BioC 3.1: CHECK report for SLGI on petty

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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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/SLGI.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.28.0’
* 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 ... [17s/17s] 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 ... [217s/218s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        37.648  5.362  43.058
siResult-class  18.448  9.728  29.010
plot            19.739  8.320  28.077
modelSLGI       18.047  8.765  26.823
compare         17.369  8.906  26.294
topInteraction   9.894  5.089  14.991
normInteraction  8.399  4.481  12.888
twoWayTable      7.478  0.223   7.705
AtongFnDomain    6.686  0.209   6.900
* 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-3.1-bioc/meat/SLGI.Rcheck/00check.log’
for details.

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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	0.010	0.004	0.014
AtongFnDomain	6.686	0.209	6.900
AtongPair	0.085	0.049	0.134
SDL	0.010	0.002	0.012
SGA	0.009	0.040	0.048
SGD.SL	0.275	0.050	0.324
TFmat	0.104	0.049	0.153
byComplex	0.869	0.138	1.007
comemberIn	0.834	0.160	0.993
compare	17.369	8.906	26.294
congruence	0.004	0.001	0.003
createSquareMatrix	0.237	0.051	0.289
domainDist	3.671	0.114	3.788
essglist	0.020	0.006	0.025
getInteraction	0.004	0.000	0.004
getSharedDomains	0.069	0.000	0.070
getSharedInteraction	0.003	0.000	0.004
getTestedPairs	0.021	0.001	0.022
getUniquePairs	0.027	0.001	0.027
gi2005	0.060	0.039	0.099
gi2007	0.192	0.049	0.241
gi2Interactome	0.004	0.000	0.003
hyperG	0.013	0.000	0.013
iSummary	37.648	5.362	43.058
modelSLGI	18.047	8.765	26.823
normInteraction	8.399	4.481	12.888
plot	19.739	8.320	28.077
seqMatcherAlign	0.002	0.000	0.002
sharedBy	4.453	0.120	4.574
sharedInt	0.007	0.001	0.007
siResult-class	18.448	9.728	29.010
test2Interact	0.005	0.000	0.005
topInteraction	9.894	5.089	14.991
twoWayTable	7.478	0.223	7.705
withinComplex	1.548	0.131	1.678

BioC 3.1: CHECK report for SLGI on petty

Summary

Command output