[PATCH 11/11] gnu: Add r-depecher.

  • Done
  • quality assurance status badge
Details
3 participants
  • Tobias Geerinckx-Rice
  • Ricardo Wurmus
  • zimoun
Owner
unassigned
Submitted by
zimoun
Severity
normal
Merged with
Z
Z
zimoun wrote on 24 Jul 2019 20:22
(address . guix-patches@gnu.org)(name . zimoun)(address . zimon.toutoune@gmail.com)
20190724182204.6818-12-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-depecher): New variable.
---
gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)

Toggle diff (54 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 64625aedd4..7c9a3b7417 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5013,3 +5013,47 @@ data sets: N-integration with variants of Generalised Canonical Correlation
Analysis and P-integration with variants of multi-group Partial Least
Squares.")
(license license:gpl2+)))
+
+(define-public r-depecher
+ (package
+ (name "r-depecher")
+ (version "1.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DepecheR" version))
+ (sha256
+ (base32
+ "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
+ (properties `((upstream-name . "DepecheR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beanplot" ,r-beanplot)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-dosnow" ,r-dosnow)
+ ("r-dplyr" ,r-dplyr)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gplots" ,r-gplots)
+ ("r-mass" ,r-mass)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-mixomics" ,r-mixomics)
+ ("r-moments" ,r-moments)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-reshape2" ,r-reshape2)
+ ("r-viridis" ,r-viridis)))
+ (home-page
+ "https://bioconductor.org/packages/DepecheR")
+ (synopsis
+ "Determination of essential phenotypic elements of clusters in high-dimensional entities")
+ (description
+ "The purpose of this package is to identify traits in a dataset that can
+separate groups. This is done on two levels. First, clustering is performed,
+using an implementation of sparse K-means. Secondly, the generated clusters
+are used to predict outcomes of groups of individuals based on their
+distribution of observations in the different clusters. As certain clusters
+with separating information will be identified, and these clusters are defined
+by a sparse number of variables, this method can reduce the complexity of
+data, to only emphasize the data that actually matters.")
+ (license license:expat)))
--
2.21.0
T
T
Tobias Geerinckx-Rice wrote on 24 Jul 2019 20:34
(no subject)
(name . GNU bug tracker automated control server)(address . control@debbugs.gnu.org)
87muh3i8nq.fsf@nckx
merge 36789 36800
T
T
Tobias Geerinckx-Rice wrote on 24 Jul 2019 20:36
(name . GNU bug tracker automated control server)(address . control@debbugs.gnu.org)
87lfwni8k4.fsf@nckx
merge 36789 36790
merge 36789 36791
merge 36789 36792
merge 36789 36793
merge 36789 36794
merge 36789 36795
merge 36789 36796
merge 36789 36797
merge 36789 36798
merge 36789 36799
-----BEGIN PGP SIGNATURE-----

iHUEARYKAB0WIQT12iAyS4c9C3o4dnINsP+IT1VteQUCXTilKwAKCRANsP+IT1Vt
efwCAPwMFfiT2lvcwMNzzwkToDSGCWdwSxssz16tTMeFjdOR8QEA/0yecSJc7Tlg
WzetWDVAWg15OT5glks97g4iaGnfGQE=
=Lk9Y
-----END PGP SIGNATURE-----

Z
Z
zimoun wrote on 24 Jul 2019 21:17
Merge 36789 36790
CAJ3okZ2J2BW+HmW+K6ziyED4x4NQb80ucCuf9Mpb+nuVBFT7Qg@mail.gmail.com
merge 36789 36790
thanks
R
R
Ricardo Wurmus wrote on 24 Jul 2019 22:49
Re: [bug#36800] [PATCH 11/11] gnu: Add r-depecher.
(address . guix-patches@gnu.org)(address . 36800@debbugs.gnu.org)
87v9vr9mzb.fsf@elephly.net
zimoun <zimon.toutoune@gmail.com> writes:

Toggle quote (2 lines)
> * gnu/packages/bioconductor.scm (r-depecher): New variable.

This package cannot actually be built:

Toggle snippet (25 lines)
…
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

I’ll modify the build phases to patch out this call to /usr/bin/strip.

--
Ricardo
Z
Z
zimoun wrote on 25 Jul 2019 11:54
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 36800@debbugs.gnu.org)
CAJ3okZ0Pudgzd9BQW0RBS80PfgDb9ZJX4Ue7G0MiyKyg6tSWNg@mail.gmail.com
Hi Ricardo,

Thank you for your quick feedback.

On Wed, 24 Jul 2019 at 22:50, Ricardo Wurmus <rekado@elephly.net> wrote:
Toggle quote (7 lines)
>
> zimoun <zimon.toutoune@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.


Toggle quote (28 lines)
> --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?


All the best,
simon
R
R
Ricardo Wurmus wrote on 25 Jul 2019 14:45
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 36800@debbugs.gnu.org)
878ssm9tad.fsf@elephly.net
Hi,

Toggle quote (11 lines)
> On Wed, 24 Jul 2019 at 22:50, Ricardo Wurmus <rekado@elephly.net> wrote:
>>
>> zimoun <zimon.toutoune@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.

Toggle quote (31 lines)
>> --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
?