BioC 3.1: CHECK report for maSigPro on petty
This page was generated on 2015-10-09 09:32:55 -0700 (Fri, 09 Oct 2015).
maSigPro 1.40.0 Maria Jose Nueda
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/maSigPro | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
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 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maSigPro_1.40.0.tar.gz
###
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* 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.
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:
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 |
|