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INSTALL report for rnaSeqMap on tokay1

This page was generated on 2019-04-13 11:21:24 -0400 (Sat, 13 Apr 2019).

Package 1330/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rnaSeqMap
Version: 2.40.1
Command: 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
StartedAt: 2019-04-12 19:41:53 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 19:43:08 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 75.6 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   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