Package: SLGI

Version: 1.18.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.18.0.tar.gz

StartedAt: 2013-03-25 04:59:18 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:07:35 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 497.1 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/SLGI.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.18.0’
* 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 whether package ‘SLGI’ can be installed ... 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        39.770  0.212  43.788
siResult-class  31.962  0.248  35.649
plot            30.510  0.076  35.129
modelSLGI       29.078  0.280  34.552
compare         28.938  0.104  32.530
topInteraction  17.253  0.052  18.890
twoWayTable     15.545  0.652  19.626
normInteraction 12.317  0.068  13.421
AtongFnDomain    8.576  0.720  11.179
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-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
   ‘SLGI.Rnw’ 
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot

* DONE (SLGI)

name	user	system	elapsed
Atong	0.008	0.004	0.016
AtongFnDomain	8.576	0.720	11.179
AtongPair	0.841	0.036	1.085
SDL	0.004	0.004	0.023
SGA	0.008	0.000	0.018
SGD.SL	0.132	0.008	0.205
TFmat	0.080	0.008	0.104
byComplex	0.732	0.052	1.007
comemberIn	1.568	0.176	2.175
compare	28.938	0.104	32.530
congruence	0.004	0.000	0.002
createSquareMatrix	0.548	0.028	0.730
domainDist	3.144	0.176	3.653
essglist	0.008	0.000	0.025
getInteraction	0.000	0.004	0.005
getSharedDomains	0.600	0.012	0.912
getSharedInteraction	0.000	0.000	0.002
getTestedPairs	0.500	0.004	0.507
getUniquePairs	0.020	0.000	0.021
gi2005	0.044	0.004	0.528
gi2007	0.116	0.004	0.440
gi2Interactome	0.000	0.000	0.001
hyperG	0.000	0.004	0.005
iSummary	39.770	0.212	43.788
modelSLGI	29.078	0.280	34.552
normInteraction	12.317	0.068	13.421
plot	30.510	0.076	35.129
seqMatcherAlign	0.004	0.000	0.001
sharedBy	3.324	0.168	4.178
sharedInt	0.004	0.000	0.004
siResult-class	31.962	0.248	35.649
test2Interact	0.004	0.000	0.003
topInteraction	17.253	0.052	18.890
twoWayTable	15.545	0.652	19.626
withinComplex	1.524	0.196	2.484