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BioC 2.13: CHECK report for eisa on perceval

This page was generated on 2014-04-05 09:52:22 -0700 (Sat, 05 Apr 2014).

Package 228/750HostnameOS / ArchBUILDCHECKBUILD BIN
eisa 1.14.0
Gabor Csardi
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/eisa
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: eisa
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch eisa_1.14.0.tar.gz
StartedAt: 2014-04-05 01:03:31 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:12:17 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 525.8 seconds
RetCode: 0
Status:  OK 
CheckDir: eisa.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/eisa.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 ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.14.0’
* 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 ‘eisa’ can be installed ... [30s/33s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Unexported objects imported by ‘:::’ calls:
  ‘Category:::getDataEnv’ ‘Category:::getKeggToProbeMap’
  ‘Category:::probeToEntrezMapHelper’
  See the note in ?`:::` about the use of this operator.
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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘EISA_biclust.Rnw’, ‘EISA_tutorial.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [208s/212s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ISA                    40.251  1.323  41.658
ISA.html               25.143  2.603  28.479
ISA.sweep              15.778  3.199  19.190
ISA.GO                 12.228  0.858  13.353
ISA.iterate            10.245  1.444  11.732
ISA.unique              9.573  1.485  11.245
gograph                 8.762  0.748   9.524
ListHyperGResult-class  7.840  0.628   8.480
ListHyperGParams-class  7.203  0.574   7.784
ISA.normalize           6.331  0.554   6.901
ISAExpressionSet        5.740  0.600   6.348
eisa.biclust            4.361  1.498   5.932
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/eisa.Rcheck/00check.log’
for details.

eisa.Rcheck/00install.out:

* installing *source* package ‘eisa’ ...
** R
** data
** inst
** preparing package for lazy loading
in method for ‘coerce’ with signature ‘"Biclust","ISAModules"’: no definition for class “Biclust”
in method for ‘coerce’ with signature ‘"ISAModules","Biclust"’: no definition for class “Biclust”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (eisa)

eisa.Rcheck/eisa-Ex.timings:

nameusersystemelapsed
ALLModules0.0270.0050.032
ISA.CHR1.8690.1232.123
ISA.GO12.228 0.85813.353
ISA.KEGG4.2390.1284.391
ISA40.251 1.32341.658
ISA.html25.143 2.60328.479
ISA.iterate10.245 1.44411.732
ISA.miRNA1.4660.1791.679
ISA.normalize6.3310.5546.901
ISA.sweep15.778 3.19919.190
ISA.unique 9.573 1.48511.245
ISA2heatmap1.1320.1271.260
ISAExpressionSet5.7400.6006.348
ISAModules-class0.0220.0200.044
ListHyperGParams-class7.2030.5747.784
ListHyperGResult-class7.8400.6288.480
cond.plot1.9340.2382.171
eisa.biclust4.3611.4985.932
enrichment0.7490.0270.777
exp.plot2.6000.2742.878
gograph8.7620.7489.524
mnplot2.4910.2542.870
overlap0.7760.9201.849
profilePlot1.1460.0991.704
robustness2.7570.2403.615