VariantAnnotation 1.14.13
Valerie Obenchain
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/VariantAnnotation | | Last Changed Rev: 107909 / Revision: 109384 | | Last Changed Date: 2015-08-28 13:56:52 -0700 (Fri, 28 Aug 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VariantAnnotation_1.14.13.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/VariantAnnotation.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantAnnotation’ version ‘1.14.13’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘VariantAnnotation’ can be installed ... [24s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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.
':::' call which should be '::': ‘DBI:::dbListFields’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘BiocGenerics:::labeledLine’ ‘BiocGenerics:::selectSome’
‘BiocGenerics:::testPackage’
‘GenomicRanges:::.SummarizedExperiment.charbound’
‘GenomicRanges:::.bind.arrays’ ‘GenomicRanges:::.cbind.DataFrame’
‘GenomicRanges:::clone’ ‘IRanges:::.expandByColumnSet’
‘Rsamtools:::.RsamtoolsFile’ ‘Rsamtools:::.RsamtoolsFileList’
‘Rsamtools:::.io_check_exists’ ‘S4Vectors:::recycleVector’
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
.predictCoding: no visible global function definition for
‘transcriptsBy’
.predictCodingGRangesList: no visible binding for global variable
‘GENETIC_CODE’
.spliceSites: no visible global function definition for ‘togroup’
VCFHeader: no visible global function definition for ‘DataFrameList’
VRangesForMatching: no visible binding for global variable ‘REF’
VRangesForMatching: no visible binding for global variable ‘ALT’
addTotalDepthRuns: no visible global function definition for ‘viewMins’
genotypeCodesToNucleotides: no visible global function definition for
‘togroup’
parseFilterStrings: no visible global function definition for ‘togroup’
probabilityToSnpMatrix: no visible global function definition for
‘post2g’
softFilter: no visible global function definition for ‘evalSeparately’
vranges2Vcf: no visible global function definition for ‘DataFrameList’
vranges2Vcf : genoArray: no visible global function definition for
‘togroup’
asVCF,VRanges : .local: no visible global function definition for
‘DataFrameList’
asVCF,VRanges : .local : genoArray: no visible global function
definition for ‘togroup’
liftOver,VRanges-Chain: no visible global function definition for
‘togroup’
locateVariants,GRanges-TxDb-IntergenicVariants : .local: no visible
global function definition for ‘transcriptsBy’
locateVariants,GRanges-TxDb-IntronVariants : .local: no visible global
function definition for ‘intronsByTranscript’
locateVariants,GRanges-TxDb-SpliceSiteVariants : .local: no visible
global function definition for ‘intronsByTranscript’
summarizeVariants,TxDb-VCF-IntronVariants: no visible global function
definition for ‘intronsByTranscript’
summarizeVariants,TxDb-VCF-SpliceSiteVariants: no visible global
function definition for ‘intronsByTranscript’
* 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
File ‘VariantAnnotation/libs/VariantAnnotation.so’:
Found non-API call to R: ‘getConnection’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [70s/107s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
locateVariants-methods 19.347 2.234 21.619
predictCoding-methods 16.700 2.112 18.847
SIFTDb-class 3.365 0.481 6.581
PolyPhenDb-class 1.208 0.340 32.986
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘VariantAnnotation_unit_tests.R’ [125s/125s]
[125s/125s] 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.
* installing *source* package ‘VariantAnnotation’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c XVector_stubs.c -o XVector_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c dna_hash.c -o dna_hash.o
dna_hash.c:10:1: warning: unused function 'kh_clear_ref' [-Wunused-function]
KHASH_MAP_INIT_STR(ref, int)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:213:1: note: expanded from here
kh_clear_ref
^
dna_hash.c:10:1: warning: unused function 'kh_del_ref' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:13:1: note: expanded from here
kh_del_ref
^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c rle.c -o rle.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c strhash.c -o strhash.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c utilities.c -o utilities.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c vcffile.c -o vcffile.o
vcffile.c:20:1: warning: unused function 'kh_clear_WARNINGS' [-Wunused-function]
KHASH_SET_INIT_STR(WARNINGS)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:89:1: note: expanded from here
kh_clear_WARNINGS
^
vcffile.c:20:1: warning: unused function 'kh_del_WARNINGS' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include/samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:103:1: note: expanded from here
kh_del_WARNINGS
^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c vcftype.c -o vcftype.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c writevcf.c -o writevcf.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o VariantAnnotation.so 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 /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-3.1-bioc/meat/VariantAnnotation.Rcheck/VariantAnnotation/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (VariantAnnotation)