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 |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings h5vc_2.0.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/h5vc.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [19s/20s] 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 ... [80s/84s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
callVariantsFisher 17.517 0.004 17.644
tallyRanges 7.956 3.112 7.731
writeToTallyFile 6.941 0.848 7.627
mismatchPlot 6.341 0.020 6.409
applyTallies 5.052 0.448 10.894
binnedAFs 5.209 0.076 5.496
* 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
‘/home/biocbuild/bbs-3.0-bioc/meat/h5vc.Rcheck/00check.log’
for details.
* installing *source* package ‘h5vc’ ...
** libs
Found /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usretc//Rsamtools.mk.
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -I/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -fpic -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:47:7: warning: unused variable ‘len’ [-Wunused-variable]
tallyBAM.cpp: In function ‘int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:96:7: warning: unused variable ‘len’ [-Wunused-variable]
tallyBAM.cpp: In function ‘int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)’:
tallyBAM.cpp:141:6: warning: unused variable ‘c’ [-Wunused-variable]
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: ‘int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)’ defined but not used [-Wunused-function]
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o h5vc.so tallyBAM.o /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
Found /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usretc//Rsamtools.mk.
installing to /home/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)