Chengyang Ji
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/sitePath |
| Branch: RELEASE_3_11 |
| Last Commit: 6c69dfc |
| Last Changed Date: 2020-06-11 02:59:43 -0400 (Thu, 11 Jun 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:49 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE sitePath PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1677/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sitePath 1.4.2 Chengyang Ji
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: sitePath |
| Version: 1.4.2 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/sitePath_1.4.2.tar.gz && rm -rf sitePath.buildbin-libdir && mkdir sitePath.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sitePath.buildbin-libdir sitePath_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL sitePath_1.4.2.zip && rm sitePath_1.4.2.tar.gz sitePath_1.4.2.zip |
| StartedAt: 2020-10-16 17:08:53 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 17:10:54 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 120.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/sitePath_1.4.2.tar.gz && rm -rf sitePath.buildbin-libdir && mkdir sitePath.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sitePath.buildbin-libdir sitePath_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL sitePath_1.4.2.zip && rm sitePath_1.4.2.tar.gz sitePath_1.4.2.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exportFunc.cpp -o exportFunc.o
exportFunc.cpp: In function 'Rcpp::ListOf<Rcpp::Vector<13> > majorSNPtips(const CharacterVector&, int)':
exportFunc.cpp:110:48: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int siteIndex = 0; siteIndex < alignedSeqs[0].size(); ++siteIndex) {
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
exportFunc.cpp: In function 'Rcpp::ListOf<Rcpp::Vector<13> > mergePaths(const Rcpp::ListOf<Rcpp::Vector<13> >&)':
exportFunc.cpp:141:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int i = 1; i < paths.size(); ++i) {
~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fixationSite.cpp -o fixationSite.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c minEntropy.cpp -o minEntropy.o
minEntropy.cpp: In function 'Rcpp::ListOf<Rcpp::Vector<13> > MinEntropy::updatedSegmentation(const Rcpp::ListOf<Rcpp::Vector<13> >&, const segment&)':
minEntropy.cpp:50:40: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int j = 0; j < aa.size(); ++j) {
~~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c searchTree.cpp -o searchTree.o
searchTree.cpp: In instantiation of 'MinEntropy::SearchTree<T>::SearchTree(unsigned int, unsigned int, const Rcpp::ListOf<Rcpp::Vector<13> >&) [with T = MinEntropy::Segmentor]':
searchTree.cpp:206:28: required from here
searchTree.cpp:20:36: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
for (unsigned int j = 0; j < aa.size(); ++j) {
~~^~~~~~~~~~~
searchTree.cpp: In instantiation of 'MinEntropy::SearchTree<T>::SearchTree(unsigned int, unsigned int, const Rcpp::ListOf<Rcpp::Vector<13> >&) [with T = MinEntropy::Amalgamator]':
searchTree.cpp:207:28: required from here
searchTree.cpp:20:36: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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 -shared -s -static-libgcc -o sitePath.dll tmp.def RcppExports.o exportFunc.o fixationSite.o minEntropy.o searchNode.o searchTree.o treemer.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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
addMSA html
extractTips html
findSites html
h3n2_align html
h3n2_align_reduced html
h3n2_tree html
h3n2_tree_reduced html
plot.lineagePath html
plot.sitePath html
plotSingleSite html
pre-assessment html
setSiteNumbering html
treemer html
zikv_align html
zikv_align_reduced html
zikv_tree html
zikv_tree_reduced 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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exportFunc.cpp -o exportFunc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fixationSite.cpp -o fixationSite.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-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 -shared -s -static-libgcc -o sitePath.dll tmp.def RcppExports.o exportFunc.o fixationSite.o minEntropy.o searchNode.o searchTree.o treemer.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/sitePath.buildbin-libdir/sitePath/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sitePath' as sitePath_1.4.2.zip
* DONE (sitePath)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'sitePath' successfully unpacked and MD5 sums checked