BioC 3.1: CHECK report for maSigPro on petty

Package: maSigPro

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maSigPro_1.40.0.tar.gz

StartedAt: 2015-10-09 00:02:50 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:05:04 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 134.0 seconds

RetCode: 0

Status:  OK

CheckDir: maSigPro.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maSigPro_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/maSigPro.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.40.0’
* 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 ‘maSigPro’ can be installed ... [6s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘stats’ ‘MASS’
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
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [41s/44s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
T.fit        13.278  0.992  14.184
maSigPro      9.418  0.696  11.433
get.siggenes  6.485  0.479   6.911
* 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-3.1-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	0.105	0.005	0.135
NBdesign	0.002	0.001	0.004
PlotGroups	0.042	0.004	0.050
PlotProfiles	0.020	0.003	0.048
T.fit	13.278	0.992	14.184
average.rows	0.009	0.000	0.010
data.abiotic	0.009	0.001	0.009
edesign.OD	0.003	0.001	0.012
edesign.abiotic	0.006	0.002	0.057
edesignCT	0.002	0.001	0.003
edesignDR	0.003	0.001	0.004
get.siggenes	6.485	0.479	6.911
i.rank	0.001	0.001	0.002
maSigPro	9.418	0.696	11.433
maSigProUsersGuide	0.005	0.003	0.017
make.design.matrix	0.018	0.011	0.035
p.vector	4.230	0.317	4.508
position	0.001	0.000	0.002
reg.coeffs	0.001	0.000	0.002
see.genes	1.354	0.184	2.145
stepback	0.060	0.004	0.064
stepfor	0.227	0.016	0.245
suma2Venn	0.009	0.003	0.252
two.ways.stepback	0.166	0.013	0.198
two.ways.stepfor	0.260	0.016	0.276