Package: SLGI

Version: 1.16.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.16.0.tar.gz

StartedAt: 2012-04-01 03:27:38 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 03:31:58 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 259.8 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/SLGI.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SLGI/DESCRIPTION' ... OK
* this is package 'SLGI' version '1.16.0'
* 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 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
* 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/hpages/test-puck5/bbs-2.10-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
Creating a generic function for 'plot' from package 'graphics' in package 'SLGI'
** 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	0.027
AtongFnDomain	4.304	0.068	4.394
AtongPair	0.364	0.004	0.386
SDL	0.008	0.000	0.030
SGA	0.008	0.000	0.029
SGD.SL	0.140	0.000	0.154
TFmat	0.072	0.012	0.105
byComplex	0.436	0.032	0.499
comemberIn	0.848	0.008	0.899
compare	14.865	0.016	14.952
congruence	0.004	0.000	0.002
createSquareMatrix	0.232	0.016	0.266
domainDist	2.064	0.028	2.112
essglist	0.004	0.004	0.029
getInteraction	0.004	0.000	0.003
getSharedDomains	0.496	0.004	0.512
getSharedInteraction	0.004	0.000	0.001
getTestedPairs	0.008	0.000	0.010
getUniquePairs	0.016	0.000	0.019
gi2005	0.040	0.004	0.074
gi2007	0.104	0.000	0.183
gi2Interactome	0	0	0
hyperG	0.004	0.000	0.005
iSummary	26.098	0.040	26.200
modelSLGI	18.909	0.008	18.987
normInteraction	5.972	0.008	6.036
plot	16.166	0.020	16.246
seqMatcherAlign	0	0	0
sharedBy	2.828	0.036	2.881
sharedInt	0.000	0.000	0.003
siResult-class	16.257	0.008	16.317
test2Interact	0.004	0.000	0.003
topInteraction	8.452	0.008	8.516
twoWayTable	8.409	0.084	8.506
withinComplex	0.760	0.020	0.812