motifRG 1.14.0
Zizhen Yao
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/motifRG | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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 motifRG.buildbin-libdir motifRG.Rcheck && mkdir motifRG.buildbin-libdir motifRG.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=motifRG.buildbin-libdir motifRG_1.14.0.tar.gz >motifRG.Rcheck\00install.out 2>&1 && cp motifRG.Rcheck\00install.out motifRG-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=motifRG.buildbin-libdir --install="check:motifRG-install.out" --force-multiarch --no-vignettes --timings motifRG_1.14.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/motifRG.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'motifRG/DESCRIPTION' ... OK
* this is package 'motifRG' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biostrings' 'IRanges' 'seqLogo' 'parallel' 'grid' 'BSgenome'
'XVector' 'BSgenome.Hsapiens.UCSC.hg19'
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 whether package 'motifRG' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'Biostrings' 'IRanges' 'seqLogo' 'parallel' 'methods' 'grid' 'graphics' 'XVector'
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
* 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' which was already attached by Depends.
Please remove these calls from your code.
Namespaces in Imports field not imported from:
'graphics' 'methods'
All declared Imports should be used.
Packages in Depends field not imported from:
'BSgenome.Hsapiens.UCSC.hg19' 'methods'
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
bestPWMMatch: no visible global function definition for 'Rle'
matchPWMCoor: no visible global function definition for 'GRanges'
my.pvec: no visible global function definition for 'mc.reset.stream'
my.pvec : <anonymous>: no visible global function definition for
'mcparallel'
my.pvec: no visible global function definition for 'mccollect'
* checking Rd files ... NOTE
prepare_Rd: YY1.control.Rd:8-9: Dropping empty section \details
prepare_Rd: YY1.peak.Rd:8-9: Dropping empty section \details
* 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' ... [109s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
findMotif 89.15 0.14 89.64
refinePWMMotif 6.34 0.17 6.59
** running examples for arch 'x64' ... [105s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
findMotif 82.86 0.14 83.4
refinePWMMotif 5.96 0.13 6.9
* 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: 5 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/motifRG.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'motifRG' ...
** 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 'motifRG' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifRG' as motifRG_1.14.0.zip
* DONE (motifRG)