Repitools 1.17.0
Mark Robinson
| Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools | | Last Changed Rev: 109592 / Revision: 109826 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | 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 Repitools_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Repitools.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.17.0’
* 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 ‘Repitools’ can be installed ... [22s/26s] 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 loading without being on the library search path ... 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
clusterPlots,ClusteredScoresList : <anonymous>: warning in axis(2, at =
c(y.min, (y.min + y.max)/2, y.max), label = score.labels): partial
argument match of 'label' to 'labels'
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for ‘nbrOfArrays’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for ‘extract’
.blocksStats,AffymetrixCelSet-GRanges: no visible binding for global
variable ‘verbose’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for ‘getCdf’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
definition for ‘extractMatrix’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
definition for ‘getCdf’
.featureScores,AffymetrixCelSet-GRanges: no visible binding for global
variable ‘verbose’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
definition for ‘extractMatrix’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
‘Arguments’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘pushState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘popState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘nbrOfArrays’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getMainCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘nbrOfUnits’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘indexOf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘enter’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getCellIndices’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘exit’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
‘AromaCellSequenceFile’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getChipType’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘countBases’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘extract’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘getNames’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
‘extractMatrix’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
‘AromaCellCpgFile’
cpgBoxplots,matrix: no visible binding for global variable ‘Arguments’
cpgBoxplots,matrix: no visible global function definition for
‘pushState’
cpgBoxplots,matrix: no visible global function definition for
‘popState’
cpgBoxplots,matrix: no visible global function definition for ‘enter’
cpgBoxplots,matrix: no visible global function definition for ‘exit’
cpgDensityCalc,GRanges-BSgenome: no visible global function definition
for ‘DNAString’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
definition for ‘getCellIndices’
getProbePositionsDf,AffymetrixCdfFile: no visible binding for global
variable ‘AromaCellPositionFile’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
definition for ‘getChipType’
regionStats,AffymetrixCelSet: no visible global function definition for
‘getCdf’
regionStats,AffymetrixCelSet: no visible global function definition for
‘getCellIndices’
regionStats,AffymetrixCelSet: no visible global function definition for
‘nbrOfArrays’
regionStats,AffymetrixCelSet: no visible binding for global variable
‘AromaCellPositionFile’
regionStats,AffymetrixCelSet: no visible global function definition for
‘getChipType’
regionStats,AffymetrixCelSet: no visible global function definition for
‘extract’
regionStats,AffymetrixCelSet: no visible global function definition for
‘extractMatrix’
sequenceCalc,GRanges-BSgenome : <anonymous>: no visible global function
definition for ‘matchPattern’
writeWig,AffymetrixCelSet: no visible global function definition for
‘getNames’
writeWig,AffymetrixCelSet: no visible global function definition for
‘extract’
writeWig,AffymetrixCelSet: no visible global function definition for
‘getCdf’
writeWig,AffymetrixCelSet: no visible global function definition for
‘extractMatrix’
Undefined global functions or variables:
Arguments AromaCellCpgFile AromaCellPositionFile
AromaCellSequenceFile DNAString countBases enter exit extract
extractMatrix getCdf getCellIndices getChipType getMainCdf getNames
indexOf matchPattern nbrOfArrays nbrOfUnits popState pushState
verbose
* 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 GNU extensions in Makefiles ... OK
* 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 ... [167s/129s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
methylEst 53.279 6.311 41.579
empBayes 21.987 4.394 21.209
cpgDensityCalc 7.580 0.591 8.218
sequenceCalc 7.520 0.635 8.212
BayMethList-class 7.072 0.340 7.489
determineOffset 4.598 0.507 5.144
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tests.R’ [83s/88s]
[83s/88s] 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
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/Repitools.Rcheck/00check.log’
for details.
* installing *source* package ‘Repitools’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -D R_NO_REMAP -I. -fPIC -Wall -mtune=core2 -g -O2 -c const.c -o const.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -D R_NO_REMAP -I. -fPIC -Wall -mtune=core2 -g -O2 -c hyp2f1.c -o hyp2f1.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -D R_NO_REMAP -I. -fPIC -Wall -mtune=core2 -g -O2 -c mtherr.c -o mtherr.o
clang -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 -o Repitools.so const.o hyp2f1.o mtherr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/Repitools.Rcheck/Repitools/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 (Repitools)