Multiple platform build/check report for BioC 3.9 - CHECK report for VariantAnnotation on tokay2

Package: VariantAnnotation

Version: 1.30.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantAnnotation.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings VariantAnnotation_1.30.1.tar.gz

StartedAt: 2019-10-16 07:47:49 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 08:13:43 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 1554.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: VariantAnnotation.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantAnnotation.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings VariantAnnotation_1.30.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/VariantAnnotation.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.30.1'
* 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-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:241: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:317: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:416: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:417: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:418: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCFHeader-class.Rd:114: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:81: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:113: file link 'FilterMatrix' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:171: file link 'FilterMatrix' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:174: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:191: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VcfFile-class.Rd:138: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/defunct.Rd:85: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:85: file link 'snpStats' in package 'snpStats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:89: file link 'snpStats' in package 'snpStats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:14: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:15: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:25: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:45: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:41: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:41: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:48: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:50: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:83: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:26: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:41: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:43: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:46: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:49: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:82: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:103: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/summarizeVariants-methods.Rd:34: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/summarizeVariants-methods.Rd:36: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-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'
  'rtracklayer:::checkArgFormat'
  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
VRangesForMatching: no visible binding for global variable 'REF'
VRangesForMatching: no visible binding for global variable 'ALT'
probabilityToSnpMatrix: no visible global function definition for
  'post2g'
Undefined global functions or variables:
  ALT REF post2g
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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-3.9-bioc/R/library/VariantAnnotation/libs/i386/VariantAnnotation.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/VariantAnnotation/libs/x64/VariantAnnotation.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'VariantAnnotation/libs/i386/VariantAnnotation.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'VariantAnnotation/libs/x64/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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
locateVariants-methods 24.56   0.58   25.14
predictCoding-methods  19.15   0.42   19.57
PROVEANDb-class         3.45   0.98  804.27
PolyPhenDb-class        1.19   0.41   19.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
locateVariants-methods 21.38   0.59   21.97
predictCoding-methods  16.76   0.46   17.21
* 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/VariantAnnotation.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/VariantAnnotation_1.30.1.tar.gz && rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.30.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL VariantAnnotation_1.30.1.zip && rm VariantAnnotation_1.30.1.tar.gz VariantAnnotation_1.30.1.zip
###
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100 1308k  100 1308k    0     0  8279k      0 --:--:-- --:--:-- --:--:-- 8662k

install for i386

* installing *source* package 'VariantAnnotation' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/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/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c dna_hash.c -o dna_hash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rle.c -o rle.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c strhash.c -o strhash.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vcffile.c -o vcffile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vcftype.c -o vcftype.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c writevcf.c -o writevcf.o
C:/Rtools/mingw_32/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 -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -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/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  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:241: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:317: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:416: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:417: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCF-class.Rd:418: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    VCFHeader-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VCFHeader-class.Rd:114: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
    VRanges-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:81: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:113: file link 'FilterMatrix' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:171: file link 'FilterMatrix' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:174: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VRanges-class.Rd:191: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    VRangesList-class                       html  
    VariantType-class                       html  
    VcfFile-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/VcfFile-class.Rd:138: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
    defunct                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/defunct.Rd:85: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    filterVcf-methods                       html  
    genotypeToSnpMatrix-methods             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:85: file link 'snpStats' in package 'snpStats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/genotypeToSnpMatrix-methods.Rd:89: file link 'snpStats' in package 'snpStats' does not exist and so has been treated as a topic
    getTranscriptSeqs-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:14: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:15: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:25: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:28: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:39: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/getTranscriptSeqs-methods.Rd:45: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    indexVcf-method                         html  
    isSNV-methods                           html  
    locateVariants-methods                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:41: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:41: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:48: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:50: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/locateVariants-methods.Rd:83: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
    predictCoding-methods                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:26: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:41: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:43: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:46: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:49: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:82: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/predictCoding-methods.Rd:103: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    probabilityToSnpMatrix                  html  
    readVcf-methods                         html  
    scanVcf-methods                         html  
    seqinfo-method                          html  
    snpSummary                              html  
    summarizeVariants-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/summarizeVariants-methods.Rd:34: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIr7GML/R.INSTALL236c288e6d97/VariantAnnotation/man/summarizeVariants-methods.Rd:36: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/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/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dna_hash.c -o dna_hash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rle.c -o rle.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c strhash.c -o strhash.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vcffile.c -o vcffile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vcftype.c -o vcftype.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c writevcf.c -o writevcf.o
C:/Rtools/mingw_64/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 -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -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/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.30.1.zip
* DONE (VariantAnnotation)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'VariantAnnotation' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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

Attaching package: 'IRanges'

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

    windows

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

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

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
starting prefilter
prefiltering 10376 records
prefiltered to C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpwDN356\file28106e4c627e
compressing and indexing 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpwDN356\file28106e4c627e'
starting filter
filtering 10376 records
completed filtering
compressing and indexing 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpwDN356\file2810ea31044'
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

[W::bcf_hdr_check_sanity] GL should be declared as Number=G
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 -- Wed Oct 16 08:12:07 2019 
*********************************************** 
Number of test functions: 99 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
VariantAnnotation RUnit Tests - 99 test functions, 0 errors, 0 failures
Number of test functions: 99 
Number of errors: 0 
Number of failures: 0 
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
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
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 7 out-of-bound ranges located on sequence
  70477. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
5: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 6 out-of-bound ranges located on sequence
  70477. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
> 
> proc.time()
   user  system elapsed 
  87.28    3.50  173.75


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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

Attaching package: 'IRanges'

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

    windows

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

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

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
starting prefilter
prefiltering 10376 records
prefiltered to C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEn5Wol\file2ea887f3178
compressing and indexing 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEn5Wol\file2ea887f3178'
starting filter
filtering 10376 records
completed filtering
compressing and indexing 'C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpEn5Wol\file2ea82e5f6da8'
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

[W::bcf_hdr_check_sanity] GL should be declared as Number=G
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 -- Wed Oct 16 08:13:33 2019 
*********************************************** 
Number of test functions: 99 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
VariantAnnotation RUnit Tests - 99 test functions, 0 errors, 0 failures
Number of test functions: 99 
Number of errors: 0 
Number of failures: 0 
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
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
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 7 out-of-bound ranges located on sequence
  70477. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
5: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 6 out-of-bound ranges located on sequence
  70477. Note that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
> 
> proc.time()
   user  system elapsed 
  83.35    1.76   85.14

name	user	system	elapsed
GLtoGP	1.52	0.47	2.30
PROVEANDb-class	3.45	0.98	804.27
PolyPhenDb-class	1.19	0.41	19.01
SIFTDb-class	0	0	0
ScanVcfParam-class	1.03	0.07	1.14
VCF-class	1.25	0.39	1.65
VCFHeader-class	0.06	0.00	0.06
VRanges-class	0.40	0.02	0.41
VRangesList-class	0.31	0.00	0.31
VariantType-class	0	0	0
VcfFile-class	0.28	0.00	0.31
filterVcf-methods	2.19	0.05	2.24
genotypeToSnpMatrix-methods	0.89	0.18	1.08
getTranscriptSeqs-methods	0	0	0
indexVcf-method	0.01	0.00	0.01
isSNV-methods	0.57	0.02	0.58
locateVariants-methods	24.56	0.58	25.14
predictCoding-methods	19.15	0.42	19.57
probabilityToSnpMatrix	0.04	0.00	0.04
readVcf-methods	2.04	0.00	2.04
scanVcf-methods	0.16	0.00	0.16
seqinfo-method	0.05	0.00	0.05
snpSummary	0.17	0.00	0.17
summarizeVariants-methods	4.90	0.07	4.97
writeVcf-methods	1.00	0.01	1.01

name	user	system	elapsed
GLtoGP	0.99	0.14	1.12
PROVEANDb-class	3.64	0.13	3.76
PolyPhenDb-class	0.47	0.03	0.50
SIFTDb-class	0	0	0
ScanVcfParam-class	0.72	0.00	0.72
VCF-class	1.03	0.06	1.10
VCFHeader-class	0.06	0.00	0.06
VRanges-class	0.28	0.00	0.28
VRangesList-class	0.38	0.00	0.37
VariantType-class	0	0	0
VcfFile-class	0.36	0.00	0.36
filterVcf-methods	1.39	0.14	1.53
genotypeToSnpMatrix-methods	0.97	0.06	1.04
getTranscriptSeqs-methods	0.01	0.00	0.01
indexVcf-method	0	0	0
isSNV-methods	0.75	0.02	0.77
locateVariants-methods	21.38	0.59	21.97
predictCoding-methods	16.76	0.46	17.21
probabilityToSnpMatrix	0.04	0.00	0.04
readVcf-methods	3.11	0.04	3.15
scanVcf-methods	0.17	0.00	0.17
seqinfo-method	0.05	0.00	0.05
snpSummary	0.2	0.0	0.2
summarizeVariants-methods	4.25	0.10	4.34
writeVcf-methods	1.25	0.00	1.25

CHECK report for VariantAnnotation on tokay2

Summary

Command output

Installation output

Tests output

Example timings