BioC 3.2: CHECK report for SLGI on oaxaca

Package: SLGI

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.29.0.tar.gz

StartedAt: 2015-08-24 04:00:36 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:05:26 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 290.2 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 SLGI_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SLGI.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.29.0’
* 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 ... [12s/12s] 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
Malformed Description field: should contain one or more complete sentences.
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 ... [152s/154s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        28.025  3.275  31.960
plot            14.107  5.581  19.837
siResult-class  12.603  6.344  19.187
modelSLGI       12.618  5.736  18.575
compare         11.594  5.721  17.874
topInteraction   6.468  3.359   9.880
normInteraction  5.701  2.860   8.605
twoWayTable      6.191  0.162   6.374
AtongFnDomain    4.853  0.120   5.040
* 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

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/SLGI.Rcheck/00check.log’
for details.

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
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 "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
* DONE (SLGI)

name	user	system	elapsed
Atong	0.009	0.005	0.013
AtongFnDomain	4.853	0.120	5.040
AtongPair	0.073	0.032	0.105
SDL	0.009	0.002	0.011
SGA	0.009	0.028	0.037
SGD.SL	0.238	0.033	0.272
TFmat	0.095	0.030	0.125
byComplex	0.622	0.093	0.740
comemberIn	0.549	0.092	0.740
compare	11.594	5.721	17.874
congruence	0.003	0.001	0.003
createSquareMatrix	0.174	0.034	0.208
domainDist	2.942	0.095	3.057
essglist	0.013	0.004	0.017
getInteraction	0.004	0.001	0.004
getSharedDomains	0.026	0.000	0.026
getSharedInteraction	0.002	0.000	0.003
getTestedPairs	0.014	0.002	0.016
getUniquePairs	0.031	0.004	0.034
gi2005	0.055	0.029	0.083
gi2007	0.142	0.025	0.167
gi2Interactome	0.002	0.000	0.002
hyperG	0.007	0.000	0.007
iSummary	28.025	3.275	31.960
modelSLGI	12.618	5.736	18.575
normInteraction	5.701	2.860	8.605
plot	14.107	5.581	19.837
seqMatcherAlign	0.002	0.001	0.002
sharedBy	3.755	0.082	3.855
sharedInt	0.004	0.000	0.004
siResult-class	12.603	6.344	19.187
test2Interact	0.005	0.000	0.005
topInteraction	6.468	3.359	9.880
twoWayTable	6.191	0.162	6.374
withinComplex	1.019	0.103	1.126