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BUILD BIN report for bsseq on tokay2

This page was generated on 2019-04-09 12:00:52 -0400 (Tue, 09 Apr 2019).

Package 188/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.19.3
Kasper Daniel Hansen
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/bsseq
Branch: master
Last Commit: d9114c7
Last Changed Date: 2019-01-31 17:38:18 -0400 (Thu, 31 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR [ OK ]
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: bsseq
Version: 1.19.3
Command: 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_1.19.3.tar.gz
StartedAt: 2019-04-09 07:32:53 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 07:36:28 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 215.2 seconds
RetCode: 0
Status:  OK  
PackageFile: bsseq_1.19.3.zip
PackageFileSize: 8.499 MiB

Command output

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###
### Running command:
###
###   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_1.19.3.tar.gz
###
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install for i386

* installing *source* package 'bsseq' ...
** 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/Rhdf5lib/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/Rhdf5lib/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/Rhdf5lib/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
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/RtmpUXP1Mf/R.INSTALL1f083c80770a/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/Rhdf5lib/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/Rhdf5lib/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/Rhdf5lib/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
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
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_1.19.3.zip
* DONE (bsseq)