Package: SLGI

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.18.0.tar.gz

StartedAt: 2013-03-25 01:18:41 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:28:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 593.4 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/SLGI.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.18.0'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
siResult-class  36.580 22.047  61.691
iSummary        42.246 14.062  59.647
plot            31.012 23.736  59.722
compare         31.171 23.452  58.997
modelSLGI       28.448 23.232  55.778
topInteraction  18.944 12.158  32.849
normInteraction 11.620 13.084  26.956
twoWayTable     15.459  0.345  15.944
AtongFnDomain    8.654  0.281   9.277
* 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
  '/Users/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	0.011	0.005	0.016
AtongFnDomain	8.654	0.281	9.277
AtongPair	0.683	0.043	0.756
SDL	0.007	0.001	0.008
SGA	0.008	0.002	0.010
SGD.SL	0.190	0.027	0.263
TFmat	0.101	0.020	0.126
byComplex	0.712	0.157	0.992
comemberIn	1.152	0.165	1.388
compare	31.171	23.452	58.997
congruence	0.003	0.000	0.003
createSquareMatrix	0.495	0.080	0.606
domainDist	3.433	0.174	3.793
essglist	0.007	0.005	0.012
getInteraction	0.003	0.000	0.003
getSharedDomains	0.837	0.015	0.860
getSharedInteraction	0.002	0.000	0.002
getTestedPairs	0.460	0.009	0.487
getUniquePairs	0.025	0.001	0.027
gi2005	0.062	0.009	0.077
gi2007	0.173	0.024	0.228
gi2Interactome	0.000	0.000	0.001
hyperG	0.007	0.000	0.008
iSummary	42.246	14.062	59.647
modelSLGI	28.448	23.232	55.778
normInteraction	11.620	13.084	26.956
plot	31.012	23.736	59.722
seqMatcherAlign	0.000	0.000	0.001
sharedBy	3.970	0.175	4.347
sharedInt	0.004	0.000	0.004
siResult-class	36.580	22.047	61.691
test2Interact	0.003	0.000	0.004
topInteraction	18.944	12.158	32.849
twoWayTable	15.459	0.345	15.944
withinComplex	1.384	0.127	1.525