Anand Mayakonda
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/maftools |
| git_branch: RELEASE_3_13 |
| git_last_commit: 0c14f2a |
| git_last_commit_date: 2021-09-07 06:38:12 -0400 (Tue, 07 Sep 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:10 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the maftools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maftools.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. |
| Package 1021/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maftools 2.8.05 (landing page) Anand Mayakonda
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: maftools |
| Version: 2.8.05 |
| Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/maftools_2.8.05.tar.gz && rm -rf maftools.buildbin-libdir && mkdir maftools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maftools.buildbin-libdir maftools_2.8.05.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL maftools_2.8.05.zip && rm maftools_2.8.05.tar.gz maftools_2.8.05.zip |
| StartedAt: 2021-10-14 08:43:44 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 08:45:06 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 81.3 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/maftools_2.8.05.tar.gz && rm -rf maftools.buildbin-libdir && mkdir maftools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maftools.buildbin-libdir maftools_2.8.05.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL maftools_2.8.05.zip && rm maftools_2.8.05.tar.gz maftools_2.8.05.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
19 6612k 19 1312k 0 0 1862k 0 0:00:03 --:--:-- 0:00:03 1862k
66 6612k 66 4428k 0 0 2608k 0 0:00:02 0:00:01 0:00:01 2607k
100 6612k 100 6612k 0 0 2922k 0 0:00:02 0:00:02 --:--:-- 2923k
install for i386
* installing *source* package 'maftools' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ntcounts.c -o ntcounts.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c somaticfreq.c -o somaticfreq.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o maftools.dll tmp.def ntcounts.o somaticfreq.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -Lc:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/maftools.buildbin-libdir/00LOCK-maftools/00new/maftools/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'maftools'
finding HTML links ... done
GISTIC-class html
MAF-class html
MAF html
OncogenicPathways html
PlotOncogenicPathways html
annovarToMaf html
bamreadcounts html
cancerhotspots html
clinicalEnrichment html
coBarplot html
coOncoplot html
compareSignatures html
drugInteractions html
estimateSignatures html
extractSignatures html
filterMaf html
forestPlot html
genesToBarcodes html
genotypeMatrix html
getClinicalData html
getCytobandSummary html
getFields html
getGeneSummary html
getSampleSummary html
gisticBubblePlot html
gisticChromPlot html
gisticOncoPlot html
icgcSimpleMutationToMAF html
inferHeterogeneity html
lollipopPlot html
lollipopPlot2 html
maf2mae html
mafCompare html
mafSummary html
mafSurvGroup html
mafSurvival html
mafbarplot html
math.score html
merge_mafs html
mutCountMatrix html
oncodrive html
oncoplot html
oncostrip html
pfamDomains html
plotApobecDiff html
plotCBSsegments html
plotClusters html
plotCophenetic html
plotEnrichmentResults html
plotOncodrive html
plotProtein html
plotSignatures html
plotTiTv html
plotVaf html
plotmafSummary html
prepareMutSig html
rainfallPlot html
read.maf html
readGistic html
setMaf html
signatureEnrichment html
somaticInteractions html
subsetMaf html
finding level-2 HTML links ... done
survGroup html
tcgaAvailable html
tcgaCompare html
tcgaDriverBP html
tcgaLoad html
titv html
tmb html
trinucleotideMatrix html
vafCompare html
write.GisticSummary html
write.mafSummary 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 'maftools' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ntcounts.c -o ntcounts.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c somaticfreq.c -o somaticfreq.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o maftools.dll tmp.def ntcounts.o somaticfreq.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/maftools.buildbin-libdir/maftools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maftools' as maftools_2.8.05.zip
* DONE (maftools)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'maftools' successfully unpacked and MD5 sums checked