h5vc 1.4.0
Paul Theodor Pyl
| 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/h5vc | | Last Changed Rev: 91797 / Revision: 95116 | | Last Changed Date: 2014-06-24 07:41:53 -0700 (Tue, 24 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 |
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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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/h5vc.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.4.0’
* 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 ... [17s/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
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’
h5dapply: no visible binding for global variable ‘Sample’
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’
* 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 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 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 ... [45s/46s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
callVariantsFisher 18.426 0.182 18.623
* 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/h5vc.Rcheck/00check.log’
for details.
* installing *source* package ‘h5vc’ ...
** libs
Found /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usretc//Rsamtools.mk.
clang++ -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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp:46:7: warning: unused variable 'len' [-Wunused-variable]
int len = nttable->end - nttable->beg;
^
tallyBAM.cpp:56:18: warning: variable 'c' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
}else if(p->indel < 0){
^˜˜˜˜˜˜˜˜˜˜˜
tallyBAM.cpp:60:16: note: uninitialized use occurs here
str += c;
^
tallyBAM.cpp:56:15: note: remove the 'if' if its condition is always true
}else if(p->indel < 0){
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tallyBAM.cpp:53:15: note: initialize the variable 'c' to silence this warning
char c;
^
= '\0'
tallyBAM.cpp:81:6: warning: unused variable 'c' [-Wunused-variable]
int c = 0;
^
3 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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
clang: warning: argument unused during compilation: '-pthread'
Found /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usretc//Rsamtools.mk.
installing to /Users/biocbuild/bbs-2.14-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)