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INSTALL report for bsseq on tokay2

This page was generated on 2019-10-16 12:26:40 -0400 (Wed, 16 Oct 2019).

Package 191/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.20.0
Kasper Daniel Hansen
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/bsseq
Branch: RELEASE_3_9
Last Commit: 07e398b
Last Changed Date: 2019-05-02 11:53:37 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bsseq
Version: 1.20.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/bsseq_1.20.0.tar.gz && rm -rf bsseq.buildbin-libdir && mkdir bsseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bsseq.buildbin-libdir bsseq_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL bsseq_1.20.0.zip && rm bsseq_1.20.0.tar.gz bsseq_1.20.0.zip
StartedAt: 2019-10-15 20:26:24 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:29:36 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 192.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/bsseq_1.20.0.tar.gz && rm -rf bsseq.buildbin-libdir && mkdir bsseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bsseq.buildbin-libdir bsseq_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL bsseq_1.20.0.zip && rm bsseq_1.20.0.tar.gz bsseq_1.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2084k  100 2084k    0     0  20.3M      0 --:--:-- --:--:-- --:--:-- 21.8M

install for i386

* installing *source* package 'bsseq' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c check_M_and_Cov.cpp -o check_M_and_Cov.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o bsseq.dll tmp.def check_M_and_Cov.o init.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.buildbin-libdir/00LOCK-bsseq/00new/bsseq/libs/i386
** R
** data
*** moving datasets to lazyload DB
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'bsseq'
    finding HTML links ... done
    BS.chr22                                html  
    BSmooth                                 html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/BSmooth.Rd:38: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/BSmooth.Rd:40: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/BSmooth.Rd:43: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/BSmooth.Rd:44: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/BSmooth.Rd:67: file link 'getRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
    BSmooth.fstat                           html  
    BSmooth.tstat                           html  
    BSseq-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/BSseq-class.Rd:137: file link 'setRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
    BSseq                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/BSseq.Rd:34: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
    BSseqStat-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/BSseqStat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
    BSseqTstat-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/BSseqTstat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
    FWGRanges-class                         html  
    computeStat                             html  
    data.frame2GRanges                      html  
    dmrFinder                               html  
    findLoci                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/findLoci.Rd:44: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/findLoci.Rd:45: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/findLoci.Rd:55: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
    fisherTests                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/fisherTests.Rd:55: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
    getCoverage                             html  
    getMeth                                 html  
    getStats                                html  
    goodnessOfFit                           html  
    hasGRanges-class                        html  
    internals                               html  
    plotRegion                              html  
    read.bismark                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/read.bismark.Rd:36: file link 'rowRanges' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/read.bismark.Rd:73: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/read.bismark.Rd:75: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/read.bismark.Rd:78: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/read.bismark.Rd:79: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/read.bismark.Rd:91: file link 'tempdir' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2rLlIb/R.INSTALL17505d6c2973/bsseq/man/read.bismark.Rd:177: file link 'getRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
    read.bsmooth                            html  
    read.umtab                              html  
    smoothSds                               html  
** 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

install for x64

* installing *source* package 'bsseq' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c check_M_and_Cov.cpp -o check_M_and_Cov.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o bsseq.dll tmp.def check_M_and_Cov.o init.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.buildbin-libdir/bsseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bsseq' as bsseq_1.20.0.zip
* DONE (bsseq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'bsseq' successfully unpacked and MD5 sums checked