BioC 3.2: CHECK report for qusage on perceval

Package: qusage

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qusage_2.2.0.tar.gz

StartedAt: 2015-10-27 11:21:29 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:23:10 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 101.1 seconds

RetCode: 0

Status:  OK

CheckDir: qusage.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qusage_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/qusage.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qusage/DESCRIPTION’ ... OK
* this is package ‘qusage’ version ‘2.2.0’
* 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 ‘qusage’ can be installed ... [4s/5s] OK
* checking installed package size ... NOTE
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
    doc    1.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: GeneSets.Rd:20: Dropping empty section \format
* 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 ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
      user system elapsed
qgen 21.36  0.744  22.106
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/qusage.Rcheck/00check.log’
for details.

* installing *source* package ‘qusage’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘head’ from package ‘utils’ in package ‘qusage’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘qusage’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qusage)

name	user	system	elapsed
aggregateGeneSet	0.417	0.016	0.433
calcVIF	0.365	0.006	0.371
combinePDFs	4.123	0.106	4.231
getXcoords	0.352	0.012	0.365
makeComparison	0.009	0.000	0.009
pVal	1.051	0.007	1.057
plotCIs	1.512	0.018	1.530
plotCIsGenes	0.270	0.003	0.273
plotCombinedPDF	4.671	0.036	4.708
plotDensityCurves	0.411	0.014	0.429
plotGeneSetDistributions	2.646	0.042	2.698
qgen	21.360	0.744	22.106
qsTable	1.116	0.060	1.177
qusage	1.015	0.018	1.033