| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:37 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
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To the developers/maintainers of the GenoGAM package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenoGAM.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 743/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenoGAM 2.12.0 (landing page) Georg Stricker
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: GenoGAM |
| Version: 2.12.0 |
| Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GenoGAM_2.12.0.tar.gz && rm -rf GenoGAM.buildbin-libdir && mkdir GenoGAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenoGAM.buildbin-libdir GenoGAM_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GenoGAM_2.12.0.zip && rm GenoGAM_2.12.0.tar.gz GenoGAM_2.12.0.zip |
| StartedAt: 2022-04-12 06:01:09 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 06:06:09 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 300.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GenoGAM_2.12.0.tar.gz && rm -rf GenoGAM.buildbin-libdir && mkdir GenoGAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenoGAM.buildbin-libdir GenoGAM_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GenoGAM_2.12.0.zip && rm GenoGAM_2.12.0.tar.gz GenoGAM_2.12.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
17 3287k 17 574k 0 0 856k 0 0:00:03 --:--:-- 0:00:03 856k
68 3287k 68 2251k 0 0 1346k 0 0:00:02 0:00:01 0:00:01 1346k
100 3287k 100 3287k 0 0 1578k 0 0:00:02 0:00:02 --:--:-- 1578k
install for i386
* installing *source* package 'GenoGAM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrixMult.cpp -o matrixMult.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
** help
*** installing help indices
converting help for package 'GenoGAM'
finding HTML links ... done
Coordinates-class html
GenoGAM-class html
GenoGAM html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/help/GenoGAM.html
GenoGAMDataSet-class html
GenoGAMDataSet-metrics html
GenoGAMDataSet-subsetting html
GenoGAMDataSetList-class html
GenoGAMDataSetList-metrics html
GenoGAMDataSetList-subsetting html
GenoGAMFamily-class html
GenoGAMList-class html
GenoGAMList-subsetting html
GenoGAMSettings-class html
asCoordinates html
callPeaks html
computeRegionSignificance html
computeSignificance html
computeSizeFactors html
fitGenoGAM html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/help/genogam.html
makeTestGenoGAM html
makeTestGenoGAMDataSet html
makeTestGenoGAMDataSetList html
makeTestGenoGAMList html
plotGenoGAM html
readData html
writeToBEDFile html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'GenoGAM' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrixMult.cpp -o matrixMult.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GenoGAM.buildbin-libdir/GenoGAM/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
* MD5 sums
packaged installation of 'GenoGAM' as GenoGAM_2.12.0.zip
* DONE (GenoGAM)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GenoGAM' successfully unpacked and MD5 sums checked