BioC 2.13: CHECK report for SLGI on perceval

Package: SLGI

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.22.0.tar.gz

StartedAt: 2014-04-05 04:26:22 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:35:18 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 535.8 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/SLGI.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 ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.22.0’
* 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 ‘SLGI’ can be installed ... [20s/21s] OK
* checking installed package size ... NOTE
  installed size is 15.9Mb
  sub-directories of 1Mb or more:
    data      4.2Mb
    extdata  11.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ScISI’ ‘lattice’ ‘GO.db’
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 ... OK
* 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’:
  ‘SLGI.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [307s/314s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        48.770  2.342  51.927
modelSLGI       28.767 11.045  40.711
siResult-class  29.809  9.595  41.372
plot            28.967 10.282  39.864
compare         29.056  9.011  38.869
topInteraction  17.286  4.317  22.054
twoWayTable     19.137  0.374  19.827
normInteraction 13.741  5.121  19.136
AtongFnDomain   11.024  0.322  11.471
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/SLGI.Rcheck/00check.log’
for details.

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot
* DONE (SLGI)

name	user	system	elapsed
Atong	0.020	0.009	0.029
AtongFnDomain	11.024	0.322	11.471
AtongPair	0.072	0.040	0.112
SDL	0.023	0.014	0.037
SGA	0.010	0.008	0.017
SGD.SL	0.152	0.021	0.173
TFmat	0.119	0.025	0.145
byComplex	0.849	0.079	0.950
comemberIn	2.048	0.152	2.223
compare	29.056	9.011	38.869
congruence	0.008	0.007	0.014
createSquareMatrix	0.664	0.076	0.747
domainDist	3.152	0.177	3.419
essglist	0.540	0.010	0.555
getInteraction	0.009	0.009	0.018
getSharedDomains	0.207	0.020	0.313
getSharedInteraction	0.004	0.008	0.013
getTestedPairs	0.019	0.006	0.025
getUniquePairs	0.048	0.014	0.064
gi2005	0.052	0.018	0.071
gi2007	0.146	0.029	0.193
gi2Interactome	0.004	0.006	0.011
hyperG	0.011	0.006	0.022
iSummary	48.770	2.342	51.927
modelSLGI	28.767	11.045	40.711
normInteraction	13.741	5.121	19.136
plot	28.967	10.282	39.864
seqMatcherAlign	0.044	0.016	0.060
sharedBy	4.541	0.159	4.803
sharedInt	0.266	0.007	0.280
siResult-class	29.809	9.595	41.372
test2Interact	0.045	0.015	0.060
topInteraction	17.286	4.317	22.054
twoWayTable	19.137	0.374	19.827
withinComplex	1.796	0.247	2.068