Moritz Gerstung
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/deepSNV |
| Branch: RELEASE_3_6 |
| Last Commit: cfa5955 |
| Last Changed Date: 2017-10-30 12:39:38 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:21:32 -0400 (Thu, 12 Apr 2018).
| Package 343/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| deepSNV 1.24.0 Moritz Gerstung
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: deepSNV |
| Version: 1.24.0 |
| Command: rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/deepSNV_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=deepSNV.buildbin-libdir --merge-multiarch deepSNV_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.24.0.zip && rm deepSNV_1.24.0.tar.gz deepSNV_1.24.0.zip |
| StartedAt: 2018-04-11 18:53:09 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:54:32 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 83.5 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/deepSNV_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=deepSNV.buildbin-libdir --merge-multiarch deepSNV_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.24.0.zip && rm deepSNV_1.24.0.tar.gz deepSNV_1.24.0.zip
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install for i386
* installing *source* package 'deepSNV' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:76:13: warning: unused variable 'iter' [-Wunused-variable]
hts_itr_t *iter = NULL;
^
bam2R.cpp:79:6: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
int i, log=0;
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'deepSNV'
finding HTML links ... done
Extract-methods html
RCC html
RF html
bam2R html
betabinLRT html
bf2Vcf html
finding level-2 HTML links ... done
consensusSequence-methods html
control-methods html
coordinates-methods html
counts html
dbetabinom html
deepSNV-class html
deepSNV-methods html
deepSNV-package html
estimateDirichlet-methods html
estimateDispersion-methods html
estimateRho html
loadAllData html
makePrior html
manhattanPlot html
mcChunk html
normalize-methods html
p.combine html
p.val-methods html
pbetabinom html
phiX html
pi html
plot.deepSNV html
qvals2Vcf html
repeatMask-methods html
shearwater html
show-deepSNV-method html
summary-methods html
test-methods html
trueSNVs html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'deepSNV' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:76:13: warning: unused variable 'iter' [-Wunused-variable]
hts_itr_t *iter = NULL;
^
bam2R.cpp:79:6: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
int i, log=0;
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deepSNV' as deepSNV_1.24.0.zip
* DONE (deepSNV)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'deepSNV' successfully unpacked and MD5 sums checked
In R CMD INSTALL