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BioC 3.4: CHECK report for VariantAnnotation on morelia

This page was generated on 2017-04-15 16:23:45 -0400 (Sat, 15 Apr 2017).

Package 1271/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.20.3
Valerie Obenchain
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/VariantAnnotation
Last Changed Rev: 127452 / Revision: 128728
Last Changed Date: 2017-03-15 22:03:50 -0400 (Wed, 15 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantAnnotation
Version: 1.20.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VariantAnnotation_1.20.3.tar.gz
StartedAt: 2017-04-15 09:10:16 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 09:19:34 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 558.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: VariantAnnotation.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VariantAnnotation_1.20.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/VariantAnnotation.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.20.3’
* 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 ... OK
* 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
* 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 '[' and siglist 'VCF,ANY,ANY,ANY'
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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
locateVariants-methods    25.791  1.311  27.910
predictCoding-methods     25.510  1.266  26.795
PROVEANDb-class            7.700  1.702  24.776
summarizeVariants-methods  8.163  0.236   8.407
PolyPhenDb-class           1.130  0.341  36.406
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.

VariantAnnotation.Rcheck/00install.out:

* 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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.3/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/3.3/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.3/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-3.4-bioc/meat/VariantAnnotation.Rcheck/VariantAnnotation/libs
** R
** inst
** preparing package for lazy loading
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
* DONE (VariantAnnotation)

VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings:

nameusersystemelapsed
GLtoGP1.5900.2031.792
PROVEANDb-class 7.700 1.70224.776
PolyPhenDb-class 1.130 0.34136.406
SIFTDb-class0.0030.0010.003
ScanVcfParam-class1.0250.0331.060
VCF-class1.4180.0361.455
VCFHeader-class0.0650.0010.066
VRanges-class0.4270.0030.429
VRangesList-class0.4180.0030.423
VariantType-class0.0110.0000.013
VcfFile-class0.3740.0190.393
filterVcf-methods3.130.133.98
genotypeToSnpMatrix-methods0.7980.0952.736
getTranscriptSeqs-methods0.0010.0000.000
isSNV-methods0.6670.0380.705
locateVariants-methods25.791 1.31127.910
predictCoding-methods25.510 1.26626.795
probabilityToSnpMatrix0.0450.0010.046
readVcf-methods3.1270.0663.199
scanVcf-methods0.1530.0040.158
snpSummary0.2370.0020.239
summarizeVariants-methods8.1630.2368.407
writeVcf-methods1.2490.0291.277