Package: SLGI

Version: 1.12.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.12.0.tar.gz

StartedAt: 2011-10-20 14:34:19 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:41:48 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 449.0 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/SLGI.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘SLGI’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 25.5Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
    data     13.8Mb
* 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 ... NOTE
'library' or 'require' call not declared from: YEAST
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "plot" in "SLGI"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (SLGI)

name	user	system	elapsed
Atong	0.020	0.000	0.019
AtongFnDomain	9.432	0.108	9.578
AtongPair	0.848	0.016	0.873
SDL	0.004	0.004	0.008
SGA	0.012	0.000	0.010
SGD.SL	0.100	0.000	0.099
TFmat	0.100	0.008	0.108
byComplex	0.840	0.040	0.888
comemberIn	1.037	0.028	1.063
compare	46.378	0.220	47.600
congruence	0.004	0.000	0.003
createSquareMatrix	0.388	0.012	0.401
domainDist	5.005	0.008	5.017
essglist	0.008	0.004	0.011
getFASTAname	6.800	0.016	6.821
getInteraction	0.000	0.004	0.004
getSharedDomains	0.108	0.000	0.108
getSharedInteraction	0.004	0.000	0.002
getTestedPairs	0.012	0.000	0.012
getUniquePairs	0.036	0.000	0.032
gi2005	0.040	0.000	0.043
gi2007	0.104	0.004	0.109
gi2Interactome	0.000	0.000	0.001
hyperG	0.004	0.000	0.006
iSummary	50.703	0.204	51.773
modelSLGI	43.939	0.176	46.608
normInteraction	19.977	0.032	20.186
plot	49.079	0.148	49.899
seqMatcherAlign	0	0	0
sharedBy	5.989	0.004	5.999
sharedInt	0.008	0.000	0.006
siResult-class	43.271	0.028	43.881
test2Interact	0.004	0.000	0.005
topInteraction	22.613	0.008	22.669
twoWayTable	14.941	0.076	15.084
withinComplex	1.364	0.012	1.388