Package: SLGI

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.12.0.tar.gz

StartedAt: 2011-10-20 17:27:05 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:39:08 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 722.2 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/SLGI.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 25.4Mb
  sub-directories of 1Mb or more:
    data     13.7Mb
    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 ... 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 sizes of PDF files under 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

* 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	0.038	0.003	0.041
AtongFnDomain	8.986	0.137	9.209
AtongPair	0.982	0.023	1.011
SDL	0.010	0.002	0.011
SGA	0.010	0.002	0.012
SGD.SL	0.176	0.011	0.188
TFmat	0.233	0.011	0.244
byComplex	1.239	0.106	1.377
comemberIn	1.248	0.120	1.395
compare	43.889	32.458	78.343
congruence	0.004	0.000	0.004
createSquareMatrix	0.411	0.072	0.494
domainDist	5.786	0.064	5.961
essglist	0.011	0.008	0.018
getFASTAname	9.589	0.086	9.732
getInteraction	0.005	0.000	0.006
getSharedDomains	0.192	0.009	0.201
getSharedInteraction	0.004	0.001	0.004
getTestedPairs	0.022	0.002	0.024
getUniquePairs	0.053	0.002	0.055
gi2005	0.094	0.007	0.102
gi2007	0.288	0.013	0.308
gi2Interactome	0.001	0.000	0.001
hyperG	0.006	0.001	0.007
iSummary	57.482	19.039	79.460
modelSLGI	52.272	33.419	91.537
normInteraction	20.935	18.355	41.366
plot	54.256	32.201	89.893
seqMatcherAlign	0.000	0.000	0.001
sharedBy	6.007	0.060	6.358
sharedInt	0.006	0.000	0.006
siResult-class	49.875	33.015	84.859
test2Interact	0.005	0.000	0.005
topInteraction	26.157	19.086	46.175
twoWayTable	14.149	0.275	14.572
withinComplex	1.660	0.131	1.817