BioC 3.0: CHECK report for SLGI on perceval

Package: SLGI

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.26.0.tar.gz

StartedAt: 2015-04-10 06:31:39 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 06:40:05 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 506.1 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SLGI.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.26.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SLGI’ can be installed ... [21s/24s] 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 ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ScISI’ ‘lattice’ ‘GO.db’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘GO.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [268s/270s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        37.372  4.694  42.172
siResult-class  26.728 10.165  36.908
plot            25.587 10.133  36.299
compare         27.373  7.740  35.182
modelSLGI       23.114 10.255  33.390
topInteraction  15.451  4.615  20.085
normInteraction 11.057  4.674  15.738
twoWayTable     14.586  0.308  15.825
AtongFnDomain    9.144  0.247   9.393
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot
* DONE (SLGI)

name	user	system	elapsed
Atong	0.010	0.007	0.016
AtongFnDomain	9.144	0.247	9.393
AtongPair	0.871	0.070	0.941
SDL	0.009	0.001	0.009
SGA	0.008	0.046	0.055
SGD.SL	0.156	0.052	0.209
TFmat	0.086	0.050	0.136
byComplex	0.755	0.130	0.901
comemberIn	1.103	0.171	1.285
compare	27.373	7.740	35.182
congruence	0.004	0.000	0.003
createSquareMatrix	0.598	0.073	0.672
domainDist	3.191	0.133	3.331
essglist	0.015	0.007	0.022
getInteraction	0.006	0.001	0.007
getSharedDomains	0.062	0.005	0.066
getSharedInteraction	0.003	0.001	0.003
getTestedPairs	0.015	0.003	0.017
getUniquePairs	0.027	0.007	0.034
gi2005	0.051	0.048	0.099
gi2007	0.131	0.049	0.181
gi2Interactome	0.002	0.000	0.002
hyperG	0.009	0.002	0.011
iSummary	37.372	4.694	42.172
modelSLGI	23.114	10.255	33.390
normInteraction	11.057	4.674	15.738
plot	25.587	10.133	36.299
seqMatcherAlign	0.002	0.000	0.001
sharedBy	4.231	0.149	4.386
sharedInt	0.005	0.000	0.005
siResult-class	26.728	10.165	36.908
test2Interact	0.006	0.000	0.006
topInteraction	15.451	4.615	20.085
twoWayTable	14.586	0.308	15.825
withinComplex	1.823	0.229	2.067