Benjamin Story
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/mitoClone2 |
| git_branch: RELEASE_3_14 |
| git_last_commit: 2b6203f |
| git_last_commit_date: 2021-10-26 13:11:28 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:55 -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 | ||||
|
To the developers/maintainers of the mitoClone2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mitoClone2.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 1177/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mitoClone2 1.0.0 (landing page) Benjamin Story
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: mitoClone2 |
| Version: 1.0.0 |
| Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/mitoClone2_1.0.0.tar.gz && rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mitoClone2.buildbin-libdir mitoClone2_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL mitoClone2_1.0.0.zip && rm mitoClone2_1.0.0.tar.gz mitoClone2_1.0.0.zip |
| StartedAt: 2022-04-12 06:40:27 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 06:44:01 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 214.1 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/mitoClone2_1.0.0.tar.gz && rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mitoClone2.buildbin-libdir mitoClone2_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL mitoClone2_1.0.0.zip && rm mitoClone2_1.0.0.tar.gz mitoClone2_1.0.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 930k 100 930k 0 0 1185k 0 --:--:-- --:--:-- --:--:-- 1187k
install for i386
* installing *source* package 'mitoClone2' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
../inst/SCITEpkg/findBestTrees.cpp:56:8: warning: built-in function 'gamma' declared as non-function [-Wbuiltin-declaration-mismatch]
double gamma = 1;
^~~~~
../inst/SCITEpkg/mcmcBinTreeMove.cpp: In function 'int pickNodeToMove(int*, int)':
../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam2R_10x.cpp -o bam2R_10x.o
bam2R_10x.cpp:6:2: warning: "/*" within comment [-Wcomment]
/**************************************************************************************
bam2R_10x.cpp:8:1: warning: "/*" within comment [-Wcomment]
/**********************************************************************
bam2R_10x.cpp: In function 'void bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable]
int bc_absent;
^~~~~~~~~
bam2R_10x.cpp: In function 'SEXPREC* bam2R_10x(SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable]
hts_itr_t *iter = NULL;
^~~~
bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mitoClone2.dll tmp.def bam2R_10x.o C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mitoClone2'
finding HTML links ... done
bam2R_10x html
baseCountsFromBamList html
clusterMetaclones html
data html
getAlleleCount html
getCloneLikelihood html
getVarsCandidate html
mitoPlot html
mut2GR html
mutationCalls-class html
mutationCallsFromCohort html
mutationCallsFromExclusionlist html
mutationCallsFromMatrix html
overwriteMetaclones html
plotClones html
pullcountsVars html
quick_cluster html
removeWindow html
setVarsCandidate html
varCluster html
*** copying figures
** 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 'mitoClone2' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
../inst/SCITEpkg/findBestTrees.cpp:56:8: warning: built-in function 'gamma' declared as non-function [-Wbuiltin-declaration-mismatch]
double gamma = 1;
^~~~~
../inst/SCITEpkg/mcmcBinTreeMove.cpp: In function 'int pickNodeToMove(int*, int)':
../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/mitoClone2/SCITE/"
cp scite "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/mitoClone2/SCITE/"
rm scite
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam2R_10x.cpp -o bam2R_10x.o
bam2R_10x.cpp:6:2: warning: "/*" within comment [-Wcomment]
/**************************************************************************************
bam2R_10x.cpp:8:1: warning: "/*" within comment [-Wcomment]
/**********************************************************************
bam2R_10x.cpp: In function 'void bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable]
int bc_absent;
^~~~~~~~~
bam2R_10x.cpp: In function 'SEXPREC* bam2R_10x(SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable]
hts_itr_t *iter = NULL;
^~~~
bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mitoClone2.dll tmp.def bam2R_10x.o C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/mitoClone2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mitoClone2' as mitoClone2_1.0.0.zip
* DONE (mitoClone2)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'mitoClone2' successfully unpacked and MD5 sums checked