Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2022-04-13 12:07:32 -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

INSTALL results for VariantAnnotation on tokay2


To the developers/maintainers of the VariantAnnotation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantAnnotation.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 2038/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.40.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/VariantAnnotation
git_branch: RELEASE_3_14
git_last_commit: 50ead7c
git_last_commit_date: 2021-10-26 11:59:51 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    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: VariantAnnotation
Version: 1.40.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/VariantAnnotation_1.40.0.tar.gz && rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL VariantAnnotation_1.40.0.zip && rm VariantAnnotation_1.40.0.tar.gz VariantAnnotation_1.40.0.zip
StartedAt: 2022-04-12 06:12:16 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:16:42 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 266.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/VariantAnnotation_1.40.0.tar.gz && rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL VariantAnnotation_1.40.0.zip && rm VariantAnnotation_1.40.0.tar.gz VariantAnnotation_1.40.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 11 1308k   11  147k    0     0   485k      0  0:00:02 --:--:--  0:00:02  486k
100 1308k  100 1308k    0     0  1035k      0  0:00:01  0:00:01 --:--:-- 1036k

install for i386

* installing *source* package 'VariantAnnotation' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c dna_hash.c -o dna_hash.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rle.c -o rle.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c strhash.c -o strhash.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utilities.c -o utilities.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c vcffile.c -o vcffile.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c vcftype.c -o vcftype.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c writevcf.c -o writevcf.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -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/VariantAnnotation.buildbin-libdir/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'tabulate' in package 'VariantAnnotation'
** help
*** installing help indices
  converting help for package 'VariantAnnotation'
    finding HTML links ... done
    GLtoGP                                  html  
    PROVEANDb-class                         html  
    PolyPhenDb-class                        html  
    PolyPhenDbColumns                       html  
    SIFTDb-class                            html  
    SIFTDbColumns                           html  
    ScanVcfParam-class                      html  
    finding level-2 HTML links ... done

    VCF-class                               html  
    VCFHeader-class                         html  
    VRanges-class                           html  
    VRangesList-class                       html  
    VariantType-class                       html  
    VcfFile-class                           html  
    defunct                                 html  
    filterVcf-methods                       html  
    genotypeToSnpMatrix-methods             html  
    getTranscriptSeqs-methods               html  
    indexVcf-method                         html  
    isSNV-methods                           html  
    locateVariants-methods                  html  
    predictCoding-methods                   html  
    probabilityToSnpMatrix                  html  
    readVcf-methods                         html  
    scanVcf-methods                         html  
    seqinfo-method                          html  
    snpSummary                              html  
    summarizeVariants-methods               html  
    writeVcf-methods                        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 'VariantAnnotation' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c dna_hash.c -o dna_hash.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rle.c -o rle.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c strhash.c -o strhash.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utilities.c -o utilities.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c vcffile.c -o vcffile.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c vcftype.c -o vcftype.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c writevcf.c -o writevcf.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -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/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.40.0.zip
* DONE (VariantAnnotation)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'VariantAnnotation' successfully unpacked and MD5 sums checked