| Message ID | 20190724182204.6818-12-zimon.toutoune@gmail.com |
|---|---|
| State | Accepted |
| Headers | show |
| Series | Add r packages to process flow cytometry data | expand |
zimoun <zimon.toutoune@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.
Hi Ricardo, Thank you for your quick feedback. 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. > --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
Hi, > 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. >> --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.
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)))