BioC 3.0: CHECK report for h5vc on perceval
This page was generated on 2015-04-10 09:59:00 -0700 (Fri, 10 Apr 2015).
h5vc 2.0.6
Paul Theodor Pyl
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/h5vc | | Last Changed Rev: 98471 / Revision: 102249 | | Last Changed Date: 2015-01-19 10:34:46 -0800 (Mon, 19 Jan 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |
Summary
| Package: h5vc |
| Version: 2.0.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch h5vc_2.0.6.tar.gz |
| StartedAt: 2015-04-10 02:35:49 -0700 (Fri, 10 Apr 2015) |
| EndedAt: 2015-04-10 02:42:02 -0700 (Fri, 10 Apr 2015) |
| EllapsedTime: 373.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: h5vc.Rcheck |
| Warnings: 1 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch h5vc_2.0.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/h5vc.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘h5vc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘h5vc’ version ‘2.0.6’
* 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 ‘h5vc’ can be installed ... [29s/32s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.h5dapplyIRanges: no visible binding for global variable ‘Sample’
callVariantsPairedFisher : <anonymous> : <anonymous>: no visible
binding for global variable ‘pValue’
callVariantsPairedFisher : <anonymous> : <anonymous>: no visible
binding for global variable ‘BlockID’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘Support’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘AF’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘SupFwd’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘SupRev’
callVariantsSingle : <anonymous> : <anonymous>: no visible binding for
global variable ‘BlockID’
h5readBlock: no visible binding for global variable ‘Sample’
mergeTallyFiles : <anonymous>: no visible binding for global variable
‘group’
mergeTallyFiles: no visible binding for global variable ‘SourceFile’
plotMutationSpectrum: no visible binding for global variable
‘altAllele’
plotMutationSpectrum: no visible binding for global variable ‘tmp’
rerunBatchTallies: no visible binding for global variable ‘regID’
resizeCohort: no visible binding for global variable ‘newSamples’
tallyRangesBatch : <anonymous>: no visible binding for global variable
‘bamFiles’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'callVariants':
vcConfParams
Code: function(minStrandCov = 5, maxStrandCov = 200,
minStrandAltSupport = 2, maxStrandAltSupportControl =
0, minStrandDelSupport = minStrandAltSupport,
maxStrandDelSupportControl =
maxStrandAltSupportControl, minStrandInsSupport =
minStrandAltSupport, maxStrandInsSupportControl =
maxStrandAltSupportControl, minStrandCovControl = 5,
maxStrandCovControl = 200, bases = 5:8,
returnDataPoints = TRUE, annotateWithBackground =
TRUE, mergeCalls = TRUE, mergeAggregator = mean,
pValueAggregator = max)
Docs: function(minStrandCov = 5, maxStrandCov = 200,
minStrandAltSupport = 2, maxStrandAltSupportControl =
0, minStrandDelSupport = minStrandAltSupport,
maxStrandDelSupportControl =
maxStrandAltSupportControl, minStrandCovControl = 5,
maxStrandCovControl = 200, bases = 5:8,
returnDataPoints = TRUE, annotateWithBackground =
TRUE, mergeCalls = TRUE, mergeAggregator = mean,
pValueAggregator = max)
Argument names in code not in docs:
minStrandInsSupport maxStrandInsSupportControl
Mismatches in argument names (first 3):
Position: 7 Code: minStrandInsSupport Docs: minStrandCovControl
Position: 8 Code: maxStrandInsSupportControl Docs: maxStrandCovControl
Position: 9 Code: minStrandCovControl Docs: bases
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [146s/134s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
tallyRanges 16.635 10.981 8.586
callVariantsFisher 20.663 0.233 20.928
writeToTallyFile 10.120 2.862 12.381
applyTallies 9.680 2.486 22.426
mergeTallies 8.125 2.850 10.997
prepareForHDF5 7.249 3.336 10.616
binnedAFs 9.077 0.481 9.934
mismatchPlot 7.255 0.363 7.674
* 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
WARNING: There was 1 warning.
NOTE: There was 1 note.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/h5vc.Rcheck/00check.log’
for details.
h5vc.Rcheck/00install.out:
* installing *source* package ‘h5vc’ ...
** libs
Found /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usretc//Rsamtools.mk.
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -I/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function ‘int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:47: warning: unused variable ‘len’
tallyBAM.cpp: In function ‘int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:96: warning: unused variable ‘len’
tallyBAM.cpp: In function ‘int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)’:
tallyBAM.cpp:141: warning: unused variable ‘c’
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43: warning: ‘int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o h5vc.so tallyBAM.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
Found /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usretc//Rsamtools.mk.
installing to /Users/biocbuild/bbs-3.0-bioc/meat/h5vc.Rcheck/h5vc/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (h5vc)
h5vc.Rcheck/h5vc-Ex.timings:
| name | user | system | elapsed
|
| applyTallies | 9.680 | 2.486 | 22.426 |
|
| batchTallies | 0.001 | 0.000 | 0.001 |
|
| binGenome | 0.865 | 0.078 | 0.946 |
|
| binnedAFs | 9.077 | 0.481 | 9.934 |
|
| callVariants | 0.956 | 0.223 | 1.432 |
|
| callVariantsFisher | 20.663 | 0.233 | 20.928 |
|
| callVariantsSingle | 1.770 | 0.263 | 2.037 |
|
| coverage | 3.617 | 0.335 | 4.062 |
|
| geom_h5vc | 0.817 | 0.064 | 0.882 |
|
| getSampleData | 0.102 | 0.003 | 0.134 |
|
| h5dapply | 1.459 | 0.072 | 1.531 |
|
| h5readBlock | 0.269 | 0.021 | 0.292 |
|
| helpers | 0.423 | 0.018 | 0.441 |
|
| mergeTallies | 8.125 | 2.850 | 10.997 |
|
| mergeTallyFiles | 0.001 | 0.000 | 0.001 |
|
| mismatchPlot | 7.255 | 0.363 | 7.674 |
|
| mutationSpectrum | 1.189 | 0.452 | 1.822 |
|
| plotMutationSpectrum | 2.484 | 0.932 | 3.439 |
|
| prepareForHDF5 | 7.249 | 3.336 | 10.616 |
|
| prepareTallyFile | 0.078 | 0.005 | 0.146 |
|
| tallyBAM | 0.152 | 0.012 | 0.165 |
|
| tallyRanges | 16.635 | 10.981 | 8.586 |
|
| writeReference | 0.590 | 0.066 | 0.728 |
|
| writeToTallyFile | 10.120 | 2.862 | 12.381 |
|