Benjamin Story
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/mitoClone2 |
| git_branch: master |
| git_last_commit: f37ba3a |
| git_last_commit_date: 2021-10-26 13:11:28 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:03 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? 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 1182/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mitoClone2 1.1.0 (landing page) Benjamin Story
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: mitoClone2 |
| Version: 1.1.0 |
| Command: rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=mitoClone2.buildbin-libdir mitoClone2_1.1.0.tar.gz |
| StartedAt: 2022-03-17 21:22:02 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 21:23:20 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 78.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: mitoClone2_1.1.0.zip |
| PackageFileSize: 3.483 MiB |
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### Running command:
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### rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=mitoClone2.buildbin-libdir mitoClone2_1.1.0.tar.gz
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* installing *source* package 'mitoClone2' ...
** using staged installation
** 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 "D:/biocbuild/bbs-3.15-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "D:/biocbuild/bbs-3.15-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 D:/biocbuild/bbs-3.15-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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/libs/x64
** 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
* MD5 sums
packaged installation of 'mitoClone2' as mitoClone2_1.1.0.zip
* DONE (mitoClone2)