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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).

Package 416/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch h5vc_2.0.6.tar.gz
###
##############################################################################
##############################################################################


* 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:

nameusersystemelapsed
applyTallies 9.680 2.48622.426
batchTallies0.0010.0000.001
binGenome0.8650.0780.946
binnedAFs9.0770.4819.934
callVariants0.9560.2231.432
callVariantsFisher20.663 0.23320.928
callVariantsSingle1.7700.2632.037
coverage3.6170.3354.062
geom_h5vc0.8170.0640.882
getSampleData0.1020.0030.134
h5dapply1.4590.0721.531
h5readBlock0.2690.0210.292
helpers0.4230.0180.441
mergeTallies 8.125 2.85010.997
mergeTallyFiles0.0010.0000.001
mismatchPlot7.2550.3637.674
mutationSpectrum1.1890.4521.822
plotMutationSpectrum2.4840.9323.439
prepareForHDF5 7.249 3.33610.616
prepareTallyFile0.0780.0050.146
tallyBAM0.1520.0120.165
tallyRanges16.63510.981 8.586
writeReference0.5900.0660.728
writeToTallyFile10.120 2.86212.381