From mboxrd@z Thu Jan 1 00:00:00 1970 From: =?UTF-8?Q?G=C3=A1bor_Boskovits?= Subject: Re: [outreach] Help trying to create R package Date: Wed, 17 Oct 2018 10:21:27 +0200 Message-ID: References: <20181016074412.54757b18@alma-ubu> <20181016082350.75757e6b@alma-ubu> <20181017001851.71543cc9@alma-ubu> <20181017091750.1c408b8d@alma-ubu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="0000000000001067820578685c98" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:49540) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gCh5K-00061H-NA for guix-devel@gnu.org; Wed, 17 Oct 2018 04:21:44 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gCh5J-00031c-68 for guix-devel@gnu.org; Wed, 17 Oct 2018 04:21:42 -0400 Received: from mail-oi1-x22a.google.com ([2607:f8b0:4864:20::22a]:40382) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gCh5I-00030v-VO for guix-devel@gnu.org; Wed, 17 Oct 2018 04:21:41 -0400 Received: by mail-oi1-x22a.google.com with SMTP id j68-v6so20373683oib.7 for ; Wed, 17 Oct 2018 01:21:40 -0700 (PDT) In-Reply-To: <20181017091750.1c408b8d@alma-ubu> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: =?UTF-8?B?QmrDtnJuIEjDtmZsaW5n?= Cc: Guix-devel , Ricardo Wurmus --0000000000001067820578685c98 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable =C3=9CHi Laura, Bj=C3=B6rn H=C3=B6fling ezt =C3=ADrta (= id=C5=91pont: 2018. okt. 17., Sze 9:17): > Hi Laura, > > On Tue, 16 Oct 2018 22:01:58 -0300 > Laura Lazzati wrote: > > > On Tue, Oct 16, 2018 at 7:19 PM Bj=C3=B6rn H=C3=B6fling > > 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=3Daspi) 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#C= ontributing > > > Bj=C3=B6rn > Best regards, g_bor > --0000000000001067820578685c98 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
=C3=9CHi Laura,



<= div class=3D"gmail_quote">
Bj=C3=B6rn H=C3=B6fling <bjoern.hoefling@bjoernhoefling.de> ezt =C3=ADrta (id=C5= =91pont: 2018. okt. 17., Sze 9:17):
Hi Laura,

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

> On Tue, Oct 16, 2018 at 7:19 PM Bj=C3=B6rn H=C3=B6fling
> <bjoern.hoefling@bjoernhoefling.de>= ; wrote:
> >
> > Hi Laura,=C2=A0
> 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-lev= el
is fine :-)

[..]

> > Here is another one:
> >
> > guix package -s "^r-" | recsel -p name| grep '\S= 9; | sort >r.txt=C2=A0
>
> 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/pack= age=3Daspi) 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-pro= ject.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 wh= ere 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 sect= ion 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<= br> > 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
<= /div>

Yes, please run gu= ix 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<= br> > 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 b= e
installed/used just at runtime. Please correct me anyone if I'm wrong,<= br> 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
>=C2=A0 =C2=A0(name "r-aspi")
>=C2=A0 =C2=A0(version "0.2.0")
>=C2=A0 =C2=A0(source
>=C2=A0 =C2=A0 =C2=A0(origin
>=C2=A0 =C2=A0 =C2=A0 =C2=A0(method url-fetch)
>=C2=A0 =C2=A0 =C2=A0 =C2=A0(uri (cran-uri "aspi" version)) >=C2=A0 =C2=A0 =C2=A0 =C2=A0(sha256
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(base32
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0"a7izhueiqsdjs2eo7dfyb63c= qje7mbqz6ennlyoynxxucbhpdnta"))))
>=C2=A0 =C2=A0(build-system r-build-system)
>=C2=A0 =C2=A0 (home-page
>=C2=A0 =C2=A0 =C2=A0"htt= ps://cran.r-project.org/web/packages/aspi/")
>=C2=A0 =C2=A0(synopsis
>=C2=A0 =C2=A0 =C2=A0"Analysis of Symmetry of Parasitic Infections&= quot;)
>=C2=A0 =C2=A0(description
>=C2=A0 =C2=A0 =C2=A0"Tools for the analysis and visualization of b= ilateral asymmetry
> in parasitic infections.")
>=C2=A0 =C2=A0(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.ht= ml#Contributing


Bj=C3=B6rn

Best regards,
g_bor
--0000000000001067820578685c98--