GNU bug report logs - #36800
[PATCH 11/11] gnu: Add r-depecher.

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 36800 <at> debbugs.gnu.org
Subject: [bug#36800] [PATCH 11/11] gnu: Add r-depecher.
Date: Thu, 25 Jul 2019 14:45:46 +0200

Hi,

> On Wed, 24 Jul 2019 at 22:50, Ricardo Wurmus <rekado <at> elephly.net> wrote:
>>
>> zimoun <zimon.toutoune <at> gmail.com> writes:
>>
>> > * gnu/packages/bioconductor.scm (r-depecher): New variable.
>>
>> This package cannot actually be built:
>
> Sorry for the annoyance.
> I missed `--pure` when I built the package.

You don’t need “--pure” because /usr won’t be available in the build
environment either way.

>> --8<---------------cut here---------------start------------->8---
>> …
>> if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug DepecheR.so; fi
>> /gnu/store/q19l04vd2za80mk1845pz7r8cz29qk43-bash-minimal-4.4.23/bin/bash: /usr/bin/strip: No such file or directory
>> make: *** [Makevars:6: strippedLib] Error 127
>> ERROR: compilation failed for package ‘DepecheR’
>> * removing ‘/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depecher-1.0.3/site-library/DepecheR’
>> Backtrace:
>>            4 (primitive-load "/gnu/store/f1ky8a22c7s5p053nci05a536j7…")
>> In ice-9/eval.scm:
>>    191:35  3 (_ #f)
>> In srfi/srfi-1.scm:
>>    863:16  2 (every1 #<procedure 725d80 at /gnu/store/4p2vk30zhkwxq…> …)
>> In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/gnu-build-system.scm:
>>    799:28  1 (_ _)
>> In /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/utils.scm:
>>     616:6  0 (invoke _ . _)
>>
>> /gnu/store/4p2vk30zhkwxqdkydn1572qz70jgvl55-module-import/guix/build/utils.scm:616:6: In procedure invoke:
>> Throw to key `srfi-34' with args `(#<condition &invoke-error [program: "R" arguments: ("CMD" "INSTALL" "--install-tests" "--library=/gnu/store/pgjzdxwn0nyanx9lvp6i9rxflabh3k21-r-depecher-1.0.3/site-library/" "--built-timestamp=1970-01-01" ".") exit-status: 1 term-signal: #f stop-signal: #f] 7c4ec0>)'.
>> builder for `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv' failed with exit code 1
>> build of /gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv failed
>> View build log at '/var/log/guix/drvs/mw/cdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv.bz2'.
>> guix build: error: build of `/gnu/store/mwcdvlm6f17i81m16w131042cmvlfh5m-r-depecher-1.0.3.drv' failed
>> --8<---------------cut here---------------end--------------->8---
>>
>> I’ll modify the build phases to patch out this call to /usr/bin/strip.
>
> Just to understand, you mean patch the file `DepecheR/src/Makevars` to
> remove the absolute path `/usr/bin/strip` to simply `strip`. Right?

The Makevars file contains a syntax error.  Instead of joining the
checks with “&&” they used “&” which is for background execution.  So
instead of checking things and proceeding only if the checks passed they
would attempt to execute /usr/bin/strip unconditionally.

I only replaced the & with the intended &&, so now the check for
/usr/bin/strip fails and it’s not executed, which is just fine.

-- 
Ricardo

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