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BioC 3.2: CHECK report for seqPattern on zin1

This page was generated on 2015-08-24 10:50:22 -0700 (Mon, 24 Aug 2015).

Package 932/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqPattern 1.1.1
Vanja Haberle
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqPattern
Last Changed Rev: 103573 / Revision: 107696
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 ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: seqPattern
Version: 1.1.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings seqPattern_1.1.1.tar.gz
StartedAt: 2015-08-24 03:41:58 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 03:43:58 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 119.4 seconds
RetCode: 0
Status:  OK 
CheckDir: seqPattern.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings seqPattern_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/seqPattern.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘seqPattern’ can be installed ... [7s/7s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plotPatternDensityMap 13.612  0.088  13.733
plotMotifDensityMap    7.186  0.032   7.232
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/5s]
 [5s/5s] 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/seqPattern.Rcheck/00check.log’
for details.


seqPattern.Rcheck/00install.out:

* 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
* DONE (seqPattern)

seqPattern.Rcheck/seqPattern-Ex.timings:

nameusersystemelapsed
getPatternOccurrenceList2.2240.0242.248
motifScanHits2.6730.0082.692
motifScanScores2.0610.0082.073
plotMotifDensityMap7.1860.0327.232
plotMotifOccurrenceAverage2.3920.0082.402
plotMotifScanScores3.1060.0153.136
plotPatternDensityMap13.612 0.08813.733
plotPatternOccurrenceAverage2.3510.0002.355