BioC 2.12: CHECK report for maSigPro on petty

Package: maSigPro

Version: 1.32.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maSigPro_1.32.3.tar.gz

StartedAt: 2013-10-08 22:59:35 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:02:17 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 162.0 seconds

RetCode: 0

Status:  OK

CheckDir: maSigPro.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/maSigPro.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [8s/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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [61s/64s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
T.fit        20.451  1.265  22.398
maSigPro     13.778  0.869  15.185
get.siggenes  9.389  0.595  10.726
p.vector      5.985  0.376   6.590
* 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
  '/Users/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	0.039	0.006	0.045
NBdesign	0.009	0.001	0.010
PlotGroups	0.167	0.005	0.181
PlotProfiles	0.053	0.004	0.057
T.fit	20.451	1.265	22.398
average.rows	0.031	0.002	0.033
data.abiotic	0.016	0.001	0.017
edesign.OD	0.016	0.001	0.018
edesign.abiotic	0.018	0.002	0.020
edesignCT	0.015	0.001	0.016
edesignDR	0.015	0.001	0.017
get.siggenes	9.389	0.595	10.726
i.rank	0.008	0.000	0.008
maSigPro	13.778	0.869	15.185
maSigProUsersGuide	0.014	0.006	0.027
make.design.matrix	0.025	0.011	0.136
p.vector	5.985	0.376	6.590
position	0.008	0.001	0.010
reg.coeffs	0.009	0.001	0.010
see.genes	2.381	0.224	2.903
stepback	0.111	0.007	0.118
stepfor	0.374	0.019	0.398
suma2Venn	0.023	0.002	0.044
two.ways.stepback	0.298	0.016	0.315
two.ways.stepfor	0.388	0.023	0.425