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BioC 2.13: CHECK report for eisa on zin1

This page was generated on 2014-04-05 09:47:48 -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: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings eisa_1.14.0.tar.gz
StartedAt: 2014-04-05 00:57:48 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:02:29 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 280.3 seconds
RetCode: 0
Status:  OK 
CheckDir: eisa.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/eisa.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [17s/17s] 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 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 ... [112s/112s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ISA                    20.557  0.080  20.686
ISA.html               14.737  0.256  15.069
ISA.sweep               9.648  0.032   9.698
ISA.GO                  6.968  0.116   7.156
gograph                 5.460  0.060   5.529
ISA.iterate             5.428  0.036   5.476
ListHyperGResult-class  5.032  0.092   5.172
* 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
  ‘/home/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
ALLModules0.240.000.24
ISA.CHR1.2520.0321.284
ISA.GO6.9680.1167.156
ISA.KEGG2.8530.0082.865
ISA20.557 0.08020.686
ISA.html14.737 0.25615.069
ISA.iterate5.4280.0365.476
ISA.miRNA0.9840.0241.025
ISA.normalize3.9530.0564.018
ISA.sweep9.6480.0329.698
ISA.unique4.7920.0324.832
ISA2heatmap1.1250.0441.181
ISAExpressionSet3.6320.0443.730
ISAModules-class0.0080.0040.013
ListHyperGParams-class4.3840.0444.438
ListHyperGResult-class5.0320.0925.172
cond.plot1.7960.0081.808
eisa.biclust2.8050.0242.848
enrichment0.4920.0000.525
exp.plot1.5080.0201.533
gograph5.4600.0605.529
mnplot1.5320.0121.546
overlap0.3120.1440.469
profilePlot1.1080.0041.113
robustness1.8040.0361.844