[bug#32192] [PATCH 0/7] Remove duplicated packages.

[bug#32192] [PATCH 0/7] Remove duplicated packages.

[Christopher Baines]

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As part of messing up packaging Ruby on Rails, I ended up duplicating
some packages, and this prompted me to look if any duplicates made it in
to guix. I ran the following command, it produces a few false positives.

  grep define-public -R | sort | uniq -d

The following patches attempt to remove the duplicates, favouring the
original package definition.

Is there any way of guarding against adding these, or more accurately
checking for duplicate definitions?

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[bug#32192] [PATCH 1/7] gnu: Remove duplicated emacs-csv-mode.

[Christopher Baines]

It was first added in 9faa46ee48d12bf55355805a84a7c533f904a39d, and then again
in 8bc8efc753605e404c1efcdc5b53a780feb0760c.

* gnu/packages/emacs.scm (emacs-csv-mode): Remove duplicated package
definition.
---
 gnu/packages/emacs.scm | 20 --------------------
 1 file changed, 20 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 20d5597f5..56decb175 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -9641,26 +9641,6 @@ buffer.")
 downloading manager for Emacs.")
       (license license:gpl3+))))
 
-(define-public emacs-csv-mode
-  (package
-    (name "emacs-csv-mode")
-    (version "1.7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "http://elpa.gnu.org/packages/csv-mode-"
-                           version ".el"))
-       (sha256
-        (base32
-         "0r4bip0w3h55i8h6sxh06czf294mrhavybz0zypzrjw91m1bi7z6"))))
-    (build-system emacs-build-system)
-    (home-page "http://elpa.gnu.org/packages/csv-mode.html")
-    (synopsis "Major mode for editing comma or char separated values")
-    (description
-     "This package provides an Emacs CSV mode, a major mode for editing
-records in a generalized CSV (character-separated values) format.")
-    (license license:gpl3+)))
-
 (define-public emacs-helpful
   (package
     (name "emacs-helpful")
-- 
2.17.1

[bug#32192] [PATCH 2/7] gnu: Remove duplicated emacs-load-relative.

[Christopher Baines]

It was first added in fa1a17b78631681a23ae1fb7b1f902148bbebdbb, and then again
in f8a88f223ea2ac36576cd92f457790df5a6f2408.

* gnu/packages/emacs.scm (emacs-load-relative): Remove duplicated package
definition.
---
 gnu/packages/emacs.scm | 26 --------------------------
 1 file changed, 26 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 56decb175..3d17375f6 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -8696,32 +8696,6 @@ region instead.")
 schema validation.")
     (license license:gpl3+)))
 
-(define-public emacs-load-relative
-  (let ((commit "738896e3da491b35399178ed2c6bc92cc728d119")
-        (revision "1"))
-    (package
-      (name "emacs-load-relative")
-      (version (string-append "0.0.1" "-" revision "."
-                              (string-take commit 7)))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/rocky/emacs-load-relative")
-               (commit commit)))
-         (file-name (string-append name "-" version "-checkout"))
-         (sha256
-          (base32
-           "1rpy5mfncncl6gqgg53d3g25g1700g4b9bivd4c0cfcv5dbxhp73"))))
-      (build-system emacs-build-system)
-      (home-page "https://github.com/rocky/emacs-load-relative")
-      (synopsis "Relative loads for Emacs Lisp files")
-      (description "@code{load-relative} allows to write small Emacs
-functions or modules in a larger multi-file Emacs package and
-facilitate running from the source tree without having to install the
-code or fiddle with evil @code{load-path}.")
-      (license license:gpl3+))))
-
 (define-public emacs-rainbow-blocks
   (let ((commit "dd435d7bb34ff6f162a5f315df308b90b7e9f842"))
     (package
-- 
2.17.1

[bug#32192] [PATCH 3/7] gnu: Remove duplicated r-psych package.

[Christopher Baines]

It was first added in cdc129dc53b1c04e9a6577f7d2b9641a0a03c32f, then again in
db80dd4a1d7e2371bc3c300f48b84a817adb3550.

* gnu/packages/cran.scm (r-psych): Remove duplicated package definition.
---
 gnu/packages/cran.scm | 33 +--------------------------------
 1 file changed, 1 insertion(+), 32 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index fc4baa5b5..e9f4f663a 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1686,7 +1686,7 @@ problems as well as resampling based estimators of prediction error.")
 (define-public r-psych
   (package
     (name "r-psych")
-    (version "1.7.8")
+    (version "1.8.4")
     (source
      (origin
        (method url-fetch)
@@ -3467,37 +3467,6 @@ filtering functions, resampling routines, and visualization of filter models.
 It also includes interpolation functions.")
     (license license:gpl2)))
 
-(define-public r-psych
-  (package
-    (name "r-psych")
-    (version "1.8.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "psych" version))
-       (sha256
-        (base32
-         "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-foreign" ,r-foreign)
-       ("r-lattice" ,r-lattice)
-       ("r-mnormt" ,r-mnormt)
-       ("r-nlme" ,r-nlme)))
-    (home-page "http://cran.r-project.org/web/packages/psych")
-    (synopsis "Procedures for psychological, psychometric, and personality research")
-    (description
-     "This package provides a general purpose toolbox for personality,
-psychometric theory and experimental psychology.  The functions are primarily
-for multivariate analysis and scale construction using factor analysis,
-principal component analysis, cluster analysis and reliability analysis,
-although others provide basic descriptive statistics.  It provides functions
-for analyzing data at multiple levels within and between group statistics,
-including correlations and factor analysis; functions for simulating and
-testing particular item and test structures are included.  Several functions
-serve as a useful front end for structural equation modeling.")
-    (license license:gpl2+)))
-
 (define-public r-gsubfn
   (package
     (name "r-gsubfn")
-- 
2.17.1

[bug#32192] [PATCH 4/7] gnu: Remove duplicated ghc-th-lift-instances.

[Christopher Baines]

It was first added in a6d1c4e75a76399c8d82a9570db5cd14351f661b, then again in
ff7dd11f0a4fd6ca947cfa40cec42628fde44667.

* gnu/packages/haskell.scm (ghc-th-lift-instances): Remove duplicated package
definition.
---
 gnu/packages/haskell.scm | 25 -------------------------
 1 file changed, 25 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 8d2dcba20..d9d39fb72 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9221,31 +9221,6 @@ connections.")
 from aeson.")
     (license license:bsd-3)))
 
-(define-public ghc-th-lift-instances
-  (package
-    (name "ghc-th-lift-instances")
-    (version "0.1.11")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/"
-                           "th-lift-instances-" version "/"
-                           "th-lift-instances-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1f56cp6ckcalld5jchv0kxpjkwcsixd7smd0g7r8cg67ppx6m90x"))))
-    (build-system haskell-build-system)
-    (inputs `(("ghc-th-lift" ,ghc-th-lift)
-              ("ghc-vector" ,ghc-vector)
-              ("ghc-text" ,ghc-text)))
-    (native-inputs `(("ghc-quickcheck" ,ghc-quickcheck)))
-    (home-page "https://github.com/bennofs/th-lift-instances")
-    (synopsis "Lift instances for template-haskell for common data types")
-    (description "Most data types in the Haskell platform do not have Lift
-instances.  This package provides orphan instances for containers, text,
-bytestring and vector.")
-    (license license:bsd-3)))
-
 (define-public ghc-generics-sop
   (package
     (name "ghc-generics-sop")
-- 
2.17.1

[bug#32192] [PATCH 5/7] gnu: Remove duplicated ghc-time-locale-compat.

[Christopher Baines]

It was first added in 5e51bcf7b38511d943f4d24621be5817144061cd, then again in
c56a30b3ba3e1e93ced3c6ba2cfb4c738b805074.

* gnu/packages/haskell.scm (ghc-time-locale-compat): Remove duplicated package
definition.
---
 gnu/packages/haskell.scm | 20 --------------------
 1 file changed, 20 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d9d39fb72..7f14c5945 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9278,26 +9278,6 @@ each constructor are represented using an n-ary product.")
 parser that uses ByteStrings for parsing and representing the URI data.")
     (license license:bsd-3)))
 
-(define-public ghc-time-locale-compat
-  (package
-    (name "ghc-time-locale-compat")
-    (version "0.1.1.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/"
-                           "time-locale-compat-" version "/"
-                           "time-locale-compat-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1vdcfr2hp9qh3ag90x6ikbdf42wiqpdylnplffna54bpnilbyi4i"))))
-    (build-system haskell-build-system)
-    (home-page "https://github.com/khibino/haskell-time-locale-compat")
-    (synopsis "Compatibility of TimeLocale between old-locale and time-1.5")
-    (description "This Haskell package contains wrapped name module for
-TimeLocale.")
-    (license license:bsd-3)))
-
 (define-public ghc-http-api-data
   (package
     (name "ghc-http-api-data")
-- 
2.17.1

[bug#32192] [PATCH 6/7] gnu: Remove duplicated perl-extutils-depends.

[Christopher Baines]

This was first added in 84e8b19fe150ae843d63ca7343aa7172f35153f3, and then
again in 017b014ce4a5defed12836886c4dfe2c5ae89d2d.

* gnu/packages/perl.scm (perl-extutils-depends): Remove duplicated package
definition.
---
 gnu/packages/perl.scm | 24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index afbe5979d..493b7860b 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -3166,30 +3166,6 @@ and alternative installers with the `installler` option.  But it's written in
 only about 40% as many lines of code and with zero non-core dependencies.")
     (license (package-license perl))))
 
-(define-public perl-extutils-depends
-  (package
-    (name "perl-extutils-depends")
-    (version "0.405")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "mirror://cpan/authors/id/X/XA/XAOC/ExtUtils-Depends-"
-             version
-             ".tar.gz"))
-       (sha256
-        (base32
-         "0b4ab9qmcihsfs2ajhn5qzg7nhazr68v3r0zvb7076smswd41mla"))))
-    (build-system perl-build-system)
-    (native-inputs
-     `(("perl-test-number-delta"
-        ,perl-test-number-delta)))
-    (home-page "http://search.cpan.org/dist/ExtUtils-Depends/")
-    (synopsis "Easily build XS extensions that depend on XS extensions")
-    (description "ExtUtils::Depends builds XS extensions that depend on XS
-extensions")
-    (license (package-license perl))))
-
 (define-public perl-extutils-installpaths
   (package
     (name "perl-extutils-installpaths")
-- 
2.17.1

[bug#32192] [PATCH 7/7] gnu: Remove duplicated python-pafy.

[Christopher Baines]

It was first added in 02f8f804f0242df885311715412a1e3ee5436f3b, then again in
2dd12924cf4a30a96262b6d392fcde58c9f10d4b.

* gnu/packages/python.scm (python-pafy): Remove duplicated package definition.
---
 gnu/packages/python.scm | 24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index fc1ef3eb2..184635bd2 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1747,30 +1747,6 @@ matching them against a list of media-ranges.")
      `(#:tests? #f
        ,@(package-arguments python2-funcsigs)))))
 
-(define-public python-pafy
-  (package
-    (name "python-pafy")
-    (version "0.5.3.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pafy" version))
-       (sha256
-        (base32
-         "1a7dxi95m1043rxx1r5x3ngb66nwlq6aqcasyqqjzmmmjps4zrim"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f)) ; Currently pafy can not find itself in the tests
-    (propagated-inputs
-     ;; Youtube-dl is a python package which is imported in the file
-     ;; "backend_youtube_dl.py", therefore it needs to be propagated.
-     `(("youtube-dl" ,youtube-dl)))
-    (home-page "https://np1.github.io/pafy/")
-    (synopsis "Retrieve YouTube content and metadata")
-    (description
-     "@code{pafy} is a python library to retrieve YouTube content and metadata.")
-    (license license:lgpl3+)))
-
 (define-public python-py
   (package
     (name "python-py")
-- 
2.17.1

[bug#32192] [PATCH 3/7] gnu: Remove duplicated r-psych package.

[Leo Famulari]

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On Tue, Jul 17, 2018 at 09:41:20PM +0100, Christopher Baines wrote:
> It was first added in cdc129dc53b1c04e9a6577f7d2b9641a0a03c32f, then again in
> db80dd4a1d7e2371bc3c300f48b84a817adb3550.
> 
> * gnu/packages/cran.scm (r-psych): Remove duplicated package definition.
> ---
>  gnu/packages/cran.scm | 33 +--------------------------------
>  1 file changed, 1 insertion(+), 32 deletions(-)
> 
> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
> index fc4baa5b5..e9f4f663a 100644
> --- a/gnu/packages/cran.scm
> +++ b/gnu/packages/cran.scm
> @@ -1686,7 +1686,7 @@ problems as well as resampling based estimators of prediction error.")
>  (define-public r-psych
>    (package
>      (name "r-psych")
> -    (version "1.7.8")
> +    (version "1.8.4")
>      (source
>       (origin
>         (method url-fetch)

Does this preserve the correct source hash?

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[bug#32192] [PATCH 0/7] Remove duplicated packages.

[Leo Famulari]

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On Tue, Jul 17, 2018 at 09:27:45PM +0100, Christopher Baines wrote:
> The following patches attempt to remove the duplicates, favouring the
> original package definition.

I sent one comment, otherwise the patches LGTM.

> Is there any way of guarding against adding these, or more accurately
> checking for duplicate definitions?

I don't know. Hopefully someone else has some ideas.

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[bug#32192] [PATCH 0/7] Remove duplicated packages.

[Ludovic Courtès]

Hello,

Leo Famulari <leo@famulari.name> skribis:

> On Tue, Jul 17, 2018 at 09:27:45PM +0100, Christopher Baines wrote:
>> The following patches attempt to remove the duplicates, favouring the
>> original package definition.
>
> I sent one comment, otherwise the patches LGTM.
>
>> Is there any way of guarding against adding these, or more accurately
>> checking for duplicate definitions?
>
> I don't know. Hopefully someone else has some ideas.

It’s terrible to see there were so many duplicate packages.

The package lookup machinery detects and warns about same-named packages
when you do things like:

  (define-public var1
    (package (name "something") …))
  (define-public var2
    (package (name "something") …))

The problem here is that duplicates were in the same module and using
the same variable name, such that the second definition would shadow the
first one, and so Guix only sees one package.

I think we should add a warning in the compiler for this situation.

Ludo’.

[bug#32192] [PATCH 0/7] Remove duplicated packages.

[Ludovic Courtès]

ludo@gnu.org (Ludovic Courtès) skribis:

> It’s terrible to see there were so many duplicate packages.
>
> The package lookup machinery detects and warns about same-named packages
> when you do things like:
>
>   (define-public var1
>     (package (name "something") …))
>   (define-public var2
>     (package (name "something") …))
>
> The problem here is that duplicates were in the same module and using
> the same variable name, such that the second definition would shadow the
> first one, and so Guix only sees one package.
>
> I think we should add a warning in the compiler for this situation.

Done!

  https://git.savannah.gnu.org/cgit/guile.git/commit/?h=stable-2.2&id=bdcd0ba8a71af24f0b64d7acac3130d8f541d26c

Now you get warnings like this:

--8<---------------cut here---------------start------------->8---
$ /data/src/guile-2.1/meta/uninstalled-env guild compile -Wshadowed-toplevel gnu/packages/haskell.scm
gnu/packages/haskell.scm:9224:0: warning: shadows previous definition of `ghc-th-lift-instances' at gnu/packages/haskell.scm:5437:0
gnu/packages/haskell.scm:9306:0: warning: shadows previous definition of `ghc-time-locale-compat' at gnu/packages/haskell.scm:2591:0
wrote `/data/src/guile-2.1/cache/guile/ccache/2.2-LE-8-3.A/home/ludo/src/guix/gnu/packages/haskell.scm.go'
$ /data/src/guile-2.1/meta/uninstalled-env guild compile -Wshadowed-toplevel gnu/packages/emacs.scm
gnu/packages/emacs.scm:8704:0: warning: shadows previous definition of `emacs-load-relative' at gnu/packages/emacs.scm:3467:0
gnu/packages/emacs.scm:9648:0: warning: shadows previous definition of `emacs-csv-mode' at gnu/packages/emacs.scm:7390:0
wrote `/data/src/guile-2.1/cache/guile/ccache/2.2-LE-8-3.A/home/ludo/src/guix/gnu/packages/emacs.scm.go'
--8<---------------cut here---------------end--------------->8---

This will be in Guile 2.2.5.

Ludo’.

[bug#32192] [PATCH 0/7] Remove duplicated packages.

[Christopher Baines]

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Ludovic Courtès <ludo@gnu.org> writes:

> ludo@gnu.org (Ludovic Courtès) skribis:
>
>> It’s terrible to see there were so many duplicate packages.
>>
>> The package lookup machinery detects and warns about same-named packages
>> when you do things like:
>>
>>   (define-public var1
>>     (package (name "something") …))
>>   (define-public var2
>>     (package (name "something") …))
>>
>> The problem here is that duplicates were in the same module and using
>> the same variable name, such that the second definition would shadow the
>> first one, and so Guix only sees one package.
>>
>> I think we should add a warning in the compiler for this situation.
>
> Done!
>
>   https://git.savannah.gnu.org/cgit/guile.git/commit/?h=stable-2.2&id=bdcd0ba8a71af24f0b64d7acac3130d8f541d26c
>
> Now you get warnings like this:
>
> --8<---------------cut here---------------start------------->8---
> $ /data/src/guile-2.1/meta/uninstalled-env guild compile -Wshadowed-toplevel gnu/packages/haskell.scm
> gnu/packages/haskell.scm:9224:0: warning: shadows previous definition of `ghc-th-lift-instances' at gnu/packages/haskell.scm:5437:0
> gnu/packages/haskell.scm:9306:0: warning: shadows previous definition of `ghc-time-locale-compat' at gnu/packages/haskell.scm:2591:0
> wrote `/data/src/guile-2.1/cache/guile/ccache/2.2-LE-8-3.A/home/ludo/src/guix/gnu/packages/haskell.scm.go'
> $ /data/src/guile-2.1/meta/uninstalled-env guild compile -Wshadowed-toplevel gnu/packages/emacs.scm
> gnu/packages/emacs.scm:8704:0: warning: shadows previous definition of `emacs-load-relative' at gnu/packages/emacs.scm:3467:0
> gnu/packages/emacs.scm:9648:0: warning: shadows previous definition of `emacs-csv-mode' at gnu/packages/emacs.scm:7390:0
> wrote `/data/src/guile-2.1/cache/guile/ccache/2.2-LE-8-3.A/home/ludo/src/guix/gnu/packages/emacs.scm.go'
> --8<---------------cut here---------------end--------------->8---
>
> This will be in Guile 2.2.5.


Awesome! Thanks Ludo’ :D


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[bug#32192] [PATCH 3/7] gnu: Remove duplicated r-psych package.

[Christopher Baines]

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Leo Famulari <leo@famulari.name> writes:

> On Tue, Jul 17, 2018 at 09:41:20PM +0100, Christopher Baines wrote:
>> It was first added in cdc129dc53b1c04e9a6577f7d2b9641a0a03c32f, then again in
>> db80dd4a1d7e2371bc3c300f48b84a817adb3550.
>>
>> * gnu/packages/cran.scm (r-psych): Remove duplicated package definition.
>> ---
>>  gnu/packages/cran.scm | 33 +--------------------------------
>>  1 file changed, 1 insertion(+), 32 deletions(-)
>>
>> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
>> index fc4baa5b5..e9f4f663a 100644
>> --- a/gnu/packages/cran.scm
>> +++ b/gnu/packages/cran.scm
>> @@ -1686,7 +1686,7 @@ problems as well as resampling based estimators of prediction error.")
>>  (define-public r-psych
>>    (package
>>      (name "r-psych")
>> -    (version "1.7.8")
>> +    (version "1.8.4")
>>      (source
>>       (origin
>>         (method url-fetch)
>
> Does this preserve the correct source hash?

It does not, good spot :) I've now fixed this to use the hash of the
removed package definition, and pushed.

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bug#32192: [PATCH 0/7] Remove duplicated packages.

[Christopher Baines]

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Leo Famulari <leo@famulari.name> writes:

> On Tue, Jul 17, 2018 at 09:27:45PM +0100, Christopher Baines wrote:
>> The following patches attempt to remove the duplicates, favouring the
>> original package definition.
>
> I sent one comment, otherwise the patches LGTM.

Thanks, I've now fixed that issue and pushed :)

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