BioC 3.0: CHECK report for SLGI on oaxaca

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 03:29:07 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:34:47 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 339.1 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-darwin13.4.0 (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 ... [16s/16s] 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 ... [160s/162s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        24.809  1.635  26.748
plot            15.671  5.215  21.046
siResult-class  15.240  5.325  21.224
compare         16.234  3.168  19.962
modelSLGI       13.564  5.321  19.027
topInteraction   8.014  2.262  10.389
twoWayTable      9.784  0.151   9.959
normInteraction  5.852  2.446   8.401
AtongFnDomain    6.001  0.123   6.159
* 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	0.011	0.005	0.014
AtongFnDomain	6.001	0.123	6.159
AtongPair	0.452	0.031	0.484
SDL	0.007	0.001	0.007
SGA	0.008	0.023	0.031
SGD.SL	0.162	0.031	0.195
TFmat	0.095	0.029	0.123
byComplex	0.403	0.078	0.483
comemberIn	0.764	0.099	0.864
compare	16.234	3.168	19.962
congruence	0.004	0.001	0.003
createSquareMatrix	0.361	0.036	0.398
domainDist	2.963	0.085	3.067
essglist	0.013	0.004	0.017
getInteraction	0.004	0.000	0.004
getSharedDomains	0.029	0.003	0.032
getSharedInteraction	0.002	0.001	0.003
getTestedPairs	0.014	0.002	0.016
getUniquePairs	0.026	0.002	0.028
gi2005	0.055	0.024	0.080
gi2007	0.262	0.026	0.294
gi2Interactome	0.002	0.000	0.002
hyperG	0.186	0.001	0.187
iSummary	24.809	1.635	26.748
modelSLGI	13.564	5.321	19.027
normInteraction	5.852	2.446	8.401
plot	15.671	5.215	21.046
seqMatcherAlign	0.001	0.000	0.002
sharedBy	3.644	0.089	3.756
sharedInt	0.005	0.001	0.006
siResult-class	15.240	5.325	21.224
test2Interact	0.004	0.000	0.005
topInteraction	8.014	2.262	10.389
twoWayTable	9.784	0.151	9.959
withinComplex	1.130	0.097	1.230