BioC 3.5: CHECK report for maSigPro on oaxaca

Package: maSigPro

Version: 1.47.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maSigPro_1.47.0.tar.gz

StartedAt: 2016-10-26 03:08:36 -0700 (Wed, 26 Oct 2016)

EndedAt: 2016-10-26 03:09:35 -0700 (Wed, 26 Oct 2016)

EllapsedTime: 59.7 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_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/maSigPro.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.47.0’
* 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 ... 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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
T.fit    7.863  0.054   7.921
maSigPro 5.540  0.035   5.579
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	0.019	0.002	0.021
NBdesign	0.002	0.000	0.003
PlotGroups	0.031	0.001	0.032
PlotProfiles	0.012	0.001	0.013
T.fit	7.863	0.054	7.921
average.rows	0.005	0.000	0.005
data.abiotic	0.005	0.001	0.006
edesign.abiotic	0.003	0.001	0.017
edesignCT	0.001	0.001	0.002
edesignDR	0.001	0.000	0.001
get.siggenes	3.677	0.018	3.696
i.rank	0.001	0.000	0.001
maSigPro	5.540	0.035	5.579
maSigProUsersGuide	0.005	0.001	0.008
make.design.matrix	0.010	0.005	0.016
p.vector	2.551	0.013	2.565
position	0.001	0.000	0.001
reg.coeffs	0.001	0.000	0.001
see.genes	0.978	0.087	1.427
stepback	0.043	0.001	0.043
stepfor	0.152	0.001	0.153
suma2Venn	0.095	0.003	0.175
two.ways.stepback	0.103	0.001	0.104
two.ways.stepfor	0.157	0.001	0.158