seqPattern 1.1.1
Vanja Haberle
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqPattern | | Last Changed Rev: 103573 / Revision: 107602 | | Last Changed Date: 2015-05-08 08:29:06 -0700 (Fri, 08 May 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf seqPattern.buildbin-libdir seqPattern.Rcheck && mkdir seqPattern.buildbin-libdir seqPattern.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=seqPattern.buildbin-libdir seqPattern_1.1.1.tar.gz >seqPattern.Rcheck\00install.out 2>&1 && cp seqPattern.Rcheck\00install.out seqPattern-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=seqPattern.buildbin-libdir --install="check:seqPattern-install.out" --force-multiarch --no-vignettes --timings seqPattern_1.1.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/seqPattern.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'seqPattern/DESCRIPTION' ... OK
* this is package 'seqPattern' version '1.1.1'
* 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 'seqPattern' can be installed ... 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'parallel' in package code.
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
.pattern.smoothscatter: no visible global function definition for
'mclapply'
getPatternOccurrenceList,DNAStringSet: no visible global function
definition for 'detectCores'
getPatternOccurrenceList,DNAStringSet: no visible global function
definition for 'mclapply'
plotPatternDensityMap,DNAStringSet: no visible global function
definition for 'detectCores'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [57s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotPatternDensityMap 16.28 3.18 19.63
plotMotifDensityMap 8.88 1.39 10.29
plotMotifScanScores 4.15 1.21 5.36
** running examples for arch 'x64' ... [71s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotPatternDensityMap 17.55 3.94 21.49
plotMotifDensityMap 10.57 1.73 15.51
plotMotifScanScores 5.59 1.30 6.88
motifScanHits 5.06 0.05 5.10
plotMotifOccurrenceAverage 4.91 0.00 6.52
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [8s]
[8s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [7s]
[8s] 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: 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/seqPattern.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'seqPattern' ...
** R
** data
** 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 'seqPattern' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqPattern' as seqPattern_1.1.1.zip
* DONE (seqPattern)