qrqc 1.20.0
Vince Buffalo
| 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/qrqc | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| 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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qrqc_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/qrqc.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 ‘qrqc/DESCRIPTION’ ... OK
* this is package ‘qrqc’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’ ‘brew’ ‘xtable’
‘Rsamtools’ ‘testthat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘qrqc’ can be installed ... [45s/48s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘brew’ ‘Rsamtools’ ‘testthat’ ‘xtable’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generateReads: no visible global function definition for ‘DNAStringSet’
generateReads: no visible global function definition for
‘write.XStringSet’
basePlot,list: no visible binding for global variable ‘base’
basePlot,SequenceSummary: no visible binding for global variable ‘base’
gcPlot,list: no visible binding for global variable ‘position’
gcPlot,SequenceSummary: no visible binding for global variable
‘position’
getBase,SequenceSummary: no visible binding for global variable ‘base’
getBaseProp,SequenceSummary: no visible binding for global variable
‘base’
kmerEntropyPlot,list: no visible binding for global variable ‘position’
kmerEntropyPlot,list: no visible binding for global variable ‘entropy’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
‘position’
kmerEntropyPlot,SequenceSummary: no visible binding for global variable
‘entropy’
kmerKLPlot,list : <anonymous>: no visible binding for global variable
‘kmer’
kmerKLPlot,list: no visible binding for global variable ‘position’
kmerKLPlot,list: no visible binding for global variable ‘kl’
kmerKLPlot,list: no visible binding for global variable ‘kmer’
kmerKLPlot,SequenceSummary: no visible binding for global variable
‘kmer’
kmerKLPlot,SequenceSummary: no visible binding for global variable
‘position’
kmerKLPlot,SequenceSummary: no visible binding for global variable ‘kl’
qualPlot,FASTQSummary: no visible binding for global variable
‘position’
qualPlot,list: no visible binding for global variable ‘position’
* 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 GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* 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 ... [70s/71s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
kmerKLPlot 15.282 0.507 15.814
getMCQual-methods 6.241 0.144 6.398
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘test-functions.R’ [21s/21s]
[22s/22s] 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
* DONE
WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/qrqc.Rcheck/00check.log’
for details.
* installing *source* package ‘qrqc’ ...
** 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/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c R_init_io.c -o R_init_io.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/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c io.c -o io.o
io.c:34: warning: ‘kseq_destroy’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 qrqc.so R_init_io.o io.o -lz /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-3.0-bioc/meat/qrqc.Rcheck/qrqc/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qrqc)