h5vc 2.16.0
Paul Theodor Pyl
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/h5vc |
| Branch: RELEASE_3_8 |
| Last Commit: fd6bd12 |
| Last Changed Date: 2018-10-30 11:41:52 -0400 (Tue, 30 Oct 2018) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/h5vc_2.16.0.tar.gz && rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=h5vc.buildbin-libdir h5vc_2.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL h5vc_2.16.0.zip && rm h5vc_2.16.0.tar.gz h5vc_2.16.0.zip
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install for i386
* installing *source* package 'h5vc' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
int len = nttable->end - nttable->beg;
^
tallyBAM.cpp: In function 'int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
int len = nttable->end - nttable->beg;
^
tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
tallyBAM.cpp:141:6: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function]
static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o h5vc.dll tmp.def tallyBAM.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/h5vc.buildbin-libdir/h5vc/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'h5vc'
finding HTML links ... done
applyTallies html
batchTallies html
binGenome html
binnedAFs html
callVariants html
callVariantsFisher html
callVariantsSingle html
coverage html
geom_h5vc html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp6BVR53/R.INSTALL1dd8cfa1179/h5vc/man/geom_h5vc.Rd:25: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
getSampleData html
h5dapply html
h5readBlock html
h5vc-package html
helpers html
mergeTallies html
mergeTallyFiles html
mismatchPlot html
mutationSpectrum html
plotMutationSpectrum html
prepareForHDF5 html
prepareTallyFile html
tallyBAM html
tallyRanges html
finding level-2 HTML links ... done
writeReference html
writeToTallyFile html
** building package indices
** installing vignettes
'h5vc.simple.genome.browser.Rmd'
'h5vc.tour.Rmd'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'h5vc' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
int len = nttable->end - nttable->beg;
^
tallyBAM.cpp: In function 'int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
int len = nttable->end - nttable->beg;
^
tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
tallyBAM.cpp:141:6: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function]
static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o h5vc.dll tmp.def tallyBAM.o C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/h5vc.buildbin-libdir/h5vc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'h5vc' as h5vc_2.16.0.zip
* DONE (h5vc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'h5vc' successfully unpacked and MD5 sums checked
In R CMD INSTALL