")
> >   (version "0.2.0")
> >   (source
> >     (origin
> >       (method url-fetch)
> >       (uri (cran-uri "aspi" version))
> >       (sha256
> >         (base32
> >           "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"))))
> >   (build-system r-build-system)
> >    (home-page
> >     "https://cran.r-project.org/web/packages/aspi/")
> >   (synopsis
> >     "Analysis of Symmetry of Parasitic Infections")
> >   (description
> >     "Tools for the analysis and visualization of bilateral asymmetry
> > in parasitic infections.")
> >   (license gpl3+)))
> > And that's were I ended up today (it is still Tuesday, almost 10pm)
>
> I haven't done a full review, but that looks good. Next you need to get
> the guix sources and prepare a patch.
>
> That's described here:
>
> https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
I have already read this chapter, but I am messed up. I have already
cloned from git, but I have some questions:
1) Do I need to install everything from the git repo in my distro?
2) How do I convert my template into a package? I can't figure out that part.
>
>
> Björn

Regards,
Laura

Re: [outreach] Help trying to create R package

[Björn Höfling]

[-- Attachment #1: Type: text/plain, Size: 2712 bytes --]

Hi Laura,

On Wed, 17 Oct 2018 22:36:02 -0300
Laura Lazzati <laura.lazzati.15@gmail.com> wrote:


> > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing  
> I have already read this chapter, but I am messed up. I have already
> cloned from git, but I have some questions:
> 1) Do I need to install everything from the git repo in my distro?

I'm not sure if I understand you right. You ask if you "need to install
everything from the git in my distro?". I don't get that. Let me tell
what I mean:

You cloned that one, right?

git clone https://git.savannah.gnu.org/git/guix.git

That is the source code of Guix. I.e. when you do a

guix package -i hello

then you use the binary "guix" command that you installed in the
beginning. And the repository you cloned is just the source code, there
is nothing in there that you need to install.


Maybe you ment the list of software that is written here:

https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git

When building Guix from a checkout, the following packages are required in addition to those mentioned in the installation instructions (see Requirements).

    GNU Autoconf;
    GNU Automake;
    GNU Gettext;
    GNU Texinfo;
    Graphviz;
    GNU Help2man (optional). 

So, yeah. In order to compile Guix from source, you need all these.

But wait, read the next sentence. You have guix already installed. Guix
provides a VERY nice command, `guix envirionment <PACKAGE>`. With that,
Guix prepares an "environment" that can be directly used to build
<PACKAGE>.

So, if you enter:

guix environment guix

then Guix will know best what software in which version it needs in
order to build guix (in this case, itself, don't get trapped by that
self-circularity :-))

When you are in, you can just follow the next steps described:

./bootstrap
./configure --localstatedir=/var
make

When that went all through well, you can install the "hello"
application:

./pre-inst-env guix package -i hello

The "./pre-inst-env" tells that you want to use the guix command that
you just built, not the one that is somewhere else on your path.

Now you just go on:

> 2) How do I convert my template into a package? I can't figure out
> that part.

You don't have to CONVERT. That template IS a package:

> > (define-public r-aspi
> > (package
> >   (name "r-aspi")

What you do is you just open the file gnu/packages/r.scm and add your
"(define... " at the end.

Ehh, wait, there is no file r.scm. It is either cran.scm or
bioinformatics.scm.

Then you are done. Try to build it:

./pre-inst-env guix build r-aspi

Björn




[-- Attachment #2: OpenPGP digital signature --]
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Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Wow, Björn, you were so fast again :)

I just got around this right now.

Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
2018. okt. 18., Cs, 8:54):
>
> Hi Laura,
>
> On Wed, 17 Oct 2018 22:36:02 -0300
> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
>
>
> > > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> > I have already read this chapter, but I am messed up. I have already
> > cloned from git, but I have some questions:
> > 1) Do I need to install everything from the git repo in my distro?
>
> I'm not sure if I understand you right. You ask if you "need to install
> everything from the git in my distro?". I don't get that. Let me tell
> what I mean:
>
> You cloned that one, right?
>
> git clone https://git.savannah.gnu.org/git/guix.git
>
> That is the source code of Guix. I.e. when you do a
>
> guix package -i hello
>
> then you use the binary "guix" command that you installed in the
> beginning. And the repository you cloned is just the source code, there
> is nothing in there that you need to install.
>
>
> Maybe you ment the list of software that is written here:
>
> https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git
>
> When building Guix from a checkout, the following packages are required in addition to those mentioned in the installation instructions (see Requirements).
>
>     GNU Autoconf;
>     GNU Automake;
>     GNU Gettext;
>     GNU Texinfo;
>     Graphviz;
>     GNU Help2man (optional).
>
> So, yeah. In order to compile Guix from source, you need all these.
>
> But wait, read the next sentence. You have guix already installed. Guix
> provides a VERY nice command, `guix envirionment <PACKAGE>`. With that,
> Guix prepares an "environment" that can be directly used to build
> <PACKAGE>.
>
> So, if you enter:
>
> guix environment guix
>
> then Guix will know best what software in which version it needs in
> order to build guix (in this case, itself, don't get trapped by that
> self-circularity :-))
>
> When you are in, you can just follow the next steps described:
>
> ./bootstrap
> ./configure --localstatedir=/var
> make
>
> When that went all through well, you can install the "hello"
> application:
>
> ./pre-inst-env guix package -i hello
>
> The "./pre-inst-env" tells that you want to use the guix command that
> you just built, not the one that is somewhere else on your path.
>
> Now you just go on:
>
> > 2) How do I convert my template into a package? I can't figure out
> > that part.
>
> You don't have to CONVERT. That template IS a package:
>
> > > (define-public r-aspi
> > > (package
> > >   (name "r-aspi")
>
> What you do is you just open the file gnu/packages/r.scm and add your
> "(define... " at the end.
>
> Ehh, wait, there is no file r.scm. It is either cran.scm or
> bioinformatics.scm.
>
> Then you are done. Try to build it:
>
> ./pre-inst-env guix build r-aspi
>
> Björn
>
>
>

Thank you!
g_bor

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Thu, Oct 18, 2018 at 4:50 AM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> Wow, Björn, you were so fast again :)
>
> I just got around this right now.
Again, thank both for being so kind :)
>
> Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
> 2018. okt. 18., Cs, 8:54):
> >
> > Hi Laura,
> >
> > On Wed, 17 Oct 2018 22:36:02 -0300
> > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> >
> >
> > > > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> > > I have already read this chapter, but I am messed up. I have already
> > > cloned from git, but I have some questions:
> > > 1) Do I need to install everything from the git repo in my distro?
> >
> > I'm not sure if I understand you right. You ask if you "need to install
> > everything from the git in my distro?". I don't get that. Let me tell
> > what I mean:
> >
> > You cloned that one, right?
> >
> > git clone https://git.savannah.gnu.org/git/guix.git
> >
> > That is the source code of Guix. I.e. when you do a
> >
> > guix package -i hello
> >
> > then you use the binary "guix" command that you installed in the
> > beginning. And the repository you cloned is just the source code, there
> > is nothing in there that you need to install.
> >
> >
> > Maybe you ment the list of software that is written here:
> >
> > https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git
> >
> > When building Guix from a checkout, the following packages are required in addition to those mentioned in the installation instructions (see Requirements).
> >
> >     GNU Autoconf;
> >     GNU Automake;
> >     GNU Gettext;
> >     GNU Texinfo;
> >     Graphviz;
> >     GNU Help2man (optional).
> >
> > So, yeah. In order to compile Guix from source, you need all these.
I was indeed trying to do this.

> >
> > But wait, read the next sentence. You have guix already installed. Guix
> > provides a VERY nice command, `guix envirionment <PACKAGE>`. With that,
> > Guix prepares an "environment" that can be directly used to build
> > <PACKAGE>.
> >
> > So, if you enter:
> >
> > guix environment guix
I have just did this :)
> >
> > then Guix will know best what software in which version it needs in
> > order to build guix (in this case, itself, don't get trapped by that
> > self-circularity :-))
> >
> > When you are in, you can just follow the next steps described:
> >
> > ./bootstrap
This worked fine.
> > ./configure --localstatedir=/var

This did not, I am getting this error:

configure: checking for guile 2.2
configure: found guile 2.2
checking for guile-2.2... /usr/bin/guile-2.2
checking for Guile version >= 2.2... 2.2.3
checking for guild-2.2... no
checking for guile-config-2.2... no
checking for guile-tools-2.2... no
configure: error: 'guild' binary not found; please check your
guile-2.x installation.

Then ran
$guix package -i guile
Same error running configure.
$guix package -s guild
$guix package -i guildhall
And my output of guix -I, however, is:
hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
recutils    1.7    out
/gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
glibc-locales    2.27    out
/gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
glibc-utf8-locales    2.27    out
/gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
nss-certs    3.36.1    out
/gnu/store/h8qlwgwhg6jr0kp5ihy90cgb6h0q1fj9-nss-certs-3.36.1
r-ade4    1.7-11    out
/gnu/store/980xl9a58nd6f22wzwsmv9mkhv7pq3hh-r-ade4-1.7-11
guile    2.2.4    out    /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4
guildhall    0-1.2fe2cc539    out
/gnu/store/kd2mvhr18yphrkiqgavw0w0r0n5bfchn-guildhall-0-1.2fe2cc539

Something weird  is that in configure output I see there is a /usr/bin
mentioned, so I went to that dir, ran
$ ll | grep guile
lrwxrwxrwx  1 root root          23 oct 10 22:55 guile ->
/etc/alternatives/guile*
lrwxrwxrwx  1 root root          43 jul 17 10:42 guile-2.2 ->
../lib/x86_64-linux-gnu/guile-2.2/bin/guile*

And can't figure out why I have that links.

> > make
> >
> > When that went all through well, you can install the "hello"
> > application:
> >
> > ./pre-inst-env guix package -i hello
> >
> > The "./pre-inst-env" tells that you want to use the guix command that
> > you just built, not the one that is somewhere else on your path.
> >
> > Now you just go on:
> >
> > > 2) How do I convert my template into a package? I can't figure out
> > > that part.
> >
> > You don't have to CONVERT. That template IS a package:
> >
> > > > (define-public r-aspi
> > > > (package
> > > >   (name "r-aspi")
> >
> > What you do is you just open the file gnu/packages/r.scm and add your
> > "(define... " at the end.
> >
> > Ehh, wait, there is no file r.scm. It is either cran.scm or
> > bioinformatics.scm.
> >
> > Then you are done. Try to build it:
> >
> > ./pre-inst-env guix build r-aspi
> >
> > Björn
> >
> >
> >
>
> Thank you!
> g_bor

Regards :)
Laura

Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Hi Laura,

Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
okt. 18., Cs, 16:49):
>
> On Thu, Oct 18, 2018 at 4:50 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> >
> > Wow, Björn, you were so fast again :)
> >
> > I just got around this right now.
> Again, thank both for being so kind :)
> >
> > Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
> > 2018. okt. 18., Cs, 8:54):
> > >
> > > Hi Laura,
> > >
> > > On Wed, 17 Oct 2018 22:36:02 -0300
> > > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> > >
> > >
> > > > > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> > > > I have already read this chapter, but I am messed up. I have already
> > > > cloned from git, but I have some questions:
> > > > 1) Do I need to install everything from the git repo in my distro?
> > >
> > > I'm not sure if I understand you right. You ask if you "need to install
> > > everything from the git in my distro?". I don't get that. Let me tell
> > > what I mean:
> > >
> > > You cloned that one, right?
> > >
> > > git clone https://git.savannah.gnu.org/git/guix.git
> > >
> > > That is the source code of Guix. I.e. when you do a
> > >
> > > guix package -i hello
> > >
> > > then you use the binary "guix" command that you installed in the
> > > beginning. And the repository you cloned is just the source code, there
> > > is nothing in there that you need to install.
> > >
> > >
> > > Maybe you ment the list of software that is written here:
> > >
> > > https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git
> > >
> > > When building Guix from a checkout, the following packages are required in addition to those mentioned in the installation instructions (see Requirements).
> > >
> > >     GNU Autoconf;
> > >     GNU Automake;
> > >     GNU Gettext;
> > >     GNU Texinfo;
> > >     Graphviz;
> > >     GNU Help2man (optional).
> > >
> > > So, yeah. In order to compile Guix from source, you need all these.
> I was indeed trying to do this.
>
> > >
> > > But wait, read the next sentence. You have guix already installed. Guix
> > > provides a VERY nice command, `guix envirionment <PACKAGE>`. With that,
> > > Guix prepares an "environment" that can be directly used to build
> > > <PACKAGE>.
> > >
> > > So, if you enter:
> > >
> > > guix environment guix
> I have just did this :)
Great.
> > >
> > > then Guix will know best what software in which version it needs in
> > > order to build guix (in this case, itself, don't get trapped by that
> > > self-circularity :-))
> > >
> > > When you are in, you can just follow the next steps described:
> > >
> > > ./bootstrap
> This worked fine.
> > > ./configure --localstatedir=/var
>
> This did not, I am getting this error:
>
> configure: checking for guile 2.2
> configure: found guile 2.2
> checking for guile-2.2... /usr/bin/guile-2.2
> checking for Guile version >= 2.2... 2.2.3
> checking for guild-2.2... no
> checking for guile-config-2.2... no
> checking for guile-tools-2.2... no
> configure: error: 'guild' binary not found; please check your
> guile-2.x installation.
>

I don't know what to make of this, but you could try guix environment
guix --ad-hoc guild.
Please see if that helps, if not then I will have a closer look at this.

> Then ran
> $guix package -i guile
> Same error running configure.
> $guix package -s guild
> $guix package -i guildhall
> And my output of guix -I, however, is:
> hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> recutils    1.7    out
> /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> glibc-locales    2.27    out
> /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> glibc-utf8-locales    2.27    out
> /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> nss-certs    3.36.1    out
> /gnu/store/h8qlwgwhg6jr0kp5ihy90cgb6h0q1fj9-nss-certs-3.36.1
> r-ade4    1.7-11    out
> /gnu/store/980xl9a58nd6f22wzwsmv9mkhv7pq3hh-r-ade4-1.7-11
> guile    2.2.4    out    /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4
> guildhall    0-1.2fe2cc539    out
> /gnu/store/kd2mvhr18yphrkiqgavw0w0r0n5bfchn-guildhall-0-1.2fe2cc539
>
> Something weird  is that in configure output I see there is a /usr/bin
> mentioned, so I went to that dir, ran
> $ ll | grep guile
> lrwxrwxrwx  1 root root          23 oct 10 22:55 guile ->
> /etc/alternatives/guile*
> lrwxrwxrwx  1 root root          43 jul 17 10:42 guile-2.2 ->
> ../lib/x86_64-linux-gnu/guile-2.2/bin/guile*
>
> And can't figure out why I have that links.
>
> > > make
> > >
> > > When that went all through well, you can install the "hello"
> > > application:
> > >
> > > ./pre-inst-env guix package -i hello
> > >
> > > The "./pre-inst-env" tells that you want to use the guix command that
> > > you just built, not the one that is somewhere else on your path.
> > >
> > > Now you just go on:
> > >
> > > > 2) How do I convert my template into a package? I can't figure out
> > > > that part.
> > >
> > > You don't have to CONVERT. That template IS a package:
> > >
> > > > > (define-public r-aspi
> > > > > (package
> > > > >   (name "r-aspi")
> > >
> > > What you do is you just open the file gnu/packages/r.scm and add your
> > > "(define... " at the end.
> > >
> > > Ehh, wait, there is no file r.scm. It is either cran.scm or
> > > bioinformatics.scm.
> > >
> > > Then you are done. Try to build it:
> > >
> > > ./pre-inst-env guix build r-aspi
> > >
> > > Björn
> > >
> > >
> > >
> >
> > Thank you!
> > g_bor
>
> Regards :)
> Laura
Best regards,
g_bor

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Thu, Oct 18, 2018 at 12:15 PM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> Hi Laura,
>
> Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> okt. 18., Cs, 16:49):
> >
> > On Thu, Oct 18, 2018 at 4:50 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> > >
> > > Wow, Björn, you were so fast again :)
> > >
> > > I just got around this right now.
> > Again, thank both for being so kind :)
> > >
> > > Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
> > > 2018. okt. 18., Cs, 8:54):
> > > >
> > > > Hi Laura,
> > > >
> > > > On Wed, 17 Oct 2018 22:36:02 -0300
> > > > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> > > >
> > > >
> > > > > > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> > > > > I have already read this chapter, but I am messed up. I have already
> > > > > cloned from git, but I have some questions:
> > > > > 1) Do I need to install everything from the git repo in my distro?
> > > >
> > > > I'm not sure if I understand you right. You ask if you "need to install
> > > > everything from the git in my distro?". I don't get that. Let me tell
> > > > what I mean:
> > > >
> > > > You cloned that one, right?
> > > >
> > > > git clone https://git.savannah.gnu.org/git/guix.git
> > > >
> > > > That is the source code of Guix. I.e. when you do a
> > > >
> > > > guix package -i hello
> > > >
> > > > then you use the binary "guix" command that you installed in the
> > > > beginning. And the repository you cloned is just the source code, there
> > > > is nothing in there that you need to install.
> > > >
> > > >
> > > > Maybe you ment the list of software that is written here:
> > > >
> > > > https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git
> > > >
> > > > When building Guix from a checkout, the following packages are required in addition to those mentioned in the installation instructions (see Requirements).
> > > >
> > > >     GNU Autoconf;
> > > >     GNU Automake;
> > > >     GNU Gettext;
> > > >     GNU Texinfo;
> > > >     Graphviz;
> > > >     GNU Help2man (optional).
> > > >
> > > > So, yeah. In order to compile Guix from source, you need all these.
> > I was indeed trying to do this.
> >
> > > >
> > > > But wait, read the next sentence. You have guix already installed. Guix
> > > > provides a VERY nice command, `guix envirionment <PACKAGE>`. With that,
> > > > Guix prepares an "environment" that can be directly used to build
> > > > <PACKAGE>.
> > > >
> > > > So, if you enter:
> > > >
> > > > guix environment guix
> > I have just did this :)
> Great.
> > > >
> > > > then Guix will know best what software in which version it needs in
> > > > order to build guix (in this case, itself, don't get trapped by that
> > > > self-circularity :-))
> > > >
> > > > When you are in, you can just follow the next steps described:
> > > >
> > > > ./bootstrap
> > This worked fine.
> > > > ./configure --localstatedir=/var
> >
> > This did not, I am getting this error:
> >
> > configure: checking for guile 2.2
> > configure: found guile 2.2
> > checking for guile-2.2... /usr/bin/guile-2.2
> > checking for Guile version >= 2.2... 2.2.3
> > checking for guild-2.2... no
> > checking for guile-config-2.2... no
> > checking for guile-tools-2.2... no
> > configure: error: 'guild' binary not found; please check your
> > guile-2.x installation.
> >
>
> I don't know what to make of this, but you could try guix environment
> guix --ad-hoc guild.
> Please see if that helps, if not then I will have a closer look at this.
I restored everything to the snapshot where I ended cloning guix.
I get this error when trying to run guix environme guix --ad-hoc guild:
guix environment: error: guild: unknown package

>
> > Then ran
> > $guix package -i guile
> > Same error running configure.
> > $guix package -s guild
> > $guix package -i guildhall
> > And my output of guix -I, however, is:
> > hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> > recutils    1.7    out
> > /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> > glibc-locales    2.27    out
> > /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> > glibc-utf8-locales    2.27    out
> > /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> > nss-certs    3.36.1    out
> > /gnu/store/h8qlwgwhg6jr0kp5ihy90cgb6h0q1fj9-nss-certs-3.36.1
> > r-ade4    1.7-11    out
> > /gnu/store/980xl9a58nd6f22wzwsmv9mkhv7pq3hh-r-ade4-1.7-11
> > guile    2.2.4    out    /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4
> > guildhall    0-1.2fe2cc539    out
> > /gnu/store/kd2mvhr18yphrkiqgavw0w0r0n5bfchn-guildhall-0-1.2fe2cc539
> >
> > Something weird  is that in configure output I see there is a /usr/bin
> > mentioned, so I went to that dir, ran
> > $ ll | grep guile
> > lrwxrwxrwx  1 root root          23 oct 10 22:55 guile ->
> > /etc/alternatives/guile*
> > lrwxrwxrwx  1 root root          43 jul 17 10:42 guile-2.2 ->
> > ../lib/x86_64-linux-gnu/guile-2.2/bin/guile*
> >
> > And can't figure out why I have that links.
> >
> > > > make
> > > >
> > > > When that went all through well, you can install the "hello"
> > > > application:
> > > >
> > > > ./pre-inst-env guix package -i hello
> > > >
> > > > The "./pre-inst-env" tells that you want to use the guix command that
> > > > you just built, not the one that is somewhere else on your path.
> > > >
> > > > Now you just go on:
> > > >
> > > > > 2) How do I convert my template into a package? I can't figure out
> > > > > that part.
> > > >
> > > > You don't have to CONVERT. That template IS a package:
> > > >
> > > > > > (define-public r-aspi
> > > > > > (package
> > > > > >   (name "r-aspi")
> > > >
> > > > What you do is you just open the file gnu/packages/r.scm and add your
> > > > "(define... " at the end.
> > > >
> > > > Ehh, wait, there is no file r.scm. It is either cran.scm or
> > > > bioinformatics.scm.
> > > >
> > > > Then you are done. Try to build it:
> > > >
> > > > ./pre-inst-env guix build r-aspi
> > > >
> > > > Björn
> > > >
> > > >
> > > >
> > >
> > > Thank you!
> > > g_bor
> >
> > Regards :)
> > Laura
> Best regards,
> g_bor

Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
okt. 18., Cs, 17:26):
>
> On Thu, Oct 18, 2018 at 12:15 PM Gábor Boskovits <boskovits@gmail.com> wrote:
> >
> > Hi Laura,
> >
> > Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> > okt. 18., Cs, 16:49):
> > >
> > > On Thu, Oct 18, 2018 at 4:50 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> > > >
> > > > Wow, Björn, you were so fast again :)
> > > >
> > > > I just got around this right now.
> > > Again, thank both for being so kind :)
> > > >
> > > > Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
> > > > 2018. okt. 18., Cs, 8:54):
> > > > >
> > > > > Hi Laura,
> > > > >
> > > > > On Wed, 17 Oct 2018 22:36:02 -0300
> > > > > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> > > > >
> > > > >
> > > > > > > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> > > > > > I have already read this chapter, but I am messed up. I have already
> > > > > > cloned from git, but I have some questions:
> > > > > > 1) Do I need to install everything from the git repo in my distro?
> > > > >
> > > > > I'm not sure if I understand you right. You ask if you "need to install
> > > > > everything from the git in my distro?". I don't get that. Let me tell
> > > > > what I mean:
> > > > >
> > > > > You cloned that one, right?
> > > > >
> > > > > git clone https://git.savannah.gnu.org/git/guix.git
> > > > >
> > > > > That is the source code of Guix. I.e. when you do a
> > > > >
> > > > > guix package -i hello
> > > > >
> > > > > then you use the binary "guix" command that you installed in the
> > > > > beginning. And the repository you cloned is just the source code, there
> > > > > is nothing in there that you need to install.
> > > > >
> > > > >
> > > > > Maybe you ment the list of software that is written here:
> > > > >
> > > > > https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git
> > > > >
> > > > > When building Guix from a checkout, the following packages are required in addition to those mentioned in the installation instructions (see Requirements).
> > > > >
> > > > >     GNU Autoconf;
> > > > >     GNU Automake;
> > > > >     GNU Gettext;
> > > > >     GNU Texinfo;
> > > > >     Graphviz;
> > > > >     GNU Help2man (optional).
> > > > >
> > > > > So, yeah. In order to compile Guix from source, you need all these.
> > > I was indeed trying to do this.
> > >
> > > > >
> > > > > But wait, read the next sentence. You have guix already installed. Guix
> > > > > provides a VERY nice command, `guix envirionment <PACKAGE>`. With that,
> > > > > Guix prepares an "environment" that can be directly used to build
> > > > > <PACKAGE>.
> > > > >
> > > > > So, if you enter:
> > > > >
> > > > > guix environment guix
> > > I have just did this :)
> > Great.
> > > > >
> > > > > then Guix will know best what software in which version it needs in
> > > > > order to build guix (in this case, itself, don't get trapped by that
> > > > > self-circularity :-))
> > > > >
> > > > > When you are in, you can just follow the next steps described:
> > > > >
> > > > > ./bootstrap
> > > This worked fine.
> > > > > ./configure --localstatedir=/var
> > >
> > > This did not, I am getting this error:
> > >
> > > configure: checking for guile 2.2
> > > configure: found guile 2.2
> > > checking for guile-2.2... /usr/bin/guile-2.2
> > > checking for Guile version >= 2.2... 2.2.3
> > > checking for guild-2.2... no
> > > checking for guile-config-2.2... no
> > > checking for guile-tools-2.2... no
> > > configure: error: 'guild' binary not found; please check your
> > > guile-2.x installation.
> > >
> >
> > I don't know what to make of this, but you could try guix environment
> > guix --ad-hoc guild.
> > Please see if that helps, if not then I will have a closer look at this.
> I restored everything to the snapshot where I ended cloning guix.
> I get this error when trying to run guix environme guix --ad-hoc guild:
> guix environment: error: guild: unknown package
>

Oops, my bad, yes. I've checked this more thoroughly, on my system
guild is provided by guile, which should be provided by guile. Could you run
a which guild and a which guile inside the guix environment guix?

> >
> > > Then ran
> > > $guix package -i guile
> > > Same error running configure.
> > > $guix package -s guild
> > > $guix package -i guildhall
> > > And my output of guix -I, however, is:
> > > hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> > > recutils    1.7    out
> > > /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> > > glibc-locales    2.27    out
> > > /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> > > glibc-utf8-locales    2.27    out
> > > /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> > > nss-certs    3.36.1    out
> > > /gnu/store/h8qlwgwhg6jr0kp5ihy90cgb6h0q1fj9-nss-certs-3.36.1
> > > r-ade4    1.7-11    out
> > > /gnu/store/980xl9a58nd6f22wzwsmv9mkhv7pq3hh-r-ade4-1.7-11
> > > guile    2.2.4    out    /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4
> > > guildhall    0-1.2fe2cc539    out
> > > /gnu/store/kd2mvhr18yphrkiqgavw0w0r0n5bfchn-guildhall-0-1.2fe2cc539
> > >
> > > Something weird  is that in configure output I see there is a /usr/bin
> > > mentioned, so I went to that dir, ran
> > > $ ll | grep guile
> > > lrwxrwxrwx  1 root root          23 oct 10 22:55 guile ->
> > > /etc/alternatives/guile*
> > > lrwxrwxrwx  1 root root          43 jul 17 10:42 guile-2.2 ->
> > > ../lib/x86_64-linux-gnu/guile-2.2/bin/guile*
> > >
> > > And can't figure out why I have that links.
> > >
> > > > > make
> > > > >
> > > > > When that went all through well, you can install the "hello"
> > > > > application:
> > > > >
> > > > > ./pre-inst-env guix package -i hello
> > > > >
> > > > > The "./pre-inst-env" tells that you want to use the guix command that
> > > > > you just built, not the one that is somewhere else on your path.
> > > > >
> > > > > Now you just go on:
> > > > >
> > > > > > 2) How do I convert my template into a package? I can't figure out
> > > > > > that part.
> > > > >
> > > > > You don't have to CONVERT. That template IS a package:
> > > > >
> > > > > > > (define-public r-aspi
> > > > > > > (package
> > > > > > >   (name "r-aspi")
> > > > >
> > > > > What you do is you just open the file gnu/packages/r.scm and add your
> > > > > "(define... " at the end.
> > > > >
> > > > > Ehh, wait, there is no file r.scm. It is either cran.scm or
> > > > > bioinformatics.scm.
> > > > >
> > > > > Then you are done. Try to build it:
> > > > >
> > > > > ./pre-inst-env guix build r-aspi
> > > > >
> > > > > Björn
> > > > >
> > > > >
> > > > >
> > > >
> > > > Thank you!
> > > > g_bor
> > >
> > > Regards :)
> > > Laura
> > Best regards,
> > g_bor

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Thu, Oct 18, 2018 at 12:40 PM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> okt. 18., Cs, 17:26):
> >
> > On Thu, Oct 18, 2018 at 12:15 PM Gábor Boskovits <boskovits@gmail.com> wrote:
> > >
> > > Hi Laura,
> > >
> > > Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> > > okt. 18., Cs, 16:49):
> > > >
> > > > On Thu, Oct 18, 2018 at 4:50 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> > > > >
> > > > > Wow, Björn, you were so fast again :)
> > > > >
> > > > > I just got around this right now.
> > > > Again, thank both for being so kind :)
> > > > >
> > > > > Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
> > > > > 2018. okt. 18., Cs, 8:54):
> > > > > >
> > > > > > Hi Laura,
> > > > > >
> > > > > > On Wed, 17 Oct 2018 22:36:02 -0300
> > > > > > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> > > > > >
> > > > > >
> > > > > > > > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> > > > > > > I have already read this chapter, but I am messed up. I have already
> > > > > > > cloned from git, but I have some questions:
> > > > > > > 1) Do I need to install everything from the git repo in my distro?
> > > > > >
> > > > > > I'm not sure if I understand you right. You ask if you "need to install
> > > > > > everything from the git in my distro?". I don't get that. Let me tell
> > > > > > what I mean:
> > > > > >
> > > > > > You cloned that one, right?
> > > > > >
> > > > > > git clone https://git.savannah.gnu.org/git/guix.git
> > > > > >
> > > > > > That is the source code of Guix. I.e. when you do a
> > > > > >
> > > > > > guix package -i hello
> > > > > >
> > > > > > then you use the binary "guix" command that you installed in the
> > > > > > beginning. And the repository you cloned is just the source code, there
> > > > > > is nothing in there that you need to install.
> > > > > >
> > > > > >
> > > > > > Maybe you ment the list of software that is written here:
> > > > > >
> > > > > > https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git
> > > > > >
> > > > > > When building Guix from a checkout, the following packages are required in addition to those mentioned in the installation instructions (see Requirements).
> > > > > >
> > > > > >     GNU Autoconf;
> > > > > >     GNU Automake;
> > > > > >     GNU Gettext;
> > > > > >     GNU Texinfo;
> > > > > >     Graphviz;
> > > > > >     GNU Help2man (optional).
> > > > > >
> > > > > > So, yeah. In order to compile Guix from source, you need all these.
> > > > I was indeed trying to do this.
> > > >
> > > > > >
> > > > > > But wait, read the next sentence. You have guix already installed. Guix
> > > > > > provides a VERY nice command, `guix envirionment <PACKAGE>`. With that,
> > > > > > Guix prepares an "environment" that can be directly used to build
> > > > > > <PACKAGE>.
> > > > > >
> > > > > > So, if you enter:
> > > > > >
> > > > > > guix environment guix
> > > > I have just did this :)
> > > Great.
> > > > > >
> > > > > > then Guix will know best what software in which version it needs in
> > > > > > order to build guix (in this case, itself, don't get trapped by that
> > > > > > self-circularity :-))
> > > > > >
> > > > > > When you are in, you can just follow the next steps described:
> > > > > >
> > > > > > ./bootstrap
> > > > This worked fine.
> > > > > > ./configure --localstatedir=/var
> > > >
> > > > This did not, I am getting this error:
> > > >
> > > > configure: checking for guile 2.2
> > > > configure: found guile 2.2
> > > > checking for guile-2.2... /usr/bin/guile-2.2
> > > > checking for Guile version >= 2.2... 2.2.3
> > > > checking for guild-2.2... no
> > > > checking for guile-config-2.2... no
> > > > checking for guile-tools-2.2... no
> > > > configure: error: 'guild' binary not found; please check your
> > > > guile-2.x installation.
> > > >
> > >
> > > I don't know what to make of this, but you could try guix environment
> > > guix --ad-hoc guild.
> > > Please see if that helps, if not then I will have a closer look at this.
> > I restored everything to the snapshot where I ended cloning guix.
> > I get this error when trying to run guix environme guix --ad-hoc guild:
> > guix environment: error: guild: unknown package
> >
>
> Oops, my bad, yes. I've checked this more thoroughly, on my system
> guild is provided by guile, which should be provided by guile. Could you run
> a which guild and a which guile inside the guix environment guix?
I went back to the previous snapshot several times.

I was cloning the  guix and throwing guix environment guix without doing cd guix
After several times, I realized that I had a warning in the output:

building /gnu/store/ilscbls919b78vn9l7b2jb72jmalbxm8-profile.drv...
warning: collision encountered:
 /gnu/store/b5x786d3h552j2zp4ppvlz9dkbiqy2ng-ld-wrapper-0/bin/ld
 /gnu/store/srmqh29dpm50j8kj1pbqg2rgh053wgyp-binutils-2.30/bin/ld
warning: choosing
/gnu/store/b5x786d3h552j2zp4ppvlz9dkbiqy2ng-ld-wrapper-0/bin/ld
successfully built /gnu/store/ilscbls919b78vn9l7b2jb72jmalbxm8-profile.drv
But I did not paid attention to that, echo $? was OK (0).
And then ran everything as I stated, facing all that issues.

Now I've cloned the repo again, removing previously the guix directory.
did cd guix
and ran guix environment guix
Did not have that warning anymore, just the usual locale warning that
happens all the time.
ran ./bootstrap

And in both cases (before restoring my VM state, and now) the result
of the which commands are:

/gnu/store/2w5kxhmkq4zkamsgx1b40vr3ii1z4dxb-profile/bin/guild
and
/gnu/store/2w5kxhmkq4zkamsgx1b40vr3ii1z4dxb-profile/bin/guile

I don't know if this is relevant or not, and if I should run the
.configure or not before you seing this.



>
> > >
> > > > Then ran
> > > > $guix package -i guile
> > > > Same error running configure.
> > > > $guix package -s guild
> > > > $guix package -i guildhall
> > > > And my output of guix -I, however, is:
> > > > hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> > > > recutils    1.7    out
> > > > /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> > > > glibc-locales    2.27    out
> > > > /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> > > > glibc-utf8-locales    2.27    out
> > > > /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> > > > nss-certs    3.36.1    out
> > > > /gnu/store/h8qlwgwhg6jr0kp5ihy90cgb6h0q1fj9-nss-certs-3.36.1
> > > > r-ade4    1.7-11    out
> > > > /gnu/store/980xl9a58nd6f22wzwsmv9mkhv7pq3hh-r-ade4-1.7-11
> > > > guile    2.2.4    out    /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4
> > > > guildhall    0-1.2fe2cc539    out
> > > > /gnu/store/kd2mvhr18yphrkiqgavw0w0r0n5bfchn-guildhall-0-1.2fe2cc539
> > > >
> > > > Something weird  is that in configure output I see there is a /usr/bin
> > > > mentioned, so I went to that dir, ran
> > > > $ ll | grep guile
> > > > lrwxrwxrwx  1 root root          23 oct 10 22:55 guile ->
> > > > /etc/alternatives/guile*
> > > > lrwxrwxrwx  1 root root          43 jul 17 10:42 guile-2.2 ->
> > > > ../lib/x86_64-linux-gnu/guile-2.2/bin/guile*
> > > >
> > > > And can't figure out why I have that links.
> > > >
> > > > > > make
> > > > > >
> > > > > > When that went all through well, you can install the "hello"
> > > > > > application:
> > > > > >
> > > > > > ./pre-inst-env guix package -i hello
> > > > > >
> > > > > > The "./pre-inst-env" tells that you want to use the guix command that
> > > > > > you just built, not the one that is somewhere else on your path.
> > > > > >
> > > > > > Now you just go on:
> > > > > >
> > > > > > > 2) How do I convert my template into a package? I can't figure out
> > > > > > > that part.
> > > > > >
> > > > > > You don't have to CONVERT. That template IS a package:
> > > > > >
> > > > > > > > (define-public r-aspi
> > > > > > > > (package
> > > > > > > >   (name "r-aspi")
> > > > > >
> > > > > > What you do is you just open the file gnu/packages/r.scm and add your
> > > > > > "(define... " at the end.
> > > > > >
> > > > > > Ehh, wait, there is no file r.scm. It is either cran.scm or
> > > > > > bioinformatics.scm.
> > > > > >
> > > > > > Then you are done. Try to build it:
> > > > > >
> > > > > > ./pre-inst-env guix build r-aspi
> > > > > >
> > > > > > Björn
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > Thank you!
> > > > > g_bor
> > > >
> > > > Regards :)
> > > > Laura
> > > Best regards,
> > > g_bor
Regards!
Laur

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Thu, Oct 18, 2018 at 1:18 PM Laura Lazzati
<laura.lazzati.15@gmail.com> wrote:
>
> On Thu, Oct 18, 2018 at 12:40 PM Gábor Boskovits <boskovits@gmail.com> wrote:
> >
> > Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> > okt. 18., Cs, 17:26):
> > >
> > > On Thu, Oct 18, 2018 at 12:15 PM Gábor Boskovits <boskovits@gmail.com> wrote:
> > > >
> > > > Hi Laura,
> > > >
> > > > Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> > > > okt. 18., Cs, 16:49):
> > > > >
> > > > > On Thu, Oct 18, 2018 at 4:50 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> > > > > >
> > > > > > Wow, Björn, you were so fast again :)
> > > > > >
> > > > > > I just got around this right now.
> > > > > Again, thank both for being so kind :)
> > > > > >
> > > > > > Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
> > > > > > 2018. okt. 18., Cs, 8:54):
> > > > > > >
> > > > > > > Hi Laura,
> > > > > > >
> > > > > > > On Wed, 17 Oct 2018 22:36:02 -0300
> > > > > > > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> > > > > > >
> > > > > > >
> > > > > > > > > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing
> > > > > > > > I have already read this chapter, but I am messed up. I have already
> > > > > > > > cloned from git, but I have some questions:
> > > > > > > > 1) Do I need to install everything from the git repo in my distro?
> > > > > > >
> > > > > > > I'm not sure if I understand you right. You ask if you "need to install
> > > > > > > everything from the git in my distro?". I don't get that. Let me tell
> > > > > > > what I mean:
> > > > > > >
> > > > > > > You cloned that one, right?
> > > > > > >
> > > > > > > git clone https://git.savannah.gnu.org/git/guix.git
> > > > > > >
> > > > > > > That is the source code of Guix. I.e. when you do a
> > > > > > >
> > > > > > > guix package -i hello
> > > > > > >
> > > > > > > then you use the binary "guix" command that you installed in the
> > > > > > > beginning. And the repository you cloned is just the source code, there
> > > > > > > is nothing in there that you need to install.
> > > > > > >
> > > > > > >
> > > > > > > Maybe you ment the list of software that is written here:
> > > > > > >
> > > > > > > https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git
> > > > > > >
> > > > > > > When building Guix from a checkout, the following packages are required in addition to those mentioned in the installation instructions (see Requirements).
> > > > > > >
> > > > > > >     GNU Autoconf;
> > > > > > >     GNU Automake;
> > > > > > >     GNU Gettext;
> > > > > > >     GNU Texinfo;
> > > > > > >     Graphviz;
> > > > > > >     GNU Help2man (optional).
> > > > > > >
> > > > > > > So, yeah. In order to compile Guix from source, you need all these.
> > > > > I was indeed trying to do this.
> > > > >
> > > > > > >
> > > > > > > But wait, read the next sentence. You have guix already installed. Guix
> > > > > > > provides a VERY nice command, `guix envirionment <PACKAGE>`. With that,
> > > > > > > Guix prepares an "environment" that can be directly used to build
> > > > > > > <PACKAGE>.
> > > > > > >
> > > > > > > So, if you enter:
> > > > > > >
> > > > > > > guix environment guix
> > > > > I have just did this :)
> > > > Great.
> > > > > > >
> > > > > > > then Guix will know best what software in which version it needs in
> > > > > > > order to build guix (in this case, itself, don't get trapped by that
> > > > > > > self-circularity :-))
> > > > > > >
> > > > > > > When you are in, you can just follow the next steps described:
> > > > > > >
> > > > > > > ./bootstrap
> > > > > This worked fine.
> > > > > > > ./configure --localstatedir=/var
> > > > >
> > > > > This did not, I am getting this error:
> > > > >
> > > > > configure: checking for guile 2.2
> > > > > configure: found guile 2.2
> > > > > checking for guile-2.2... /usr/bin/guile-2.2
> > > > > checking for Guile version >= 2.2... 2.2.3
> > > > > checking for guild-2.2... no
> > > > > checking for guile-config-2.2... no
> > > > > checking for guile-tools-2.2... no
> > > > > configure: error: 'guild' binary not found; please check your
> > > > > guile-2.x installation.
> > > > >
> > > >
> > > > I don't know what to make of this, but you could try guix environment
> > > > guix --ad-hoc guild.
> > > > Please see if that helps, if not then I will have a closer look at this.
> > > I restored everything to the snapshot where I ended cloning guix.
> > > I get this error when trying to run guix environme guix --ad-hoc guild:
> > > guix environment: error: guild: unknown package
> > >
> >
> > Oops, my bad, yes. I've checked this more thoroughly, on my system
> > guild is provided by guile, which should be provided by guile. Could you run
> > a which guild and a which guile inside the guix environment guix?
> I went back to the previous snapshot several times.
>
> I was cloning the  guix and throwing guix environment guix without doing cd guix
> After several times, I realized that I had a warning in the output:
>
> building /gnu/store/ilscbls919b78vn9l7b2jb72jmalbxm8-profile.drv...
> warning: collision encountered:
>  /gnu/store/b5x786d3h552j2zp4ppvlz9dkbiqy2ng-ld-wrapper-0/bin/ld
>  /gnu/store/srmqh29dpm50j8kj1pbqg2rgh053wgyp-binutils-2.30/bin/ld
> warning: choosing
> /gnu/store/b5x786d3h552j2zp4ppvlz9dkbiqy2ng-ld-wrapper-0/bin/ld
> successfully built /gnu/store/ilscbls919b78vn9l7b2jb72jmalbxm8-profile.drv
> But I did not paid attention to that, echo $? was OK (0).
> And then ran everything as I stated, facing all that issues.
>
> Now I've cloned the repo again, removing previously the guix directory.
> did cd guix
> and ran guix environment guix
> Did not have that warning anymore, just the usual locale warning that
> happens all the time.
> ran ./bootstrap
>
> And in both cases (before restoring my VM state, and now) the result
> of the which commands are:
>
> /gnu/store/2w5kxhmkq4zkamsgx1b40vr3ii1z4dxb-profile/bin/guild
> and
> /gnu/store/2w5kxhmkq4zkamsgx1b40vr3ii1z4dxb-profile/bin/guile
>
> I don't know if this is relevant or not, and if I should run the
> .configure or not before you seing this.
I answer myself:
ran
$./configure --localstatedir=/var
And same output.
>
>
>
> >
> > > >
> > > > > Then ran
> > > > > $guix package -i guile
> > > > > Same error running configure.
> > > > > $guix package -s guild
> > > > > $guix package -i guildhall
> > > > > And my output of guix -I, however, is:
> > > > > hello    2.10    out    /gnu/store/bihfrh609gkxb9dp7n96wlpigiv3krfy-hello-2.10
> > > > > recutils    1.7    out
> > > > > /gnu/store/6h02na6yz9smc7c7g62ss03kp4yhqpc1-recutils-1.7
> > > > > glibc-locales    2.27    out
> > > > > /gnu/store/s28fmfrq8r0c688x59cj0fcyh2pv87nj-glibc-locales-2.27
> > > > > glibc-utf8-locales    2.27    out
> > > > > /gnu/store/mbns811n696fl7g060cx6jqjh75mlj8i-glibc-utf8-locales-2.27
> > > > > nss-certs    3.36.1    out
> > > > > /gnu/store/h8qlwgwhg6jr0kp5ihy90cgb6h0q1fj9-nss-certs-3.36.1
> > > > > r-ade4    1.7-11    out
> > > > > /gnu/store/980xl9a58nd6f22wzwsmv9mkhv7pq3hh-r-ade4-1.7-11
> > > > > guile    2.2.4    out    /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4
> > > > > guildhall    0-1.2fe2cc539    out
> > > > > /gnu/store/kd2mvhr18yphrkiqgavw0w0r0n5bfchn-guildhall-0-1.2fe2cc539
> > > > >
> > > > > Something weird  is that in configure output I see there is a /usr/bin
> > > > > mentioned, so I went to that dir, ran
> > > > > $ ll | grep guile
> > > > > lrwxrwxrwx  1 root root          23 oct 10 22:55 guile ->
> > > > > /etc/alternatives/guile*
> > > > > lrwxrwxrwx  1 root root          43 jul 17 10:42 guile-2.2 ->
> > > > > ../lib/x86_64-linux-gnu/guile-2.2/bin/guile*
> > > > >
> > > > > And can't figure out why I have that links.
> > > > >
> > > > > > > make
> > > > > > >
> > > > > > > When that went all through well, you can install the "hello"
> > > > > > > application:
> > > > > > >
> > > > > > > ./pre-inst-env guix package -i hello
> > > > > > >
> > > > > > > The "./pre-inst-env" tells that you want to use the guix command that
> > > > > > > you just built, not the one that is somewhere else on your path.
> > > > > > >
> > > > > > > Now you just go on:
> > > > > > >
> > > > > > > > 2) How do I convert my template into a package? I can't figure out
> > > > > > > > that part.
> > > > > > >
> > > > > > > You don't have to CONVERT. That template IS a package:
> > > > > > >
> > > > > > > > > (define-public r-aspi
> > > > > > > > > (package
> > > > > > > > >   (name "r-aspi")
> > > > > > >
> > > > > > > What you do is you just open the file gnu/packages/r.scm and add your
> > > > > > > "(define... " at the end.
> > > > > > >
> > > > > > > Ehh, wait, there is no file r.scm. It is either cran.scm or
> > > > > > > bioinformatics.scm.
> > > > > > >
> > > > > > > Then you are done. Try to build it:
> > > > > > >
> > > > > > > ./pre-inst-env guix build r-aspi
> > > > > > >
> > > > > > > Björn
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > Thank you!
> > > > > > g_bor
> > > > >
> > > > > Regards :)
> > > > > Laura
> > > > Best regards,
> > > > g_bor
> Regards!
> Laur

Re: [outreach] Help trying to create R package

[Björn Höfling]

[-- Attachment #1: Type: text/plain, Size: 8088 bytes --]

On Thu, 18 Oct 2018 14:26:50 -0300
Laura Lazzati <laura.lazzati.15@gmail.com> wrote:

> On Thu, Oct 18, 2018 at 1:18 PM Laura Lazzati
> <laura.lazzati.15@gmail.com> wrote:
> >
> > On Thu, Oct 18, 2018 at 12:40 PM Gábor Boskovits
> > <boskovits@gmail.com> wrote:  
> > >
> > > Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont:
> > > 2018. okt. 18., Cs, 17:26):  
> > > >
> > > > On Thu, Oct 18, 2018 at 12:15 PM Gábor Boskovits
> > > > <boskovits@gmail.com> wrote:  
> > > > >
> > > > > Hi Laura,
> > > > >
> > > > > Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont:
> > > > > 2018. okt. 18., Cs, 16:49):  
> > > > > >
> > > > > > On Thu, Oct 18, 2018 at 4:50 AM Gábor Boskovits
> > > > > > <boskovits@gmail.com> wrote:  
> > > > > > >
> > > > > > > Wow, Björn, you were so fast again :)
> > > > > > >
> > > > > > > I just got around this right now.  
> > > > > > Again, thank both for being so kind :)  
> > > > > > >
> > > > > > > Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt
> > > > > > > írta (időpont: 2018. okt. 18., Cs, 8:54):  
> > > > > > > >
> > > > > > > > Hi Laura,
> > > > > > > >
> > > > > > > > On Wed, 17 Oct 2018 22:36:02 -0300
> > > > > > > > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> > > > > > > >
> > > > > > > >  
> > > > > > > > > > https://www.gnu.org/software/guix/manual/en/html_node/Contributing.html#Contributing  
> > > > > > > > > I have already read this chapter, but I am messed up.
> > > > > > > > > I have already cloned from git, but I have some
> > > > > > > > > questions: 1) Do I need to install everything from
> > > > > > > > > the git repo in my distro?  
> > > > > > > >
> > > > > > > > I'm not sure if I understand you right. You ask if you
> > > > > > > > "need to install everything from the git in my
> > > > > > > > distro?". I don't get that. Let me tell what I mean:
> > > > > > > >
> > > > > > > > You cloned that one, right?
> > > > > > > >
> > > > > > > > git clone https://git.savannah.gnu.org/git/guix.git
> > > > > > > >
> > > > > > > > That is the source code of Guix. I.e. when you do a
> > > > > > > >
> > > > > > > > guix package -i hello
> > > > > > > >
> > > > > > > > then you use the binary "guix" command that you
> > > > > > > > installed in the beginning. And the repository you
> > > > > > > > cloned is just the source code, there is nothing in
> > > > > > > > there that you need to install.
> > > > > > > >
> > > > > > > >
> > > > > > > > Maybe you ment the list of software that is written
> > > > > > > > here:
> > > > > > > >
> > > > > > > > https://www.gnu.org/software/guix/manual/en/guix.html#Building-from-Git
> > > > > > > >
> > > > > > > > When building Guix from a checkout, the following
> > > > > > > > packages are required in addition to those mentioned in
> > > > > > > > the installation instructions (see Requirements).
> > > > > > > >
> > > > > > > >     GNU Autoconf;
> > > > > > > >     GNU Automake;
> > > > > > > >     GNU Gettext;
> > > > > > > >     GNU Texinfo;
> > > > > > > >     Graphviz;
> > > > > > > >     GNU Help2man (optional).
> > > > > > > >
> > > > > > > > So, yeah. In order to compile Guix from source, you
> > > > > > > > need all these.  
> > > > > > I was indeed trying to do this.
> > > > > >  
> > > > > > > >
> > > > > > > > But wait, read the next sentence. You have guix already
> > > > > > > > installed. Guix provides a VERY nice command, `guix
> > > > > > > > envirionment <PACKAGE>`. With that, Guix prepares an
> > > > > > > > "environment" that can be directly used to build
> > > > > > > > <PACKAGE>.
> > > > > > > >
> > > > > > > > So, if you enter:
> > > > > > > >
> > > > > > > > guix environment guix  
> > > > > > I have just did this :)  
> > > > > Great.  
> > > > > > > >
> > > > > > > > then Guix will know best what software in which version
> > > > > > > > it needs in order to build guix (in this case, itself,
> > > > > > > > don't get trapped by that self-circularity :-))
> > > > > > > >
> > > > > > > > When you are in, you can just follow the next steps
> > > > > > > > described:
> > > > > > > >
> > > > > > > > ./bootstrap  
> > > > > > This worked fine.  
> > > > > > > > ./configure --localstatedir=/var  
> > > > > >
> > > > > > This did not, I am getting this error:
> > > > > >
> > > > > > configure: checking for guile 2.2
> > > > > > configure: found guile 2.2
> > > > > > checking for guile-2.2... /usr/bin/guile-2.2
> > > > > > checking for Guile version >= 2.2... 2.2.3
> > > > > > checking for guild-2.2... no
> > > > > > checking for guile-config-2.2... no
> > > > > > checking for guile-tools-2.2... no
> > > > > > configure: error: 'guild' binary not found; please check
> > > > > > your guile-2.x installation.
> > > > > >  
> > > > >
> > > > > I don't know what to make of this, but you could try guix
> > > > > environment guix --ad-hoc guild.
> > > > > Please see if that helps, if not then I will have a closer
> > > > > look at this.  
> > > > I restored everything to the snapshot where I ended cloning
> > > > guix. I get this error when trying to run guix environme guix
> > > > --ad-hoc guild: guix environment: error: guild: unknown package
> > > >  
> > >
> > > Oops, my bad, yes. I've checked this more thoroughly, on my system
> > > guild is provided by guile, which should be provided by guile.
> > > Could you run a which guild and a which guile inside the guix
> > > environment guix?  
> > I went back to the previous snapshot several times.
> >
> > I was cloning the  guix and throwing guix environment guix without
> > doing cd guix After several times, I realized that I had a warning
> > in the output:
> >
> > building /gnu/store/ilscbls919b78vn9l7b2jb72jmalbxm8-profile.drv...
> > warning: collision encountered:
> >  /gnu/store/b5x786d3h552j2zp4ppvlz9dkbiqy2ng-ld-wrapper-0/bin/ld
> >  /gnu/store/srmqh29dpm50j8kj1pbqg2rgh053wgyp-binutils-2.30/bin/ld
> > warning: choosing
> > /gnu/store/b5x786d3h552j2zp4ppvlz9dkbiqy2ng-ld-wrapper-0/bin/ld
> > successfully
> > built /gnu/store/ilscbls919b78vn9l7b2jb72jmalbxm8-profile.drv But I
> > did not paid attention to that, echo $? was OK (0). And then ran
> > everything as I stated, facing all that issues.
> >
> > Now I've cloned the repo again, removing previously the guix
> > directory. did cd guix
> > and ran guix environment guix
> > Did not have that warning anymore, just the usual locale warning
> > that happens all the time.
> > ran ./bootstrap
> >
> > And in both cases (before restoring my VM state, and now) the result
> > of the which commands are:
> >
> > /gnu/store/2w5kxhmkq4zkamsgx1b40vr3ii1z4dxb-profile/bin/guild
> > and
> > /gnu/store/2w5kxhmkq4zkamsgx1b40vr3ii1z4dxb-profile/bin/guile
> >
> > I don't know if this is relevant or not, and if I should run the
> > .configure or not before you seing this.  
> I answer myself:
> ran
> $./configure --localstatedir=/var
> And same output.

Sad.

OK, first check again that you are working with the "right" guix:

Check 'which guix' and it should be the one in ~/.config/guix/bin/guix
If not, it was somewhere in the discussion already (Excuse my brevity,
need to go soon).

If that doesn't fix, I suppose still you have the "wrong" guile,
somehwere from Ubuntu. Try this:

guix environment --pure guix

or even stronger:

guix environment -C guix

These are stronger environments, the last one even a container (that
could cause even more trouble, ah, yes, the container will cause
trouble because it cannot access the build daemon, damn.)

The --pure and -C have the feature that they will blend out everything
from your current environment. Even "normal" stuff like ls, which, etc.

But you can enrich again your environment:

guix environment --pure guix --ad-hoc coreutils findutils which 

would be a good starter.

Read in manual about guix environment.

Hope this brings you a step further.

Again, sorry for brevity.

Björn

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Re: [outreach] Help trying to create R package

[Ricardo Wurmus]

Hi Laura,

> configure: checking for guile 2.2
> configure: found guile 2.2
> checking for guile-2.2... /usr/bin/guile-2.2
> checking for Guile version >= 2.2... 2.2.3
> checking for guild-2.2... no
> checking for guile-config-2.2... no
> checking for guile-tools-2.2... no
> configure: error: 'guild' binary not found; please check your
> guile-2.x installation.

I recommend using “guix environment --pure guix” when on a foreign
distribution.

-- 
Ricardo

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Thu, Oct 18, 2018 at 3:15 PM Ricardo Wurmus <rekado@elephly.net> wrote:
>
>
> Hi Laura,
>
> > configure: checking for guile 2.2
> > configure: found guile 2.2
> > checking for guile-2.2... /usr/bin/guile-2.2
> > checking for Guile version >= 2.2... 2.2.3
> > checking for guild-2.2... no
> > checking for guile-config-2.2... no
> > checking for guile-tools-2.2... no
> > configure: error: 'guild' binary not found; please check your
> > guile-2.x installation.
>
> I recommend using “guix environment --pure guix” when on a foreign
> distribution.
Yes, I am trying that right now :) I'll let you know after reading
Invoking guix environment and trying that. Hope this works
>
> --
> Ricardo
>

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Thu, Oct 18, 2018 at 3:17 PM Laura Lazzati
<laura.lazzati.15@gmail.com> wrote:
>
> On Thu, Oct 18, 2018 at 3:15 PM Ricardo Wurmus <rekado@elephly.net> wrote:
> >
> >
> > Hi Laura,
> >
> > > configure: checking for guile 2.2
> > > configure: found guile 2.2
> > > checking for guile-2.2... /usr/bin/guile-2.2
> > > checking for Guile version >= 2.2... 2.2.3
> > > checking for guild-2.2... no
> > > checking for guile-config-2.2... no
> > > checking for guile-tools-2.2... no
> > > configure: error: 'guild' binary not found; please check your
> > > guile-2.x installation.
> >
> > I recommend using “guix environment --pure guix” when on a foreign
> > distribution.
> Yes, I am trying that right now :) I'll let you know after reading
> Invoking guix environment and trying that. Hope this works
> >
I have tried lots of things today, not successfully.

with guix environment guix, I get the same output that I get without
using guix environment (I mean, it uses the installed guix that I tend
to use generally)
the output of which guix in both cases is:
/home/laura/.config/guix/current/bin/guix

with guix environment --pure guix --ad-hoc coreutils findutils which (or -C)
I get, the output:
Command 'lesspipe' is available in the following places
 * /bin/lesspipe
 * /usr/bin/lesspipe
The command could not be located because '/bin:/usr/bin' is not
included in the PATH environment variable.
lesspipe: command not found
There, I run which guix and get:
which: no guix in
(/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)

The closest I got was by setting:
PATH=$PATH:/usr/bin/:/bin
PATH=$PATH:/usr/local/bin
And since I still got the issue with guile, I went to
/usr/bin/
and created a symlink
sudo ln -s /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4 guile-2.2.4
(setting guile-2.2 that whas already there to a hidden file)
 Then the ./configure --localstatedir=/var
Worked fine, as well as the make (echo $? of both 0)
There, the result of which guix is:
/usr/local/bin/guix
( a symlink to -> /var/guix/profiles/per-user/root/guix-profile/bin/guix)
I could run the ./pre-inst-env guix package -i hello, took a while but worked.
Complained about having to do:
export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
Did so.
And finally I appended my r-aspi definition to cran.scm
However, everything went wrong when trying to run: (sorry, the output
is long and I also get the same output with ./pre-inst-env lint
r-aspi)
./pre-inst-env guix build r-aspi
;;; note: source file /home/laura/guix/gnu/packages/cran.scm
;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
guix build: warning: failed to load '(gnu packages abiword)':
exception thrown: #<condition &invalid-base32-character [character:
#\t string: "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"]
262f6c0>
guix build: warning: failed to load '(gnu packages android)':
In procedure module-lookup: Unbound variable: googletest
guix build: warning: failed to load '(gnu packages avr)':
In procedure module-lookup: Unbound variable: binutils
guix build: warning: failed to load '(gnu packages axoloti)':
In procedure module-lookup: Unbound variable: gcc-4.9
guix build: warning: failed to load '(gnu packages bioconductor)':
In procedure module-lookup: Unbound variable: perl-module-build
guix build: warning: failed to load '(gnu packages bootloaders)':
no binding `bc' in module (gnu packages algebra)
guix build: warning: failed to load '(gnu packages chemistry)':
In procedure module-lookup: Unbound variable: python2-numpy
guix build: warning: failed to load '(gnu packages commencement)':
In procedure module-lookup: Unbound variable: gnu-make
guix build: warning: failed to load '(gnu packages debug)':
In procedure module-lookup: Unbound variable: gnu-make
guix build: warning: failed to load '(gnu packages display-managers)':
In procedure module-lookup: Unbound variable: gpgme
guix build: warning: failed to load '(gnu packages games)':
In procedure module-lookup: Unbound variable: unzip
guix build: warning: failed to load '(gnu packages image-viewers)':
In procedure module-lookup: Unbound variable: curl
guix build: warning: failed to load '(gnu packages license)':
In procedure module-lookup: Unbound variable: perl
guix build: warning: failed to load '(gnu packages make-bootstrap)':
In procedure module-lookup: Unbound variable: coreutils
guix build: warning: failed to load '(gnu packages maven)':
In procedure module-lookup: Unbound variable: java-plexus-container-default
guix build: warning: failed to load '(gnu packages syndication)':
In procedure module-lookup: Unbound variable: curl
guix build: warning: failed to load '(gnu packages unrtf)':
In procedure module-lookup: Unbound variable: coreutils
guix build: error: r-aspi: unknown package




> >
> > Ricardo
> >
Regards,
Laura

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Thu, Oct 18, 2018 at 10:05 PM Laura Lazzati
<laura.lazzati.15@gmail.com> wrote:
>
> On Thu, Oct 18, 2018 at 3:17 PM Laura Lazzati
> <laura.lazzati.15@gmail.com> wrote:
> >
> > On Thu, Oct 18, 2018 at 3:15 PM Ricardo Wurmus <rekado@elephly.net> wrote:
> > >
> > >
> > > Hi Laura,
> > >
> > > > configure: checking for guile 2.2
> > > > configure: found guile 2.2
> > > > checking for guile-2.2... /usr/bin/guile-2.2
> > > > checking for Guile version >= 2.2... 2.2.3
> > > > checking for guild-2.2... no
> > > > checking for guile-config-2.2... no
> > > > checking for guile-tools-2.2... no
> > > > configure: error: 'guild' binary not found; please check your
> > > > guile-2.x installation.
> > >
> > > I recommend using “guix environment --pure guix” when on a foreign
> > > distribution.
> > Yes, I am trying that right now :) I'll let you know after reading
> > Invoking guix environment and trying that. Hope this works
> > >
> I have tried lots of things today, not successfully.
>
> with guix environment guix, I get the same output that I get without
> using guix environment (I mean, it uses the installed guix that I tend
> to use generally)
> the output of which guix in both cases is:
> /home/laura/.config/guix/current/bin/guix
>
> with guix environment --pure guix --ad-hoc coreutils findutils which (or -C)
> I get, the output:
> Command 'lesspipe' is available in the following places
>  * /bin/lesspipe
>  * /usr/bin/lesspipe
> The command could not be located because '/bin:/usr/bin' is not
> included in the PATH environment variable.
> lesspipe: command not found
> There, I run which guix and get:
> which: no guix in
> (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
>
> The closest I got was by setting:
> PATH=$PATH:/usr/bin/:/bin
> PATH=$PATH:/usr/local/bin
> And since I still got the issue with guile, I went to
> /usr/bin/
> and created a symlink
> sudo ln -s /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4 guile-2.2.4
> (setting guile-2.2 that whas already there to a hidden file)
>  Then the ./configure --localstatedir=/var
> Worked fine, as well as the make (echo $? of both 0)
> There, the result of which guix is:
> /usr/local/bin/guix
> ( a symlink to -> /var/guix/profiles/per-user/root/guix-profile/bin/guix)
> I could run the ./pre-inst-env guix package -i hello, took a while but worked.
> Complained about having to do:
> export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> Did so.
> And finally I appended my r-aspi definition to cran.scm
> However, everything went wrong when trying to run: (sorry, the output
> is long and I also get the same output with ./pre-inst-env lint
> r-aspi)
> ./pre-inst-env guix build r-aspi
> ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> guix build: warning: failed to load '(gnu packages abiword)':
> exception thrown: #<condition &invalid-base32-character [character:
> #\t string: "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"]
I have an update here, sorry, I can't help trying to figure out what's
wrong. In the definition of my r-aspi, I found that the base32 was not
well calculated, and I have already corrected that. Now this line does
not appear anymore when throwing the same commands. the other warnings
do. and the In procedure module-lookup: Unbound variable: continue
too.  I also tried generating the new cran.go with guild compile
cran.scm but the output was really awful. If you need it, when you
answer back I paste it.
> 262f6c0>
> guix build: warning: failed to load '(gnu packages android)':
> In procedure module-lookup: Unbound variable: googletest
> guix build: warning: failed to load '(gnu packages avr)':
> In procedure module-lookup: Unbound variable: binutils
> guix build: warning: failed to load '(gnu packages axoloti)':
> In procedure module-lookup: Unbound variable: gcc-4.9
> guix build: warning: failed to load '(gnu packages bioconductor)':
> In procedure module-lookup: Unbound variable: perl-module-build
> guix build: warning: failed to load '(gnu packages bootloaders)':
> no binding `bc' in module (gnu packages algebra)
> guix build: warning: failed to load '(gnu packages chemistry)':
> In procedure module-lookup: Unbound variable: python2-numpy
> guix build: warning: failed to load '(gnu packages commencement)':
> In procedure module-lookup: Unbound variable: gnu-make
> guix build: warning: failed to load '(gnu packages debug)':
> In procedure module-lookup: Unbound variable: gnu-make
> guix build: warning: failed to load '(gnu packages display-managers)':
> In procedure module-lookup: Unbound variable: gpgme
> guix build: warning: failed to load '(gnu packages games)':
> In procedure module-lookup: Unbound variable: unzip
> guix build: warning: failed to load '(gnu packages image-viewers)':
> In procedure module-lookup: Unbound variable: curl
> guix build: warning: failed to load '(gnu packages license)':
> In procedure module-lookup: Unbound variable: perl
> guix build: warning: failed to load '(gnu packages make-bootstrap)':
> In procedure module-lookup: Unbound variable: coreutils
> guix build: warning: failed to load '(gnu packages maven)':
> In procedure module-lookup: Unbound variable: java-plexus-container-default
> guix build: warning: failed to load '(gnu packages syndication)':
> In procedure module-lookup: Unbound variable: curl
> guix build: warning: failed to load '(gnu packages unrtf)':
> In procedure module-lookup: Unbound variable: coreutils
> guix build: error: r-aspi: unknown package
>
>
>
>
> > >
> > > Ricardo
> > >
> Regards,
> Laura
Regards,
Laura

Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Helllo Laura,

Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
okt. 19., P, 5:48):
>
> On Thu, Oct 18, 2018 at 10:05 PM Laura Lazzati
> <laura.lazzati.15@gmail.com> wrote:
> >
> > On Thu, Oct 18, 2018 at 3:17 PM Laura Lazzati
> > <laura.lazzati.15@gmail.com> wrote:
> > >
> > > On Thu, Oct 18, 2018 at 3:15 PM Ricardo Wurmus <rekado@elephly.net> wrote:
> > > >
> > > >
> > > > Hi Laura,
> > > >
> > > > > configure: checking for guile 2.2
> > > > > configure: found guile 2.2
> > > > > checking for guile-2.2... /usr/bin/guile-2.2
> > > > > checking for Guile version >= 2.2... 2.2.3
> > > > > checking for guild-2.2... no
> > > > > checking for guile-config-2.2... no
> > > > > checking for guile-tools-2.2... no
> > > > > configure: error: 'guild' binary not found; please check your
> > > > > guile-2.x installation.
> > > >
> > > > I recommend using “guix environment --pure guix” when on a foreign
> > > > distribution.
> > > Yes, I am trying that right now :) I'll let you know after reading
> > > Invoking guix environment and trying that. Hope this works
> > > >
> > I have tried lots of things today, not successfully.
> >
> > with guix environment guix, I get the same output that I get without
> > using guix environment (I mean, it uses the installed guix that I tend
> > to use generally)
> > the output of which guix in both cases is:
> > /home/laura/.config/guix/current/bin/guix
> >
> > with guix environment --pure guix --ad-hoc coreutils findutils which (or -C)
> > I get, the output:
> > Command 'lesspipe' is available in the following places
> >  * /bin/lesspipe
> >  * /usr/bin/lesspipe
> > The command could not be located because '/bin:/usr/bin' is not
> > included in the PATH environment variable.
> > lesspipe: command not found
> > There, I run which guix and get:
> > which: no guix in
> > (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
> >
> > The closest I got was by setting:
> > PATH=$PATH:/usr/bin/:/bin
> > PATH=$PATH:/usr/local/bin
> > And since I still got the issue with guile, I went to
> > /usr/bin/
> > and created a symlink
> > sudo ln -s /gnu/store/p9wm67w3rfw3hlb9iljgvsfn84mz4w9d-guile-2.2.4 guile-2.2.4
> > (setting guile-2.2 that whas already there to a hidden file)
> >  Then the ./configure --localstatedir=/var
> > Worked fine, as well as the make (echo $? of both 0)
> > There, the result of which guix is:
> > /usr/local/bin/guix
> > ( a symlink to -> /var/guix/profiles/per-user/root/guix-profile/bin/guix)
> > I could run the ./pre-inst-env guix package -i hello, took a while but worked.
> > Complained about having to do:
> > export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> > Did so.

This seems to be ok so far.

> > And finally I appended my r-aspi definition to cran.scm
> > However, everything went wrong when trying to run: (sorry, the output
> > is long and I also get the same output with ./pre-inst-env lint
> > r-aspi)
> > ./pre-inst-env guix build r-aspi
> > ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> > ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> > guix build: warning: failed to load '(gnu packages abiword)':
> > exception thrown: #<condition &invalid-base32-character [character:
> > #\t string: "a7izhueiqsdjs2eo7dfyb63cqje7mbqz6ennlyoynxxucbhpdnta"]

If I get you right, then the problem is introduced when you add the
package definition to cran.scm, since
./pre-inst-env guix package -i hello worked.

Since essentially everything is broken by the change, it is most
probable that you have some forms that
is not closed properly.
I would at first check for mismatching parenthesis.

If you can see nothing suspicious, then could you send a diff, so that
I can have a look?

> I have an update here, sorry, I can't help trying to figure out what's
> wrong. In the definition of my r-aspi, I found that the base32 was not
> well calculated, and I have already corrected that. Now this line does
> not appear anymore when throwing the same commands. the other warnings
> do. and the In procedure module-lookup: Unbound variable: continue
> too.  I also tried generating the new cran.go with guild compile
> cran.scm but the output was really awful. If you need it, when you
> answer back I paste it.
> > 262f6c0>
> > guix build: warning: failed to load '(gnu packages android)':
> > In procedure module-lookup: Unbound variable: googletest
> > guix build: warning: failed to load '(gnu packages avr)':
> > In procedure module-lookup: Unbound variable: binutils
> > guix build: warning: failed to load '(gnu packages axoloti)':
> > In procedure module-lookup: Unbound variable: gcc-4.9
> > guix build: warning: failed to load '(gnu packages bioconductor)':
> > In procedure module-lookup: Unbound variable: perl-module-build
> > guix build: warning: failed to load '(gnu packages bootloaders)':
> > no binding `bc' in module (gnu packages algebra)
> > guix build: warning: failed to load '(gnu packages chemistry)':
> > In procedure module-lookup: Unbound variable: python2-numpy
> > guix build: warning: failed to load '(gnu packages commencement)':
> > In procedure module-lookup: Unbound variable: gnu-make
> > guix build: warning: failed to load '(gnu packages debug)':
> > In procedure module-lookup: Unbound variable: gnu-make
> > guix build: warning: failed to load '(gnu packages display-managers)':
> > In procedure module-lookup: Unbound variable: gpgme
> > guix build: warning: failed to load '(gnu packages games)':
> > In procedure module-lookup: Unbound variable: unzip
> > guix build: warning: failed to load '(gnu packages image-viewers)':
> > In procedure module-lookup: Unbound variable: curl
> > guix build: warning: failed to load '(gnu packages license)':
> > In procedure module-lookup: Unbound variable: perl
> > guix build: warning: failed to load '(gnu packages make-bootstrap)':
> > In procedure module-lookup: Unbound variable: coreutils
> > guix build: warning: failed to load '(gnu packages maven)':
> > In procedure module-lookup: Unbound variable: java-plexus-container-default
> > guix build: warning: failed to load '(gnu packages syndication)':
> > In procedure module-lookup: Unbound variable: curl
> > guix build: warning: failed to load '(gnu packages unrtf)':
> > In procedure module-lookup: Unbound variable: coreutils
> > guix build: error: r-aspi: unknown package
> >
> >
> >
> >
> > > >
> > > > Ricardo
> > > >
> > Regards,
> > Laura
> Regards,
> Laura

Best regards,
g_bor

Re: [outreach] Help trying to create R package

[Ricardo Wurmus]

Hi Laura,

> with guix environment --pure guix --ad-hoc coreutils findutils which (or -C)
> I get, the output:
> Command 'lesspipe' is available in the following places
>  * /bin/lesspipe
>  * /usr/bin/lesspipe
> The command could not be located because '/bin:/usr/bin' is not
> included in the PATH environment variable.
> lesspipe: command not found

This is because your shell initialization code (e.g. to set up the
prompt) refers to lesspipe.  You can ignore this or remove the fancy
initialization.

> There, I run which guix and get:
> which: no guix in
> (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)

That’s because “--pure” resets the PATH; that’s by design.  The only
problem you have is that your Guix is located elsewhere.  But why do you
need Guix itself inside of an environment to build Guix?

The point of using “guix environment --pure guix” is only to enter a
clean environment containing everything you need to build Guix from
source.  So once you’re inside of this environment you can run the
bootstrap and configure scripts, and run make to compile the sources.

To *use* that Guix you just built you need to use “./pre-inst-env guix”
from the source directory.

> The closest I got was by setting:
> PATH=$PATH:/usr/bin/:/bin
> PATH=$PATH:/usr/local/bin

This defeats the purpose of using “--pure” as these directories contain
all sorts of things on a foreign distro, so you lose control over the
environment.

--
Ricardo

Re: [outreach] Help trying to create R package

[Gábor Boskovits]

[-- Attachment #1: Type: text/plain, Size: 1815 bytes --]

Hello Ricardo,

Ricardo Wurmus <rekado@elephly.net> ezt írta (időpont: 2018. okt. 19., P
9:10):

>
> Hi Laura,
>
> > with guix environment --pure guix --ad-hoc coreutils findutils which (or
> -C)
> > I get, the output:
> > Command 'lesspipe' is available in the following places
> >  * /bin/lesspipe
> >  * /usr/bin/lesspipe
> > The command could not be located because '/bin:/usr/bin' is not
> > included in the PATH environment variable.
> > lesspipe: command not found
>
> This is because your shell initialization code (e.g. to set up the
> prompt) refers to lesspipe.  You can ignore this or remove the fancy
> initialization.
>
> > There, I run which guix and get:
> > which: no guix in
> >
> (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
>
> That’s because “--pure” resets the PATH; that’s by design.  The only
> problem you have is that your Guix is located elsewhere.  But why do you
> need Guix itself inside of an environment to build Guix?
>
> The point of using “guix environment --pure guix” is only to enter a
> clean environment containing everything you need to build Guix from
> source.  So once you’re inside of this environment you can run the
> bootstrap and configure scripts, and run make to compile the sources.
>
> To *use* that Guix you just built you need to use “./pre-inst-env guix”
> from the source directory.
>
> > The closest I got was by setting:
> > PATH=$PATH:/usr/bin/:/bin
> > PATH=$PATH:/usr/local/bin
>
> This defeats the purpose of using “--pure” as these directories contain
> all sorts of things on a foreign distro, so you lose control over the
> environment.
>

Sorry, my bad, I missed that.


> --
> Ricardo
>
g_bor

>

[-- Attachment #2: Type: text/html, Size: 2630 bytes --]

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Fri, Oct 19, 2018 at 4:29 AM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> Hello Ricardo,
>
> Ricardo Wurmus <rekado@elephly.net> ezt írta (időpont: 2018. okt. 19., P 9:10):
>>
>>
>> Hi Laura,
>>
>> > with guix environment --pure guix --ad-hoc coreutils findutils which (or -C)
>> > I get, the output:
>> > Command 'lesspipe' is available in the following places
>> >  * /bin/lesspipe
>> >  * /usr/bin/lesspipe
>> > The command could not be located because '/bin:/usr/bin' is not
>> > included in the PATH environment variable.
>> > lesspipe: command not found
>>
>> This is because your shell initialization code (e.g. to set up the
>> prompt) refers to lesspipe.  You can ignore this or remove the fancy
>> initialization.
>>
>> > There, I run which guix and get:
>> > which: no guix in
>> > (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
>>
>> That’s because “--pure” resets the PATH; that’s by design.  The only
>> problem you have is that your Guix is located elsewhere.  But why do you
>> need Guix itself inside of an environment to build Guix?
>>
>> The point of using “guix environment --pure guix” is only to enter a
>> clean environment containing everything you need to build Guix from
>> source.  So once you’re inside of this environment you can run the
>> bootstrap and configure scripts, and run make to compile the sources.
>>
>> To *use* that Guix you just built you need to use “./pre-inst-env guix”
>> from the source directory.
>>
>> > The closest I got was by setting:
>> > PATH=$PATH:/usr/bin/:/bin
>> > PATH=$PATH:/usr/local/bin
>>
>> This defeats the purpose of using “--pure” as these directories contain
>> all sorts of things on a foreign distro, so you lose control over the
>> environment.

I am glad to tell you that I have followed all the commands, I will
copy some of them here just in case, and saved the output in my daily
journal of everything :)

guix environment --pure guix --ad-hoc coreutils findutils which
./bootstrap
./configure --localstatedir=/var
make
echo $? ->got 0
which guix -> got
no guix in (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
./pre-inst-env guix package --help -> worked fine!
./pre-inst-env guix package -i hello -> the same
./pre-inst-env guix package -i emacs
export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
export INFOPATH="/home/laura/.guix-profile/share/info${INFOPATH:+:}$INFOPATH"
(with this two exports, I could run hello and emacs without problems)
./pre-inst-env guix package -i nss-certs
Played a lot with
./pre-inst-env guix build r-aspi
and
emacs gnu/packages/cran.scm
until I found out that there were syntax errors, mismatches in
parenthesis and so on, and in the last
./pre-inst-env guix build r-aspi got:
;;; note: source file /home/laura/guix/gnu/packages/cran.scm
;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
(still that) but:
successfully built /gnu/store/bmapswnk9li1nscfpirgzsy3npw9hyql-r-aspi-0.2.0.drv
/gnu/store/a3apqwf4hy67ms462hn802gk89x99mzh-r-aspi-0.2.0

I am following the contribution guide now, to send the patch, I ran
./pre-inst-env guix lint r-aspi
;;; note: source file /home/laura/guix/gnu/packages/cran.scm
;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
fetching CVE database for 2018...
fetching CVE database for 2017...
fetching CVE database for 2016...
fetching CVE database for 2015...

Is this output OK?

>
>
> Sorry, my bad, I missed that.
>
>>
>> --
>> Ricardo
>
> g_bor

Regards!
Laura

Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Hello Laura,

Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
okt. 19., P, 20:37):
>
> On Fri, Oct 19, 2018 at 4:29 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> >
> > Hello Ricardo,
> >
> > Ricardo Wurmus <rekado@elephly.net> ezt írta (időpont: 2018. okt. 19., P 9:10):
> >>
> >>
> >> Hi Laura,
> >>
> >> > with guix environment --pure guix --ad-hoc coreutils findutils which (or -C)
> >> > I get, the output:
> >> > Command 'lesspipe' is available in the following places
> >> >  * /bin/lesspipe
> >> >  * /usr/bin/lesspipe
> >> > The command could not be located because '/bin:/usr/bin' is not
> >> > included in the PATH environment variable.
> >> > lesspipe: command not found
> >>
> >> This is because your shell initialization code (e.g. to set up the
> >> prompt) refers to lesspipe.  You can ignore this or remove the fancy
> >> initialization.
> >>
> >> > There, I run which guix and get:
> >> > which: no guix in
> >> > (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
> >>
> >> That’s because “--pure” resets the PATH; that’s by design.  The only
> >> problem you have is that your Guix is located elsewhere.  But why do you
> >> need Guix itself inside of an environment to build Guix?
> >>
> >> The point of using “guix environment --pure guix” is only to enter a
> >> clean environment containing everything you need to build Guix from
> >> source.  So once you’re inside of this environment you can run the
> >> bootstrap and configure scripts, and run make to compile the sources.
> >>
> >> To *use* that Guix you just built you need to use “./pre-inst-env guix”
> >> from the source directory.
> >>
> >> > The closest I got was by setting:
> >> > PATH=$PATH:/usr/bin/:/bin
> >> > PATH=$PATH:/usr/local/bin
> >>
> >> This defeats the purpose of using “--pure” as these directories contain
> >> all sorts of things on a foreign distro, so you lose control over the
> >> environment.
>
> I am glad to tell you that I have followed all the commands, I will
> copy some of them here just in case, and saved the output in my daily
> journal of everything :)
>
> guix environment --pure guix --ad-hoc coreutils findutils which
> ./bootstrap
> ./configure --localstatedir=/var
> make
> echo $? ->got 0
> which guix -> got
> no guix in (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
> ./pre-inst-env guix package --help -> worked fine!
> ./pre-inst-env guix package -i hello -> the same
> ./pre-inst-env guix package -i emacs
> export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> export INFOPATH="/home/laura/.guix-profile/share/info${INFOPATH:+:}$INFOPATH"
> (with this two exports, I could run hello and emacs without problems)
> ./pre-inst-env guix package -i nss-certs
> Played a lot with
> ./pre-inst-env guix build r-aspi
> and
> emacs gnu/packages/cran.scm
> until I found out that there were syntax errors, mismatches in
> parenthesis and so on, and in the last
> ./pre-inst-env guix build r-aspi got:
> ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> (still that) but:

This is not a problem, it just indicates that you modified cran.scm, and it will
use the .scm file instead, as the .go file was compiled from an older source.

> successfully built /gnu/store/bmapswnk9li1nscfpirgzsy3npw9hyql-r-aspi-0.2.0.drv
> /gnu/store/a3apqwf4hy67ms462hn802gk89x99mzh-r-aspi-0.2.0
>

That's great!

> I am following the contribution guide now, to send the patch, I ran
> ./pre-inst-env guix lint r-aspi
> ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> fetching CVE database for 2018...
> fetching CVE database for 2017...
> fetching CVE database for 2016...
> fetching CVE database for 2015...
>
> Is this output OK?
>

Yes, this output is just fine.

> >
> >
> > Sorry, my bad, I missed that.
> >
> >>
> >> --
> >> Ricardo
> >
> > g_bor
>
> Regards!
> Laura
Best regards,
g_bor

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Fri, Oct 19, 2018 at 3:45 PM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> Hello Laura,
>
> Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> okt. 19., P, 20:37):
> >
> > On Fri, Oct 19, 2018 at 4:29 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> > >
> > > Hello Ricardo,
> > >
> > > Ricardo Wurmus <rekado@elephly.net> ezt írta (időpont: 2018. okt. 19., P 9:10):
> > >>
> > >>
> > >> Hi Laura,
> > >>
> > >> > with guix environment --pure guix --ad-hoc coreutils findutils which (or -C)
> > >> > I get, the output:
> > >> > Command 'lesspipe' is available in the following places
> > >> >  * /bin/lesspipe
> > >> >  * /usr/bin/lesspipe
> > >> > The command could not be located because '/bin:/usr/bin' is not
> > >> > included in the PATH environment variable.
> > >> > lesspipe: command not found
> > >>
> > >> This is because your shell initialization code (e.g. to set up the
> > >> prompt) refers to lesspipe.  You can ignore this or remove the fancy
> > >> initialization.
> > >>
> > >> > There, I run which guix and get:
> > >> > which: no guix in
> > >> > (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
> > >>
> > >> That’s because “--pure” resets the PATH; that’s by design.  The only
> > >> problem you have is that your Guix is located elsewhere.  But why do you
> > >> need Guix itself inside of an environment to build Guix?
> > >>
> > >> The point of using “guix environment --pure guix” is only to enter a
> > >> clean environment containing everything you need to build Guix from
> > >> source.  So once you’re inside of this environment you can run the
> > >> bootstrap and configure scripts, and run make to compile the sources.
> > >>
> > >> To *use* that Guix you just built you need to use “./pre-inst-env guix”
> > >> from the source directory.
> > >>
> > >> > The closest I got was by setting:
> > >> > PATH=$PATH:/usr/bin/:/bin
> > >> > PATH=$PATH:/usr/local/bin
> > >>
> > >> This defeats the purpose of using “--pure” as these directories contain
> > >> all sorts of things on a foreign distro, so you lose control over the
> > >> environment.
> >
> > I am glad to tell you that I have followed all the commands, I will
> > copy some of them here just in case, and saved the output in my daily
> > journal of everything :)
> >
> > guix environment --pure guix --ad-hoc coreutils findutils which
> > ./bootstrap
> > ./configure --localstatedir=/var
> > make
> > echo $? ->got 0
> > which guix -> got
> > no guix in (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
> > ./pre-inst-env guix package --help -> worked fine!
> > ./pre-inst-env guix package -i hello -> the same
> > ./pre-inst-env guix package -i emacs
> > export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> > export INFOPATH="/home/laura/.guix-profile/share/info${INFOPATH:+:}$INFOPATH"
> > (with this two exports, I could run hello and emacs without problems)
> > ./pre-inst-env guix package -i nss-certs
> > Played a lot with
> > ./pre-inst-env guix build r-aspi
> > and
> > emacs gnu/packages/cran.scm
> > until I found out that there were syntax errors, mismatches in
> > parenthesis and so on, and in the last
> > ./pre-inst-env guix build r-aspi got:
> > ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> > ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> > (still that) but:
>
> This is not a problem, it just indicates that you modified cran.scm, and it will
> use the .scm file instead, as the .go file was compiled from an older source.
>
> > successfully built /gnu/store/bmapswnk9li1nscfpirgzsy3npw9hyql-r-aspi-0.2.0.drv
> > /gnu/store/a3apqwf4hy67ms462hn802gk89x99mzh-r-aspi-0.2.0
> >
>
> That's great!
>
> > I am following the contribution guide now, to send the patch, I ran
> > ./pre-inst-env guix lint r-aspi
> > ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> > ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> > fetching CVE database for 2018...
> > fetching CVE database for 2017...
> > fetching CVE database for 2016...
> > fetching CVE database for 2015...
> >
> > Is this output OK?
> >
>
> Yes, this output is just fine.
I have already run all the commands suggested in
https://www.gnu.org/software/guix/manual/en/html_node/Submitting-Patches.html#Submitting-Patches
I have never used git format-patch before, I am reading documentation
about it but I am not very sure about how to apply it to my package,
could you help me in clarifying this last step?
>
> > >
> > >
> > > Sorry, my bad, I missed that.
> > >
> > >>
> > >> --
> > >> Ricardo
> > >
> > > g_bor
> >
> > Regards!
> > Laura
> Best regards,
> g_bor

Regards :)
Laura

Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Hello Laura,

Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
okt. 19., P, 22:35):
>
> On Fri, Oct 19, 2018 at 3:45 PM Gábor Boskovits <boskovits@gmail.com> wrote:
> >
> > Hello Laura,
> >
> > Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> > okt. 19., P, 20:37):
> > >
> > > On Fri, Oct 19, 2018 at 4:29 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> > > >
> > > > Hello Ricardo,
> > > >
> > > > Ricardo Wurmus <rekado@elephly.net> ezt írta (időpont: 2018. okt. 19., P 9:10):
> > > >>
> > > >>
> > > >> Hi Laura,
> > > >>
> > > >> > with guix environment --pure guix --ad-hoc coreutils findutils which (or -C)
> > > >> > I get, the output:
> > > >> > Command 'lesspipe' is available in the following places
> > > >> >  * /bin/lesspipe
> > > >> >  * /usr/bin/lesspipe
> > > >> > The command could not be located because '/bin:/usr/bin' is not
> > > >> > included in the PATH environment variable.
> > > >> > lesspipe: command not found
> > > >>
> > > >> This is because your shell initialization code (e.g. to set up the
> > > >> prompt) refers to lesspipe.  You can ignore this or remove the fancy
> > > >> initialization.
> > > >>
> > > >> > There, I run which guix and get:
> > > >> > which: no guix in
> > > >> > (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
> > > >>
> > > >> That’s because “--pure” resets the PATH; that’s by design.  The only
> > > >> problem you have is that your Guix is located elsewhere.  But why do you
> > > >> need Guix itself inside of an environment to build Guix?
> > > >>
> > > >> The point of using “guix environment --pure guix” is only to enter a
> > > >> clean environment containing everything you need to build Guix from
> > > >> source.  So once you’re inside of this environment you can run the
> > > >> bootstrap and configure scripts, and run make to compile the sources.
> > > >>
> > > >> To *use* that Guix you just built you need to use “./pre-inst-env guix”
> > > >> from the source directory.
> > > >>
> > > >> > The closest I got was by setting:
> > > >> > PATH=$PATH:/usr/bin/:/bin
> > > >> > PATH=$PATH:/usr/local/bin
> > > >>
> > > >> This defeats the purpose of using “--pure” as these directories contain
> > > >> all sorts of things on a foreign distro, so you lose control over the
> > > >> environment.
> > >
> > > I am glad to tell you that I have followed all the commands, I will
> > > copy some of them here just in case, and saved the output in my daily
> > > journal of everything :)
> > >
> > > guix environment --pure guix --ad-hoc coreutils findutils which
> > > ./bootstrap
> > > ./configure --localstatedir=/var
> > > make
> > > echo $? ->got 0
> > > which guix -> got
> > > no guix in (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
> > > ./pre-inst-env guix package --help -> worked fine!
> > > ./pre-inst-env guix package -i hello -> the same
> > > ./pre-inst-env guix package -i emacs
> > > export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> > > export INFOPATH="/home/laura/.guix-profile/share/info${INFOPATH:+:}$INFOPATH"
> > > (with this two exports, I could run hello and emacs without problems)
> > > ./pre-inst-env guix package -i nss-certs
> > > Played a lot with
> > > ./pre-inst-env guix build r-aspi
> > > and
> > > emacs gnu/packages/cran.scm
> > > until I found out that there were syntax errors, mismatches in
> > > parenthesis and so on, and in the last
> > > ./pre-inst-env guix build r-aspi got:
> > > ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> > > ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> > > (still that) but:
> >
> > This is not a problem, it just indicates that you modified cran.scm, and it will
> > use the .scm file instead, as the .go file was compiled from an older source.
> >
> > > successfully built /gnu/store/bmapswnk9li1nscfpirgzsy3npw9hyql-r-aspi-0.2.0.drv
> > > /gnu/store/a3apqwf4hy67ms462hn802gk89x99mzh-r-aspi-0.2.0
> > >
> >
> > That's great!
> >
> > > I am following the contribution guide now, to send the patch, I ran
> > > ./pre-inst-env guix lint r-aspi
> > > ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> > > ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> > > fetching CVE database for 2018...
> > > fetching CVE database for 2017...
> > > fetching CVE database for 2016...
> > > fetching CVE database for 2015...
> > >
> > > Is this output OK?
> > >
> >
> > Yes, this output is just fine.
> I have already run all the commands suggested in
> https://www.gnu.org/software/guix/manual/en/html_node/Submitting-Patches.html#Submitting-Patches
> I have never used git format-patch before, I am reading documentation
> about it but I am not very sure about how to apply it to my package,
> could you help me in clarifying this last step?

Once you made a commit, and you are statisfied with it, then you can run:
git format-patch -1
to create a patch form the last commit.
I would store it somewhere outside the repository, so that it does not
get in your way later as an utracked file.
You can also specify the output directory directly with -o.

Once this is done, a patch file is created, with a name resembling the
commit message.
You can then do:
git send-email <patch-filename>

It will ask for the e-mail address you want to send to, you should
specify the guix-patches mailinglist.

Hope that helps.

> >
> > > >
> > > >
> > > > Sorry, my bad, I missed that.
> > > >
> > > >>
> > > >> --
> > > >> Ricardo
> > > >
> > > > g_bor
> > >
> > > Regards!
> > > Laura
> > Best regards,
> > g_bor
>
> Regards :)
> Laura
Best regards,
g_bor

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Fri, Oct 19, 2018 at 6:25 PM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> Hello Laura,
>
> Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> okt. 19., P, 22:35):
> >
> > On Fri, Oct 19, 2018 at 3:45 PM Gábor Boskovits <boskovits@gmail.com> wrote:
> > >
> > > Hello Laura,
> > >
> > > Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
> > > okt. 19., P, 20:37):
> > > >
> > > > On Fri, Oct 19, 2018 at 4:29 AM Gábor Boskovits <boskovits@gmail.com> wrote:
> > > > >
> > > > > Hello Ricardo,
> > > > >
> > > > > Ricardo Wurmus <rekado@elephly.net> ezt írta (időpont: 2018. okt. 19., P 9:10):
> > > > >>
> > > > >>
> > > > >> Hi Laura,
> > > > >>
> > > > >> > with guix environment --pure guix --ad-hoc coreutils findutils which (or -C)
> > > > >> > I get, the output:
> > > > >> > Command 'lesspipe' is available in the following places
> > > > >> >  * /bin/lesspipe
> > > > >> >  * /usr/bin/lesspipe
> > > > >> > The command could not be located because '/bin:/usr/bin' is not
> > > > >> > included in the PATH environment variable.
> > > > >> > lesspipe: command not found
> > > > >>
> > > > >> This is because your shell initialization code (e.g. to set up the
> > > > >> prompt) refers to lesspipe.  You can ignore this or remove the fancy
> > > > >> initialization.
> > > > >>
> > > > >> > There, I run which guix and get:
> > > > >> > which: no guix in
> > > > >> > (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
> > > > >>
> > > > >> That’s because “--pure” resets the PATH; that’s by design.  The only
> > > > >> problem you have is that your Guix is located elsewhere.  But why do you
> > > > >> need Guix itself inside of an environment to build Guix?
> > > > >>
> > > > >> The point of using “guix environment --pure guix” is only to enter a
> > > > >> clean environment containing everything you need to build Guix from
> > > > >> source.  So once you’re inside of this environment you can run the
> > > > >> bootstrap and configure scripts, and run make to compile the sources.
> > > > >>
> > > > >> To *use* that Guix you just built you need to use “./pre-inst-env guix”
> > > > >> from the source directory.
> > > > >>
> > > > >> > The closest I got was by setting:
> > > > >> > PATH=$PATH:/usr/bin/:/bin
> > > > >> > PATH=$PATH:/usr/local/bin
> > > > >>
> > > > >> This defeats the purpose of using “--pure” as these directories contain
> > > > >> all sorts of things on a foreign distro, so you lose control over the
> > > > >> environment.
> > > >
> > > > I am glad to tell you that I have followed all the commands, I will
> > > > copy some of them here just in case, and saved the output in my daily
> > > > journal of everything :)
> > > >
> > > > guix environment --pure guix --ad-hoc coreutils findutils which
> > > > ./bootstrap
> > > > ./configure --localstatedir=/var
> > > > make
> > > > echo $? ->got 0
> > > > which guix -> got
> > > > no guix in (/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/bin:/gnu/store/khk3lpx1li9y5zxzdppn9wi4n5g1qsgs-profile/sbin)
> > > > ./pre-inst-env guix package --help -> worked fine!
> > > > ./pre-inst-env guix package -i hello -> the same
> > > > ./pre-inst-env guix package -i emacs
> > > > export PATH="/home/laura/.guix-profile/bin${PATH:+:}$PATH"
> > > > export INFOPATH="/home/laura/.guix-profile/share/info${INFOPATH:+:}$INFOPATH"
> > > > (with this two exports, I could run hello and emacs without problems)
> > > > ./pre-inst-env guix package -i nss-certs
> > > > Played a lot with
> > > > ./pre-inst-env guix build r-aspi
> > > > and
> > > > emacs gnu/packages/cran.scm
> > > > until I found out that there were syntax errors, mismatches in
> > > > parenthesis and so on, and in the last
> > > > ./pre-inst-env guix build r-aspi got:
> > > > ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> > > > ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> > > > (still that) but:
> > >
> > > This is not a problem, it just indicates that you modified cran.scm, and it will
> > > use the .scm file instead, as the .go file was compiled from an older source.
> > >
> > > > successfully built /gnu/store/bmapswnk9li1nscfpirgzsy3npw9hyql-r-aspi-0.2.0.drv
> > > > /gnu/store/a3apqwf4hy67ms462hn802gk89x99mzh-r-aspi-0.2.0
> > > >
> > >
> > > That's great!
> > >
> > > > I am following the contribution guide now, to send the patch, I ran
> > > > ./pre-inst-env guix lint r-aspi
> > > > ;;; note: source file /home/laura/guix/gnu/packages/cran.scm
> > > > ;;;       newer than compiled /home/laura/guix/gnu/packages/cran.go
> > > > fetching CVE database for 2018...
> > > > fetching CVE database for 2017...
> > > > fetching CVE database for 2016...
> > > > fetching CVE database for 2015...
> > > >
> > > > Is this output OK?
> > > >
> > >
> > > Yes, this output is just fine.
> > I have already run all the commands suggested in
> > https://www.gnu.org/software/guix/manual/en/html_node/Submitting-Patches.html#Submitting-Patches
> > I have never used git format-patch before, I am reading documentation
> > about it but I am not very sure about how to apply it to my package,
> > could you help me in clarifying this last step?
>
> Once you made a commit, and you are statisfied with it, then you can run:
> git format-patch -1
> to create a patch form the last commit.
> I would store it somewhere outside the repository, so that it does not
> get in your way later as an utracked file.
> You can also specify the output directory directly with -o.
>
> Once this is done, a patch file is created, with a name resembling the
> commit message.
> You can then do:
> git send-email <patch-filename>
>
> It will ask for the e-mail address you want to send to, you should
> specify the guix-patches mailinglist.
>
> Hope that helps.
I ended up sending the patch in plain text mode directly from my
email, because even I installed the send-mail command for git, my
second factor authenticator complained. I will take a look about how
to configure the command properly.
Please, let me know if you received it fine, and if so, if you would
like me to work on other contributions meanwhile (maybe another r
package, or let me know what alse would you like me to do)

> > >
> > > > >
> > > > >
> > > > > Sorry, my bad, I missed that.
> > > > >
> > > > >>
> > > > >> --
> > > > >> Ricardo
> > > > >
> > > > > g_bor
> > > >
> > > > Regards!
> > > > Laura
> > > Best regards,
> > > g_bor
> >
> > Regards :)
> > Laura
> Best regards,
> g_bor

Regards!
Laura

Re: [outreach] Help trying to create R package

[Björn Höfling]

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Hi Laura,

On Fri, 19 Oct 2018 20:10:03 -0300
Laura Lazzati <laura.lazzati.15@gmail.com> wrote:


> I ended up sending the patch in plain text mode directly from my
> email, because even I installed the send-mail command for git, my
> second factor authenticator complained. I will take a look about how
> to configure the command properly.
> Please, let me know if you received it fine, and if so, if you would
> like me to work on other contributions meanwhile (maybe another r
> package, or let me know what alse would you like me to do)

Congratulations! Your patch went through:

https://debbugs.gnu.org/cgi/bugreport.cgi?bug=33099

Either follow its status on that page and/or subscribe to the
guix-patches list:

https://lists.gnu.org/mailman/listinfo/guix-patches

Someone will review it and give you feedback.

For Outreachy it is important to document your contributions. So,
please also go to the Guix-Outreachy page, there you should find a link
to formally report your contribution. When I have understood that
right, it is not important that your contribution really get's accepted
for that, just that you made one.

Björn


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Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Hello Laura,

Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
2018. okt. 20., Szo, 8:08):
>
> Hi Laura,
>
> On Fri, 19 Oct 2018 20:10:03 -0300
> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
>
>
> > I ended up sending the patch in plain text mode directly from my
> > email, because even I installed the send-mail command for git, my
> > second factor authenticator complained. I will take a look about how
> > to configure the command properly.

I guess you are using gmail with two factor authentication.
Then you will have to create an app password, and after that
you can use git credentials to set up authentication using the app
password, but sending as plain text is fine for now.

> > Please, let me know if you received it fine, and if so, if you would
> > like me to work on other contributions meanwhile (maybe another r
> > package, or let me know what alse would you like me to do)

Another R package would be great, in the meanwhile I will have a look
around what else to do.

>
> Congratulations! Your patch went through:
>
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=33099
>

That is great!

> Either follow its status on that page and/or subscribe to the
> guix-patches list:
>
> https://lists.gnu.org/mailman/listinfo/guix-patches
>
> Someone will review it and give you feedback.
>

I will review it later today.

> For Outreachy it is important to document your contributions. So,
> please also go to the Guix-Outreachy page, there you should find a link
> to formally report your contribution. When I have understood that
> right, it is not important that your contribution really get's accepted
> for that, just that you made one.
>

Yes, now you can record this contribution.

> Björn
>
Best regards,
g_bor

Re: [outreach] Help trying to create R package

[Laura Lazzati]

On Sat, Oct 20, 2018 at 3:34 AM Gábor Boskovits <boskovits@gmail.com> wrote:
>
> Hello Laura,
>
> Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ezt írta (időpont:
> 2018. okt. 20., Szo, 8:08):
> >
> > Hi Laura,
> >
> > On Fri, 19 Oct 2018 20:10:03 -0300
> > Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
> >
> >
> > > I ended up sending the patch in plain text mode directly from my
> > > email, because even I installed the send-mail command for git, my
> > > second factor authenticator complained. I will take a look about how
> > > to configure the command properly.
>
> I guess you are using gmail with two factor authentication.
> Then you will have to create an app password, and after that
> you can use git credentials to set up authentication using the app
> password, but sending as plain text is fine for now.
Yes, I will try that for a second commit
>
> > > Please, let me know if you received it fine, and if so, if you would
> > > like me to work on other contributions meanwhile (maybe another r
> > > package, or let me know what alse would you like me to do)
>
> Another R package would be great, in the meanwhile I will have a look
> around what else to do.
Sure, as I said before, once I learn how to package one, I will be
able to package more. I will take a look at the page and check other
packages that are not already in guix. And yes, if you find other
tasks that I can do it is fine for me. I would like to go on
contributing even after November 6th (the outreachy deadline for
applying). Maybe after that I can go on playing with GuixSD and
reading the whole documentation ;)
>
> >
> > Congratulations! Your patch went through:
> >
> > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=33099
> >
>
> That is great!
>
> > Either follow its status on that page and/or subscribe to the
> > guix-patches list:
> >
> > https://lists.gnu.org/mailman/listinfo/guix-patches
> >
> > Someone will review it and give you feedback.
Thank you, I saw that they wrote about it :) But I will ask in that
thread of mails about how to make my changes to be accespted
> >
>
> I will review it later today.
>
> > For Outreachy it is important to document your contributions. So,
> > please also go to the Guix-Outreachy page, there you should find a link
> > to formally report your contribution. When I have understood that
> > right, it is not important that your contribution really get's accepted
> > for that, just that you made one.
Yes, I reported the in progress contribution.
> >
>
> Yes, now you can record this contribution.
>
> > Björn
> >
> Best regards,
> g_bor
Regards :)

Laura

Re: [outreach] Help trying to create R package

[Ludovic Courtès]

Hello!

Björn Höfling <bjoern.hoefling@bjoernhoefling.de> skribis:

> On Fri, 19 Oct 2018 20:10:03 -0300
> Laura Lazzati <laura.lazzati.15@gmail.com> wrote:
>
>
>> I ended up sending the patch in plain text mode directly from my
>> email, because even I installed the send-mail command for git, my
>> second factor authenticator complained. I will take a look about how
>> to configure the command properly.
>> Please, let me know if you received it fine, and if so, if you would
>> like me to work on other contributions meanwhile (maybe another r
>> package, or let me know what alse would you like me to do)
>
> Congratulations! Your patch went through:
>
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=33099

Or, for a nicer view:

  https://issues.guix.info/issue/33099

Thank you for this first patch, Laura!

Ludo’.

Re: [outreach] Help trying to create R package

[Laura Lazzati]

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>
>
> I tracked it down:
>
> The cause is that:
>
> guix/import/cran.scm:
>
> (define (latest-bioconductor-package-version name)
>   "Return the version string corresponding to the latest release of the
> bioconductor package NAME, or #F if the package is unknown."
>
> actually returns #f. It's a bit said that this #f is not checked
> further down. The problem is the package name. If you add an "r" before
> the package name, it should work (suppose you fixed the first problem):
>
> guix import cran --archive=bioconductor rtracklayer
>
Sorry for writing again on this topic.
Today I wanted to practice packaging an r package belonging to
bioconductor, to then go on and read and work with texinfo.
After writing on IRC channel, I realized I already had this exact problem,
but thought it was a problem of other packages.
I ran again this same command, and I am getting:

$guix import cran -a bioconductor rtracklayer
guile: warning: failed to install locale
hint: Consider installing the `glibc-utf8-locales' or `glibc-locales'
package and defining `GUIX_LOCPATH', along these lines:

     guix package -i glibc-utf8-locales
     export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"

See the "Application Setup" section in the manual, for more info.



Starting download of /tmp/guix-file.kBVFop
From
https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz.
..
download failed "
https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz"
404 "Not Found"
failed to download "/tmp/guix-file.kBVFop" from "
https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz
"
Backtrace
(and the backtrace is the same).

I am also new to schemas, but opened guix/import/cran.scm and saw what
Bjorn was saying. I don't know why if it is not the latest package there
should be a false condition, but I don't know either why I am not getting
the latest version from bioconductor if it is real that, for tracklayer the
latest is 42 and that file does not exist.
Any ideas? Should I spend more time trying to figure this out or should I
move on to another task, like knowing guix more deeply or learning texinfo?


Regards!
Laura

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Re: [outreach] Help trying to create R package

[Gábor Boskovits]

Hello Laura,

Laura Lazzati <laura.lazzati.15@gmail.com> ezt írta (időpont: 2018.
nov. 2., P, 20:45):
>>
>>
>> I tracked it down:
>>
>> The cause is that:
>>
>> guix/import/cran.scm:
>>
>> (define (latest-bioconductor-package-version name)
>>   "Return the version string corresponding to the latest release of the
>> bioconductor package NAME, or #F if the package is unknown."
>>
>> actually returns #f. It's a bit said that this #f is not checked
>> further down. The problem is the package name. If you add an "r" before
>> the package name, it should work (suppose you fixed the first problem):
>>
>> guix import cran --archive=bioconductor rtracklayer
>
> Sorry for writing again on this topic.
> Today I wanted to practice packaging an r package belonging to bioconductor, to then go on and read and work with texinfo.
> After writing on IRC channel, I realized I already had this exact problem, but thought it was a problem of other packages.
> I ran again this same command, and I am getting:
>
> $guix import cran -a bioconductor rtracklayer
> guile: warning: failed to install locale
> hint: Consider installing the `glibc-utf8-locales' or `glibc-locales' package and defining `GUIX_LOCPATH', along these lines:
>
>      guix package -i glibc-utf8-locales
>      export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"
>
> See the "Application Setup" section in the manual, for more info.
>
>
>
> Starting download of /tmp/guix-file.kBVFop
> From https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz...
> download failed "https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz" 404 "Not Found"
> failed to download "/tmp/guix-file.kBVFop" from "https://bioconductor.org/packages/release/bioc/src/contrib/rtracklayer_1.40.6.tar.gz"
> Backtrace
> (and the backtrace is the same).
>
> I am also new to schemas, but opened guix/import/cran.scm and saw what Bjorn was saying. I don't know why if it is not the latest package there should be a false condition, but I don't know either why I am not getting the latest version from bioconductor if it is real that, for tracklayer the latest is 42 and that file does not exist.
> Any ideas? Should I spend more time trying to figure this out or should I move on to another task, like knowing guix more deeply or learning texinfo?
>

This is not your fault, you were simply at the wrong place at the wrong time :)
Bioconductor 3.8 was released on October 31., so the importer, and
most probably all packages not having the substitues from
bioconductor are off. (It seems the release tarballs from 3.7 were
removed.) There is a comment in the importer that all bioconductor
packages should be updated together. We should ask Ricardo later how
to proceed regarding this.

>
> Regards!
> Laura

Best regards,
g_bor

Re: [outreach] Help trying to create R package

[Laura Lazzati]

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Thank you :)
Ok, i'll move to the texinfo task.
Regards!
Laura

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