BioC 2.12: CHECK report for maSigPro on george2

Package: maSigPro

Version: 1.32.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings maSigPro_1.32.3.tar.gz

StartedAt: 2013-10-09 03:02:48 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:05:28 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 160.0 seconds

RetCode: 0

Status:  OK

CheckDir: maSigPro.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/maSigPro.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maSigPro/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maSigPro’ version ‘1.32.3’
* 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 ‘maSigPro’ can be installed ... [7s/8s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... NOTE
see.genes: warning in mfuzz(signif, c = k, m = m): partial argument
  match of 'c' to 'centers'
* 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 examples ... [68s/72s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
T.fit        20.441  0.728  21.329
see.genes    12.568  0.932  16.567
maSigPro     11.972  0.316  12.348
get.siggenes  9.577  0.332   9.920
p.vector      5.585  0.164   5.864
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/maSigPro.Rcheck/00check.log’
for details.

* installing *source* package ‘maSigPro’ ...
** 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 (maSigPro)

name	user	system	elapsed
NBdata	0.048	0.000	0.058
NBdesign	0.012	0.004	0.017
PlotGroups	0.092	0.000	0.122
PlotProfiles	0.068	0.000	0.071
T.fit	20.441	0.728	21.329
average.rows	0.252	0.012	0.264
data.abiotic	0.012	0.004	0.018
edesign.OD	0.016	0.000	0.017
edesign.abiotic	0.016	0.000	0.016
edesignCT	0.016	0.000	0.015
edesignDR	0.012	0.000	0.013
get.siggenes	9.577	0.332	9.920
i.rank	0.020	0.000	0.022
maSigPro	11.972	0.316	12.348
maSigProUsersGuide	0.036	0.008	0.047
make.design.matrix	0.032	0.008	0.039
p.vector	5.585	0.164	5.864
position	0.016	0.004	0.019
reg.coeffs	0.012	0.000	0.012
see.genes	12.568	0.932	16.567
stepback	0.333	0.016	0.350
stepfor	0.320	0.004	0.329
suma2Venn	0.260	0.016	0.336
two.ways.stepback	0.280	0.008	0.287
two.ways.stepfor	0.320	0.008	0.324