BioC 3.1: CHECK report for SLGI on morelia

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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 (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 ‘1.28.0’
* 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 ... [10s/10s] 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 ... [107s/107s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        16.842  2.468  19.370
plot             9.763  4.480  14.244
compare          9.740  3.669  13.413
siResult-class   8.392  4.697  13.090
modelSLGI        8.364  4.434  12.799
topInteraction   4.403  2.194   6.597
normInteraction  3.966  2.075   6.041
* 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	0.009	0.003	0.013
AtongFnDomain	3.345	0.190	3.535
AtongPair	0.057	0.035	0.092
SDL	0.004	0.002	0.007
SGA	0.006	0.019	0.025
SGD.SL	0.171	0.038	0.210
TFmat	0.072	0.037	0.109
byComplex	0.409	0.069	0.488
comemberIn	0.409	0.111	0.520
compare	9.740	3.669	13.413
congruence	0.002	0.001	0.002
createSquareMatrix	0.252	0.026	0.278
domainDist	2.654	0.280	2.935
essglist	0.008	0.003	0.010
getInteraction	0.002	0.000	0.003
getSharedDomains	0.020	0.001	0.020
getSharedInteraction	0.002	0.000	0.003
getTestedPairs	0.013	0.000	0.013
getUniquePairs	0.017	0.004	0.020
gi2005	0.042	0.032	0.073
gi2007	0.111	0.038	0.149
gi2Interactome	0.002	0.000	0.002
hyperG	0.007	0.000	0.006
iSummary	16.842	2.468	19.370
modelSLGI	8.364	4.434	12.799
normInteraction	3.966	2.075	6.041
plot	9.763	4.480	14.244
seqMatcherAlign	0.001	0.000	0.001
sharedBy	2.529	0.122	2.652
sharedInt	0.003	0.001	0.004
siResult-class	8.392	4.697	13.090
test2Interact	0.003	0.000	0.002
topInteraction	4.403	2.194	6.597
twoWayTable	4.050	0.233	4.282
withinComplex	0.635	0.044	0.678

BioC 3.1: CHECK report for SLGI on morelia

Summary

Command output