rnaSeqMap 2.40.1
Michal Okoniewski
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/rnaSeqMap |
| Branch: RELEASE_3_8 |
| Last Commit: c122d64 |
| Last Changed Date: 2019-01-04 13:47:21 -0400 (Fri, 04 Jan 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | 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/rnaSeqMap_2.40.1.tar.gz && rm -rf rnaSeqMap.buildbin-libdir && mkdir rnaSeqMap.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rnaSeqMap.buildbin-libdir rnaSeqMap_2.40.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL rnaSeqMap_2.40.1.zip && rm rnaSeqMap_2.40.1.tar.gz rnaSeqMap_2.40.1.zip
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install for i386
* installing *source* package 'rnaSeqMap' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Rinit.c -o Rinit.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c gcoverage.c -o gcoverage.o
gcoverage.c: In function 'gcoverage':
gcoverage.c:7:31: warning: variable 'nc' set but not used [-Wunused-but-set-variable]
int start, i, j, na, nb, nc, nwyn;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ghistogram.c -o ghistogram.o
ghistogram.c: In function 'ghistogram':
ghistogram.c:9:10: warning: variable 'xa' set but not used [-Wunused-but-set-variable]
int *xa, *xb, *xab;
^
ghistogram.c:8:20: warning: variable 'nb' set but not used [-Wunused-but-set-variable]
int i, j, l , na, nb, nab, Is;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c regionmining.c -o regionmining.o
regionmining.c: In function 'regionmining':
regionmining.c:22:18: warning: variable 'start' set but not used [-Wunused-but-set-variable]
int current, start, param, minsup,*xwyn;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c splicingind.c -o splicingind.o
splicingind.c: In function 'splicingind':
splicingind.c:8:13: warning: variable 'nb' set but not used [-Wunused-but-set-variable]
int j, na, nb, nab;
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o rnaSeqMap.dll tmp.def Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -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/rnaSeqMap.buildbin-libdir/rnaSeqMap/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rnaSeqMap'
finding HTML links ... done
NDplots html
NucleotideDistr-class html
RleList2matrix html
SeqReds html
addBamData html
addDataToReadset html
addExperimentsToReadset html
averageND html
bam2sig html
buildDESeq html
buildDGEList html
findRegionsAsIR html
findRegionsAsND html
fiveCol2GRanges html
gRanges2CamelMeasures html
geneInChromosome html
generators html
getBamData html
getCoverageFromRS html
getData html
getExpDescription html
getFCFromND html
getSIFromND html
getSumsExp html
measures html
normalizations html
normalizeBySum html
parseGff3 html
plotGeneCoverage html
readsInRange html
regionBasedCoverage html
regionCoverage html
rs.list html
setData html
setSAXPYData html
setSpecies html
simplePlot html
spaceInChromosome html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'rnaSeqMap' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rinit.c -o Rinit.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c gcoverage.c -o gcoverage.o
gcoverage.c: In function 'gcoverage':
gcoverage.c:7:31: warning: variable 'nc' set but not used [-Wunused-but-set-variable]
int start, i, j, na, nb, nc, nwyn;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ghistogram.c -o ghistogram.o
ghistogram.c: In function 'ghistogram':
ghistogram.c:9:10: warning: variable 'xa' set but not used [-Wunused-but-set-variable]
int *xa, *xb, *xab;
^
ghistogram.c:8:20: warning: variable 'nb' set but not used [-Wunused-but-set-variable]
int i, j, l , na, nb, nab, Is;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c regionmining.c -o regionmining.o
regionmining.c: In function 'regionmining':
regionmining.c:22:18: warning: variable 'start' set but not used [-Wunused-but-set-variable]
int current, start, param, minsup,*xwyn;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c splicingind.c -o splicingind.o
splicingind.c: In function 'splicingind':
splicingind.c:8:13: warning: variable 'nb' set but not used [-Wunused-but-set-variable]
int j, na, nb, nab;
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o rnaSeqMap.dll tmp.def Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -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/rnaSeqMap.buildbin-libdir/rnaSeqMap/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rnaSeqMap' as rnaSeqMap_2.40.1.zip
* DONE (rnaSeqMap)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'rnaSeqMap' successfully unpacked and MD5 sums checked
In R CMD INSTALL