Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:06:02 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for CGEN on tokay2


To the developers/maintainers of the CGEN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGEN.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 285/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGEN 3.30.0  (landing page)
Justin Lee
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/CGEN
git_branch: RELEASE_3_14
git_last_commit: 15192e1
git_last_commit_date: 2021-10-26 13:08:59 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CGEN
Version: 3.30.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CGEN_3.30.0.tar.gz && rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGEN.buildbin-libdir CGEN_3.30.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CGEN_3.30.0.zip && rm CGEN_3.30.0.tar.gz CGEN_3.30.0.zip
StartedAt: 2022-01-16 04:17:48 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 04:19:51 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 123.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CGEN_3.30.0.tar.gz && rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGEN.buildbin-libdir CGEN_3.30.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CGEN_3.30.0.zip && rm CGEN_3.30.0.tar.gz CGEN_3.30.0.zip
###
##############################################################################
##############################################################################


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install for i386

* installing *source* package 'CGEN' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Additive.c -o Additive.o
Additive.c: In function 'compute_g':
Additive.c:233:19: warning: 'et22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x    = et12 + et22 - 1;
              ~~~~~^~~~~~
Additive.c:235:25: warning: 't22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       *g22 = logx - t12 - t22;
              ~~~~~~~~~~~^~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CML.c -o CML.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ccl.c -o ccl.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c csclust.f -o csclust.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fsclust.c -o fsclust.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hcl.c -o hcl.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pmatch.c -o pmatch.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score.c -o score.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/CGEN.buildbin-libdir/00LOCK-CGEN/00new/CGEN/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CGEN'
    finding HTML links ... done
    CGEN                                    html  
    GxE.scan                                html  
    GxE.scan.combine                        html  
    GxE.scan.partition                      html  
    LocusMapData                            html  
    QQ.plot                                 html  
    Xdata                                   html  
    Xdata2                                  html  
    additive.test                           html  
    chromosome.plot                         html  
    getMatchedSets                          html  
    getSummary                              html  
    getWaldTest                             html  
    locusMap.list                           html  
    pheno.list                              html  
    printEffects                            html  
    snp.effects                             html  
    snp.effects.plot                        html  
    snp.list                                html  
    snp.logistic                            html  
    snp.matched                             html  
    snp.score                               html  
    subject.list                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CGEN' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Additive.c -o Additive.o
Additive.c: In function 'compute_g':
Additive.c:233:19: warning: 'et22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x    = et12 + et22 - 1;
              ~~~~~^~~~~~
Additive.c:235:25: warning: 't22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       *g22 = logx - t12 - t22;
              ~~~~~~~~~~~^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c CML.c -o CML.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ccl.c -o ccl.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c csclust.f -o csclust.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fsclust.c -o fsclust.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hcl.c -o hcl.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pmatch.c -o pmatch.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score.c -o score.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/CGEN.buildbin-libdir/CGEN/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGEN' as CGEN_3.30.0.zip
* DONE (CGEN)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CGEN' successfully unpacked and MD5 sums checked