GNU bug report logs -
#36800
[PATCH 11/11] gnu: Add r-depecher.
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Reported by: zimoun <zimon.toutoune <at> gmail.com>
Date: Wed, 24 Jul 2019 18:23:10 UTC
Severity: normal
Tags: patch
Merged with 36789,
36790,
36791,
36792,
36793,
36794,
36795,
36796,
36797,
36798,
36799
Done: zimoun <zimon.toutoune <at> gmail.com>
Bug is archived. No further changes may be made.
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(Wed, 24 Jul 2019 18:23:10 GMT)
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(Wed, 24 Jul 2019 18:23:10 GMT)
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
* gnu/packages/bioconductor.scm (r-depecher): New variable.
---
gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
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
Merged 36789 36800.
Request was from
Tobias Geerinckx-Rice <me <at> tobias.gr>
to
control <at> debbugs.gnu.org
.
(Wed, 24 Jul 2019 18:35:03 GMT)
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Merged 36789 36790 36800.
Request was from
Tobias Geerinckx-Rice <me <at> tobias.gr>
to
control <at> debbugs.gnu.org
.
(Wed, 24 Jul 2019 18:37:02 GMT)
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(Wed, 24 Jul 2019 20:50:01 GMT)
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Message #32 received at submit <at> debbugs.gnu.org (full text, mbox):
zimoun <zimon.toutoune <at> gmail.com> writes:
> * gnu/packages/bioconductor.scm (r-depecher): New variable.
This package cannot actually be built:
--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.
--
Ricardo
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(Wed, 24 Jul 2019 20:50:02 GMT)
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(Thu, 25 Jul 2019 09:56:01 GMT)
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Message #38 received at 36800 <at> debbugs.gnu.org (full text, mbox):
Hi Ricardo,
Thank you for your quick feedback.
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.
> --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
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(Thu, 25 Jul 2019 12:47:02 GMT)
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Message #41 received at 36800 <at> debbugs.gnu.org (full text, mbox):
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
bug archived.
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Debbugs Internal Request <help-debbugs <at> gnu.org>
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(Sat, 21 Mar 2020 11:24:03 GMT)
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This bug report was last modified 4 years and 37 days ago.
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