BioC 2.13: CHECK report for maSigPro on perceval

Package: maSigPro

Version: 1.34.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maSigPro_1.34.1.tar.gz

StartedAt: 2014-04-05 02:26:16 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:28:28 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 132.1 seconds

RetCode: 0

Status:  OK

CheckDir: maSigPro.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/maSigPro.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.34.1’
* 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/7s] 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘maSigPro.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [47s/49s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
T.fit        16.153  1.108  17.740
maSigPro      9.756  0.748  11.606
get.siggenes  6.999  0.520   7.853
* 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.037	0.006	0.044
NBdesign	0.006	0.001	0.009
PlotGroups	0.052	0.003	0.056
PlotProfiles	0.044	0.003	0.048
T.fit	16.153	1.108	17.740
average.rows	0.016	0.002	0.019
data.abiotic	0.014	0.002	0.016
edesign.OD	0.010	0.001	0.011
edesign.abiotic	0.012	0.002	0.014
edesignCT	0.008	0.001	0.009
edesignDR	0.010	0.001	0.012
get.siggenes	6.999	0.520	7.853
i.rank	0.008	0.001	0.008
maSigPro	9.756	0.748	11.606
maSigProUsersGuide	0.019	0.004	0.030
make.design.matrix	0.021	0.009	0.069
p.vector	4.463	0.315	4.912
position	0.007	0.000	0.008
reg.coeffs	0.007	0.000	0.008
see.genes	1.452	0.162	1.855
stepback	0.096	0.007	0.103
stepfor	0.280	0.025	0.308
suma2Venn	0.019	0.002	0.035
two.ways.stepback	0.236	0.023	0.260
two.ways.stepfor	0.281	0.023	0.311