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INSTALL report for hapFabia on tokay2

This page was generated on 2020-10-17 11:56:48 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE hapFabia PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 800/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hapFabia 1.30.0
Andreas Mitterecker
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/hapFabia
Branch: RELEASE_3_11
Last Commit: 9c7681b
Last Changed Date: 2020-04-27 14:31:07 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hapFabia
Version: 1.30.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/hapFabia_1.30.0.tar.gz && rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hapFabia.buildbin-libdir hapFabia_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL hapFabia_1.30.0.zip && rm hapFabia_1.30.0.tar.gz hapFabia_1.30.0.zip
StartedAt: 2020-10-16 17:08:45 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 17:09:45 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 60.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/hapFabia_1.30.0.tar.gz && rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hapFabia.buildbin-libdir hapFabia_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL hapFabia_1.30.0.zip && rm hapFabia_1.30.0.tar.gz hapFabia_1.30.0.zip
###
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100  959k  100  959k    0     0  12.5M      0 --:--:-- --:--:-- --:--:-- 13.7M

install for i386

* installing *source* package 'hapFabia' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interfaceR.c -o interfaceR.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c split_sparse_matrixB.c -o split_sparse_matrixB.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftoFABIAB.c -o vcftoFABIAB.o
vcftoFABIAB.c: In function 'getdelimS':
vcftoFABIAB.c:50:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
       if (ch == EOF)
       ^~
vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
          while (idx > *linebufsz - 2) {
          ^~~~~
vcftoFABIAB.c: In function 'vcftoFABIAB':
vcftoFABIAB.c:394:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
     strncat(format[j],Iformat,19);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:382:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
     strncat(info[j],Iinfo,190);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:372:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
     strncat(filter[j],Ifilter,19);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:362:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
     strncat(qual[j],Iqual,19);
     ^~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:352:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
     strncat(minor[j],Iminor,190);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:342:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
     strncat(major[j],Imajor,190);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:332:5: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
     strncat(snpName[j],IsnpName,49);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/hapFabia.buildbin-libdir/00LOCK-hapFabia/00new/hapFabia/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'hapFabia'
    finding HTML links ... done
    IBDsegment-class                        html  
    IBDsegmentList-class                    html  
    IBDsegmentList2excel                    html  
    analyzeIBDsegments                      html  
    chr1ASW1000G                            html  
    compareIBDsegmentLists                  html  
    extractIBDsegments                      html  
    findDenseRegions                        html  
    hapFabia                                html  
    hapFabiaVersion                         html  
    hapRes                                  html  
    identifyDuplicates                      html  
    iterateIntervals                        html  
    makePipelineFile                        html  
    matrixPlot                              html  
    mergeIBDsegmentLists                    html  
    mergedIBDsegmentList                    html  
    plotIBDsegment                          html  
    res                                     html  
    setAnnotation                           html  
    setStatistics                           html  
    sim                                     html  
    simu                                    html  
    simulateIBDsegments                     html  
    simulateIBDsegmentsFabia                html  
    split_sparse_matrix                     html  
    toolsFactorizationClass                 html  
    vcftoFABIA                              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 'hapFabia' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interfaceR.c -o interfaceR.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c split_sparse_matrixB.c -o split_sparse_matrixB.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vcftoFABIAB.c -o vcftoFABIAB.o
vcftoFABIAB.c: In function 'getdelimS':
vcftoFABIAB.c:50:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
       if (ch == EOF)
       ^~
vcftoFABIAB.c:54:10: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
          while (idx > *linebufsz - 2) {
          ^~~~~
vcftoFABIAB.c: In function 'vcftoFABIAB':
vcftoFABIAB.c:394:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
     strncat(format[j],Iformat,19);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:382:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 19999 [-Wstringop-truncation]
     strncat(info[j],Iinfo,190);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:372:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
     strncat(filter[j],Ifilter,19);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:362:5: warning: 'strncat' output may be truncated copying 19 bytes from a string of length 1999 [-Wstringop-truncation]
     strncat(qual[j],Iqual,19);
     ^~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:352:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
     strncat(minor[j],Iminor,190);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:342:5: warning: 'strncat' output may be truncated copying 190 bytes from a string of length 1999999 [-Wstringop-truncation]
     strncat(major[j],Imajor,190);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
vcftoFABIAB.c:332:5: warning: 'strncat' output may be truncated copying 49 bytes from a string of length 4999 [-Wstringop-truncation]
     strncat(snpName[j],IsnpName,49);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hapFabia' as hapFabia_1.30.0.zip
* DONE (hapFabia)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'hapFabia' successfully unpacked and MD5 sums checked