Chengyang Ji
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/sitePath |
| git_branch: RELEASE_3_13 |
| git_last_commit: cb9e231 |
| git_last_commit_date: 2021-09-16 01:59:30 -0400 (Thu, 16 Sep 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:23 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the sitePath package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sitePath.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 1784/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sitePath 1.8.4 (landing page) Chengyang Ji
| 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: sitePath |
| Version: 1.8.4 |
| Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/sitePath_1.8.4.tar.gz && rm -rf sitePath.buildbin-libdir && mkdir sitePath.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sitePath.buildbin-libdir sitePath_1.8.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL sitePath_1.8.4.zip && rm sitePath_1.8.4.tar.gz sitePath_1.8.4.zip |
| StartedAt: 2021-10-14 09:36:39 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 09:41:02 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 263.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/sitePath_1.8.4.tar.gz && rm -rf sitePath.buildbin-libdir && mkdir sitePath.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sitePath.buildbin-libdir sitePath_1.8.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL sitePath_1.8.4.zip && rm sitePath_1.8.4.tar.gz sitePath_1.8.4.zip
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install for i386
* installing *source* package 'sitePath' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lumpyCluster.cpp -o lumpyCluster.o
lumpyCluster.cpp: In member function 'void LumpyCluster::Base::mergeClusters(const clusters&, int)':
lumpyCluster.cpp:96:24: warning: comparison of integer expressions of different signedness: 'std::vector<Treemer::TipSeqLinker*>::size_type' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
if (allTips.size() >= m_maxSNPnum) {
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c minEntropy.cpp -o minEntropy.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c searchNode.cpp -o searchNode.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c searchTree.cpp -o searchTree.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c treemer.cpp -o treemer.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o sitePath.dll tmp.def RcppExports.o lumpyCluster.o minEntropy.o searchNode.o searchTree.o treemer.o util.o -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/sitePath.buildbin-libdir/00LOCK-sitePath/00new/sitePath/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'sitePath'
finding HTML links ... done
SNPsites html
addMSA html
finding level-2 HTML links ... done
allSitesName html
as.data.frame html
extractSite html
extractTips html
fixationIndels html
fixationPath html
fixationSites html
groupTips html
h3n2_align html
h3n2_tree html
lineagePath html
paraFixSites html
parallelSites html
plotFunctions html
plotMutSites html
plotSingleSite html
reexports html
sars2_align html
sars2_tree html
setSiteNumbering html
similarityMatrix html
sitePath-deprecated html
sitesMinEntropy html
zikv_align html
zikv_tree 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 'sitePath' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lumpyCluster.cpp -o lumpyCluster.o
lumpyCluster.cpp: In member function 'void LumpyCluster::Base::mergeClusters(const clusters&, int)':
lumpyCluster.cpp:96:24: warning: comparison of integer expressions of different signedness: 'std::vector<Treemer::TipSeqLinker*>::size_type' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
if (allTips.size() >= m_maxSNPnum) {
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c minEntropy.cpp -o minEntropy.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c searchNode.cpp -o searchNode.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c searchTree.cpp -o searchTree.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c treemer.cpp -o treemer.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o sitePath.dll tmp.def RcppExports.o lumpyCluster.o minEntropy.o searchNode.o searchTree.o treemer.o util.o -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/sitePath.buildbin-libdir/sitePath/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sitePath' as sitePath_1.8.4.zip
* DONE (sitePath)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'sitePath' successfully unpacked and MD5 sums checked