BioC 2.14: CHECK report for VariantAnnotation on petty
This page was generated on 2014-10-08 08:59:41 -0700 (Wed, 08 Oct 2014).
VariantAnnotation 1.10.5
Valerie Obenchain
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/VariantAnnotation | | Last Changed Rev: 91895 / Revision: 95116 | | Last Changed Date: 2014-06-26 05:58:14 -0700 (Thu, 26 Jun 2014) |
| zin2 | Linux (Ubuntu 12.04.4 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 |
Summary
| Package: VariantAnnotation |
| Version: 1.10.5 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch VariantAnnotation_1.10.5.tar.gz |
| StartedAt: 2014-10-08 00:33:34 -0700 (Wed, 08 Oct 2014) |
| EndedAt: 2014-10-08 00:48:11 -0700 (Wed, 08 Oct 2014) |
| EllapsedTime: 877.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: VariantAnnotation.Rcheck |
| Warnings: 0 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch VariantAnnotation_1.10.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/VariantAnnotation.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.10.5’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘VariantAnnotation’ can be installed ... [51s/53s] 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
':::' 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’
‘GenomicFeatures:::.makeUCSCTxListFromGRangesList’
‘GenomicRanges:::.cbind.DataFrame’
‘GenomicRanges:::.cbind.SummarizedExperiment’
‘GenomicRanges:::.rbind.SummarizedExperiment’
‘GenomicRanges:::.SummarizedExperiment.charbound’
‘GenomicRanges:::clone’ ‘IRanges:::.expandByColumnSet’
‘IRanges:::recycleVector’
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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 ... [173s/208s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
locateVariants-methods 41.412 2.645 44.211
predictCoding-methods 19.135 1.390 20.553
getTranscriptSeqs-methods 15.971 0.618 16.625
summarizeVariants-methods 14.732 1.067 15.810
SIFTDb-class 10.356 0.476 13.821
refLocsToLocalLocs-methods 5.981 0.435 6.418
readVcf-methods 6.072 0.048 6.125
genotypeToSnpMatrix-methods 5.549 0.314 5.876
PolyPhenDb-class 3.243 0.495 34.465
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘VariantAnnotation_unit_tests.R’ [232s/232s]
[232s/232s] 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
NOTE: There was 1 note.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.
VariantAnnotation.Rcheck/00install.out:
* installing *source* package ‘VariantAnnotation’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c dna_hash.c -o dna_hash.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c rle.c -o rle.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c strhash.c -o strhash.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c utilities.c -o utilities.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c vcffile.c -o vcffile.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c vcftype.c -o vcftype.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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 /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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:
| name | user | system | elapsed
|
| GLtoGP | 1.524 | 0.268 | 1.795 |
|
| PROVEANDb-class | 0.002 | 0.001 | 0.002 |
|
| PolyPhenDb-class | 3.243 | 0.495 | 34.465 |
|
| SIFTDb-class | 10.356 | 0.476 | 13.821 |
|
| ScanVcfParam-class | 2.313 | 0.087 | 2.411 |
|
| VCF-class | 4.775 | 0.060 | 4.839 |
|
| VCFHeader-class | 0.159 | 0.002 | 0.162 |
|
| VRanges-class | 0.820 | 0.003 | 0.826 |
|
| VRangesList-class | 0.933 | 0.008 | 0.943 |
|
| VariantType-class | 0.026 | 0.001 | 0.028 |
|
| filterVcf-methods | 3.765 | 0.095 | 3.866 |
|
| genotypeToSnpMatrix-methods | 5.549 | 0.314 | 5.876 |
|
| getTranscriptSeqs-methods | 15.971 | 0.618 | 16.625 |
|
| isSNV-methods | 2.259 | 0.034 | 2.294 |
|
| locateVariants-methods | 41.412 | 2.645 | 44.211 |
|
| predictCoding-methods | 19.135 | 1.390 | 20.553 |
|
| probabilityToSnpMatrix | 0.218 | 0.004 | 0.221 |
|
| readVcf-methods | 6.072 | 0.048 | 6.125 |
|
| refLocsToLocalLocs-methods | 5.981 | 0.435 | 6.418 |
|
| scanVcf-methods | 0.411 | 0.019 | 0.430 |
|
| snpSummary | 0.463 | 0.017 | 0.480 |
|
| summarizeVariants-methods | 14.732 | 1.067 | 15.810 |
|
| writeVcf-methods | 3.969 | 0.036 | 4.004 |
|