BioC 2.14: CHECK report for maSigPro on petty

Package: maSigPro

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maSigPro_1.36.0.tar.gz

StartedAt: 2014-10-07 22:46:43 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:49:34 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 170.8 seconds

RetCode: 0

Status:  OK

CheckDir: maSigPro.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maSigPro_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/maSigPro.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.36.0’
* 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 ... [9s/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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
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 ... [58s/63s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
T.fit        19.427  1.166  21.547
maSigPro     12.922  0.905  15.285
get.siggenes  9.108  0.585  10.303
p.vector      5.963  0.402   6.844
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.047	0.005	0.072
NBdesign	0.004	0.001	0.004
PlotGroups	0.065	0.008	0.077
PlotProfiles	0.028	0.003	0.034
T.fit	19.427	1.166	21.547
average.rows	0.015	0.001	0.017
data.abiotic	0.009	0.001	0.011
edesign.OD	0.004	0.001	0.005
edesign.abiotic	0.006	0.001	0.008
edesignCT	0.004	0.001	0.005
edesignDR	0.003	0.001	0.005
get.siggenes	9.108	0.585	10.303
i.rank	0.001	0.001	0.001
maSigPro	12.922	0.905	15.285
maSigProUsersGuide	0.011	0.005	0.024
make.design.matrix	0.019	0.010	0.044
p.vector	5.963	0.402	6.844
position	0.002	0.000	0.001
reg.coeffs	0.002	0.000	0.002
see.genes	2.133	0.232	2.858
stepback	0.078	0.005	0.083
stepfor	0.341	0.021	0.391
suma2Venn	0.014	0.003	0.060
two.ways.stepback	0.278	0.019	0.318
two.ways.stepfor	0.362	0.022	0.389