BioC 2.13: CHECK report for eisa on zin1

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

* 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.

* 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)

name	user	system	elapsed
ALLModules	0.24	0.00	0.24
ISA.CHR	1.252	0.032	1.284
ISA.GO	6.968	0.116	7.156
ISA.KEGG	2.853	0.008	2.865
ISA	20.557	0.080	20.686
ISA.html	14.737	0.256	15.069
ISA.iterate	5.428	0.036	5.476
ISA.miRNA	0.984	0.024	1.025
ISA.normalize	3.953	0.056	4.018
ISA.sweep	9.648	0.032	9.698
ISA.unique	4.792	0.032	4.832
ISA2heatmap	1.125	0.044	1.181
ISAExpressionSet	3.632	0.044	3.730
ISAModules-class	0.008	0.004	0.013
ListHyperGParams-class	4.384	0.044	4.438
ListHyperGResult-class	5.032	0.092	5.172
cond.plot	1.796	0.008	1.808
eisa.biclust	2.805	0.024	2.848
enrichment	0.492	0.000	0.525
exp.plot	1.508	0.020	1.533
gograph	5.460	0.060	5.529
mnplot	1.532	0.012	1.546
overlap	0.312	0.144	0.469
profilePlot	1.108	0.004	1.113
robustness	1.804	0.036	1.844