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BioC 3.0: CHECK report for maSigPro on zin1

This page was generated on 2015-04-10 09:37:10 -0700 (Fri, 10 Apr 2015).

Package 509/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maSigPro 1.38.0
Maria Jose Nueda
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/maSigPro
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: maSigPro
Version: 1.38.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings maSigPro_1.38.0.tar.gz
StartedAt: 2015-04-10 01:36:27 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:37:51 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 83.8 seconds
RetCode: 0
Status:  OK 
CheckDir: maSigPro.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings maSigPro_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/maSigPro.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.38.0’
* 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 ... [4s/4s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/38s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
see.genes 11.225  0.288  12.734
T.fit      8.932  0.324   9.287
maSigPro   5.741  0.180   5.939
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/maSigPro.Rcheck/00check.log’
for details.

maSigPro.Rcheck/00install.out:

* 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)

maSigPro.Rcheck/maSigPro-Ex.timings:

nameusersystemelapsed
NBdata0.0160.0040.018
NBdesign0.0000.0000.002
PlotGroups0.0240.0000.025
PlotProfiles0.0120.0040.013
T.fit8.9320.3249.287
average.rows0.0080.0000.005
data.abiotic0.0040.0000.005
edesign.OD0.0000.0000.002
edesign.abiotic0.0040.0000.021
edesignCT0.0000.0000.002
edesignDR0.0000.0000.002
get.siggenes4.0920.1244.225
i.rank0.0000.0000.001
maSigPro5.7410.1805.939
maSigProUsersGuide0.0040.0040.012
make.design.matrix0.0040.0080.012
p.vector2.6840.1202.827
position000
reg.coeffs000
see.genes11.225 0.28812.734
stepback0.0320.0040.037
stepfor0.1520.0040.159
suma2Venn0.2120.0120.244
two.ways.stepback0.1280.0080.135
two.ways.stepfor0.1600.0080.170