Multiple platform build/check report for BioC 3.6 - CHECK report for VariantAnnotation on tokay1

Package: VariantAnnotation

Version: 1.24.5

Command: rm -rf VariantAnnotation.buildbin-libdir VariantAnnotation.Rcheck && mkdir VariantAnnotation.buildbin-libdir VariantAnnotation.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.24.5.tar.gz >VariantAnnotation.Rcheck\00install.out 2>&1 && cp VariantAnnotation.Rcheck\00install.out VariantAnnotation-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=VariantAnnotation.buildbin-libdir --install="check:VariantAnnotation-install.out" --force-multiarch --no-vignettes --timings VariantAnnotation_1.24.5.tar.gz

StartedAt: 2018-04-12 03:46:28 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 04:12:02 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 1533.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: VariantAnnotation.Rcheck

Warnings: 2

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###
### Running command:
###
###   rm -rf VariantAnnotation.buildbin-libdir VariantAnnotation.Rcheck && mkdir VariantAnnotation.buildbin-libdir VariantAnnotation.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.24.5.tar.gz >VariantAnnotation.Rcheck\00install.out 2>&1 && cp VariantAnnotation.Rcheck\00install.out VariantAnnotation-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=VariantAnnotation.buildbin-libdir --install="check:VariantAnnotation-install.out" --force-multiarch --no-vignettes --timings VariantAnnotation_1.24.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/VariantAnnotation.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'VariantAnnotation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VariantAnnotation' version '1.24.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'VariantAnnotation' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VCF-class.Rd:307: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VCF-class.Rd:404: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VCF-class.Rd:405: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VCF-class.Rd:406: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:81: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:113: missing file link 'FilterMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:171: missing file link 'FilterMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:174: missing file link 'FilterRules'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:191: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/defunct.Rd:89: missing file link 'mapToTranscripts'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:85: missing file link 'snpStats'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:89: missing file link 'snpStats'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:14: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:15: missing file link 'FaFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:25: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: missing file link 'FaFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: missing file link 'FaFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:45: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:41: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:41: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:48: missing file link 'TxDb'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:50: missing file link 'TxDb'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:83: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:26: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:41: missing file link 'TxDb'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:43: missing file link 'TxDb'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:46: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:49: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:82: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:103: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/summarizeVariants-methods.Rd:34: missing file link 'TxDb'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/summarizeVariants-methods.Rd:36: missing file link 'TxDb'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/VariantAnnotation.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'snpStats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'BiocGenerics:::testPackage'
  'Rsamtools:::.RsamtoolsFile' 'Rsamtools:::.RsamtoolsFileList'
  'Rsamtools:::.io_check_exists' 'S4Vectors:::expandByColumnSet'
  'S4Vectors:::labeledLine' 'S4Vectors:::recycleVector'
  'S4Vectors:::selectSome'
  'SummarizedExperiment:::.SummarizedExperiment.charbound'
  'SummarizedExperiment:::.cbind.DataFrame'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.predictCodingGRangesList: no visible binding for global variable
  'GENETIC_CODE'
VRangesForMatching: no visible binding for global variable 'REF'
VRangesForMatching: no visible binding for global variable 'ALT'
probabilityToSnpMatrix: no visible global function definition for
  'post2g'
import,VcfFile-ANY-ANY: no visible global function definition for
  'checkArgFormat'
Undefined global functions or variables:
  ALT GENETIC_CODE REF checkArgFormat post2g
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'mcols<-' and siglist 'VCF'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386/VariantAnnotation.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
File 'VariantAnnotation/libs/i386/VariantAnnotation.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
locateVariants-methods    19.95   0.58   20.53
predictCoding-methods     16.47   0.39   16.86
summarizeVariants-methods  5.64   0.07    5.72
PROVEANDb-class            4.16   0.72  639.59
PolyPhenDb-class           0.53   0.15   25.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
locateVariants-methods    19.73   0.83   20.56
predictCoding-methods     15.02   0.73   15.75
summarizeVariants-methods  5.42   0.12    5.54
PROVEANDb-class            4.89   0.28    5.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'VariantAnnotation_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'VariantAnnotation_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/VariantAnnotation.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'VariantAnnotation' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c dna_hash.c -o dna_hash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rle.c -o rle.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c strhash.c -o strhash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vcffile.c -o vcffile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vcftype.c -o vcftype.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c writevcf.c -o writevcf.o
C:/Rtools/mingw_32/bin/g++ -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-3.6-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386
** R
** inst
** preparing 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  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VCF-class.Rd:307: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VCF-class.Rd:404: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VCF-class.Rd:405: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VCF-class.Rd:406: missing file link 'RangedSummarizedExperiment'
    VCFHeader-class                         html  
    VRanges-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:81: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:113: missing file link 'FilterMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:171: missing file link 'FilterMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:174: missing file link 'FilterRules'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/VRanges-class.Rd:191: missing file link 'GenomicRanges'
    VRangesList-class                       html  
    VariantType-class                       html  
    VcfFile-class                           html  
    defunct                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/defunct.Rd:89: missing file link 'mapToTranscripts'
    filterVcf-methods                       html  
    genotypeToSnpMatrix-methods             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:85: missing file link 'snpStats'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:89: missing file link 'snpStats'
    getTranscriptSeqs-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:14: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:15: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:25: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:45: missing file link 'DNAStringSet'
    indexVcf-method                         html  
    isSNV-methods                           html  
    locateVariants-methods                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:41: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:41: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:48: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:50: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/locateVariants-methods.Rd:83: missing file link 'Hits'
    predictCoding-methods                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:26: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:41: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:43: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:46: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:49: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:82: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/predictCoding-methods.Rd:103: missing file link 'GRanges'
    probabilityToSnpMatrix                  html  
    readVcf-methods                         html  
    scanVcf-methods                         html  
    seqinfo-method                          html  
    snpSummary                              html  
    summarizeVariants-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/summarizeVariants-methods.Rd:34: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcR2cMp/R.INSTALL21b426c64fc6/VariantAnnotation/man/summarizeVariants-methods.Rd:36: missing file link 'TxDb'
    writeVcf-methods                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'VariantAnnotation' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dna_hash.c -o dna_hash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rle.c -o rle.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c strhash.c -o strhash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vcffile.c -o vcffile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vcftype.c -o vcftype.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c writevcf.c -o writevcf.o
C:/Rtools/mingw_64/bin/g++ -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-3.6-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.24.5.zip
* DONE (VariantAnnotation)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("VariantAnnotation") || stop("unable to load VariantAnnotation package")
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

[1] TRUE
> VariantAnnotation:::.test()
Loading required package: RSQLite
Loading required package: survival
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:VariantAnnotation':

    expand

The following object is masked from 'package:S4Vectors':

    expand

non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
'select()' returned 1:1 mapping between keys and columns
Loading required package: BSgenome
Loading required package: rtracklayer
'select()' returned many:1 mapping between keys and columns


RUNIT TEST PROTOCOL -- Thu Apr 12 04:09:51 2018 
*********************************************** 
Number of test functions: 92 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
VariantAnnotation RUnit Tests - 92 test functions, 0 errors, 0 failures
Number of test functions: 92 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: info fields with no header: noMatch 
2: In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames
3: In DataFrame(..., check.names = FALSE) : NAs introduced by coercion
> 
> proc.time()
   user  system elapsed 
 106.84    1.82  173.14


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("VariantAnnotation") || stop("unable to load VariantAnnotation package")
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

[1] TRUE
> VariantAnnotation:::.test()
Loading required package: RSQLite
Loading required package: survival
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:VariantAnnotation':

    expand

The following object is masked from 'package:S4Vectors':

    expand

non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
'select()' returned 1:1 mapping between keys and columns
Loading required package: BSgenome
Loading required package: rtracklayer
'select()' returned many:1 mapping between keys and columns


RUNIT TEST PROTOCOL -- Thu Apr 12 04:11:56 2018 
*********************************************** 
Number of test functions: 92 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
VariantAnnotation RUnit Tests - 92 test functions, 0 errors, 0 failures
Number of test functions: 92 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: info fields with no header: noMatch 
2: In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames
3: In DataFrame(..., check.names = FALSE) : NAs introduced by coercion
> 
> proc.time()
   user  system elapsed 
 122.06    1.96  124.01

name	user	system	elapsed
GLtoGP	2.20	0.11	2.31
PROVEANDb-class	4.16	0.72	639.59
PolyPhenDb-class	0.53	0.15	25.97
SIFTDb-class	0	0	0
ScanVcfParam-class	0.82	0.13	0.94
VCF-class	1.09	0.02	1.11
VCFHeader-class	0.05	0.00	0.04
VRanges-class	0.33	0.01	0.35
VRangesList-class	0.48	0.02	0.50
VariantType-class	0.02	0.00	0.01
VcfFile-class	0.20	0.00	0.21
filterVcf-methods	2.16	0.12	2.28
genotypeToSnpMatrix-methods	0.68	0.10	0.78
getTranscriptSeqs-methods	0	0	0
indexVcf-method	0.02	0.00	0.01
isSNV-methods	0.65	0.01	0.68
locateVariants-methods	19.95	0.58	20.53
predictCoding-methods	16.47	0.39	16.86
probabilityToSnpMatrix	0.03	0.00	0.03
readVcf-methods	1.53	0.02	1.55
scanVcf-methods	0.13	0.00	0.12
seqinfo-method	0.03	0.00	0.04
snpSummary	0.13	0.00	0.12
summarizeVariants-methods	5.64	0.07	5.72
writeVcf-methods	0.83	0.00	0.82

name	user	system	elapsed
GLtoGP	2.40	0.08	2.49
PROVEANDb-class	4.89	0.28	5.18
PolyPhenDb-class	0.69	0.04	0.73
SIFTDb-class	0	0	0
ScanVcfParam-class	1.00	0.02	1.02
VCF-class	1.92	0.03	1.95
VCFHeader-class	0.01	0.02	0.03
VRanges-class	0.43	0.00	0.42
VRangesList-class	0.48	0.01	0.50
VariantType-class	0	0	0
VcfFile-class	0.27	0.02	0.28
filterVcf-methods	1.73	0.09	1.83
genotypeToSnpMatrix-methods	0.88	0.06	0.95
getTranscriptSeqs-methods	0	0	0
indexVcf-method	0.00	0.02	0.02
isSNV-methods	0.87	0.00	0.88
locateVariants-methods	19.73	0.83	20.56
predictCoding-methods	15.02	0.73	15.75
probabilityToSnpMatrix	0.02	0.02	0.03
readVcf-methods	1.89	0.01	1.91
scanVcf-methods	0.14	0.00	0.14
seqinfo-method	0.04	0.00	0.04
snpSummary	0.19	0.02	0.21
summarizeVariants-methods	5.42	0.12	5.54
writeVcf-methods	0.98	0.02	1.00

CHECK report for VariantAnnotation on tokay1

Summary

Command output

Installation output

Tests output

Example timings