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This page was generated on 2022-04-13 12:06:41 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for hapFabia on tokay2


To the developers/maintainers of the hapFabia package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hapFabia.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 851/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hapFabia 1.36.0  (landing page)
Andreas Mitterecker
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/hapFabia
git_branch: RELEASE_3_14
git_last_commit: b5514bc
git_last_commit_date: 2021-10-26 12:04:29 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hapFabia
Version: 1.36.0
Command: rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hapFabia.buildbin-libdir hapFabia_1.36.0.tar.gz
StartedAt: 2022-04-13 06:23:39 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 06:24:07 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 27.2 seconds
RetCode: 0
Status:   OK  
PackageFile: hapFabia_1.36.0.zip
PackageFileSize: 1.829 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hapFabia.buildbin-libdir hapFabia_1.36.0.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'hapFabia' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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  
REDIRECT:topic	 IBDsegment,numeric,numeric,character,numeric,numeric,numeric,numeric,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector,vector-method -> IBDsegment-class.html [ FAIL ]
    IBDsegmentList-class                    html  
    IBDsegmentList2excel                    html  
    analyzeIBDsegments                      html  
    chr1ASW1000G                            html  
    compareIBDsegmentLists                  html  
    extractIBDsegments                      html  
REDIRECT:topic	 extractIBDsegments,Factorization,list,data.frame,character,matrix,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric-method -> extractIBDsegments.html [ FAIL ]
    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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hapFabia' as hapFabia_1.36.0.zip
* DONE (hapFabia)