PWMEnrich 4.9.2
Robert Stojnic
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PWMEnrich | | Last Changed Rev: 117512 / Revision: 121152 | | Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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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### rm -rf PWMEnrich.buildbin-libdir PWMEnrich.Rcheck && mkdir PWMEnrich.buildbin-libdir PWMEnrich.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PWMEnrich.buildbin-libdir PWMEnrich_4.9.2.tar.gz >PWMEnrich.Rcheck\00install.out 2>&1 && cp PWMEnrich.Rcheck\00install.out PWMEnrich-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=PWMEnrich.buildbin-libdir --install="check:PWMEnrich-install.out" --force-multiarch --no-vignettes --timings PWMEnrich_4.9.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/PWMEnrich.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PWMEnrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PWMEnrich' version '4.9.2'
* 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 whether package 'PWMEnrich' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
doc 1.5Mb
extdata 3.4Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
'library' or 'require' calls in package code:
'PWMEnrich.Dmelanogaster.background' 'PWMEnrich.Hsapiens.background'
'PWMEnrich.Mmusculus.background' 'parallel'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colMedians: no visible binding for global variable 'median'
colSds: no visible binding for global variable 'sd'
getPromoters: no visible global function definition for
'providerVersion'
getPromoters: no visible global function definition for 'data'
gevPerSequence: no visible global function definition for 'predict.lm'
logNormPval: no visible global function definition for 'plnorm'
makePWMGEVBackground : <anonymous>: no visible global function
definition for 'lm'
makePWMLognBackground : dlnorm.lcen: no visible global function
definition for 'dlnorm'
makePWMLognBackground : dlnorm.lcen: no visible global function
definition for 'plnorm'
makePWMLognBackground: no visible binding for global variable 'sd'
makePWMLognBackground: no visible global function definition for
'quantile'
makePWMLognBackground: no visible global function definition for
'median'
makePWMLognBackground: no visible global function definition for
'optimize'
makePWMPvalCutoffBackground: no visible global function definition for
'quantile'
makePWMPvalCutoffBackground: no visible global function definition for
'ecdf'
makePWMPvalCutoffBackgroundFromSeq: no visible global function
definition for 'na.omit'
makePWMPvalCutoffBackgroundFromSeq: no visible global function
definition for 'quantile'
makePWMPvalCutoffBackgroundFromSeq: no visible global function
definition for 'ecdf'
matrixShuffleZscorePerSequence: no visible binding for global variable
'sd'
motifEcdf : <anonymous>: no visible global function definition for
'na.omit'
motifEcdf: no visible binding for global variable 'ecdf'
motifEnrichment: no visible binding for global variable 'qlnorm'
motifEnrichment : <anonymous>: no visible global function definition
for 'pchisq'
motifScores: no visible global function definition for 'mclapply'
motifScoresBigMemory: no visible global function definition for
'mclapply'
motifSimilarity: no visible binding for global variable 'sd'
plotMotifScores: no visible global function definition for 'palette'
plotMotifScores: no visible global function definition for 'col2rgb'
plotMotifScores: no visible global function definition for 'rgb'
plotMotifScores: no visible global function definition for 'par'
plotMotifScores: no visible global function definition for 'lines'
plotMotifScores: no visible global function definition for 'polygon'
plotMotifScores: no visible global function definition for 'rect'
plotMotifScores: no visible global function definition for 'text'
registerCoresPWMEnrich: no visible global function definition for
'detectCores'
tryAllMotifAlignments : <anonymous>: no visible global function
definition for 'cor'
Undefined global functions or variables:
col2rgb cor data detectCores dlnorm ecdf lines lm mclapply median
na.omit optimize palette par pchisq plnorm polygon predict.lm
providerVersion qlnorm quantile rect rgb sd text
Consider adding
importFrom("grDevices", "col2rgb", "palette", "rgb")
importFrom("graphics", "lines", "par", "polygon", "rect", "text")
importFrom("stats", "cor", "dlnorm", "ecdf", "lm", "median", "na.omit",
"optimize", "pchisq", "plnorm", "predict.lm", "qlnorm",
"quantile", "sd")
importFrom("utils", "data")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
motifScores 5.38 0.02 5.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
OK
** running tests for arch 'x64' ...
Running 'test-all.R'
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: 3 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/PWMEnrich.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'PWMEnrich' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'PWMEnrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PWMEnrich' as PWMEnrich_4.9.2.zip
* DONE (PWMEnrich)