BioC 3.2: CHECK report for SLGI on oaxaca

Package: SLGI

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.30.0.tar.gz

StartedAt: 2016-04-23 04:33:02 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:37:36 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 274.0 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_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SLGI.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.30.0’
* 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/13s] 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 ... [139s/142s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        26.897  2.208  31.136
siResult-class  12.452  5.715  18.188
modelSLGI       11.375  6.092  17.554
plot            11.292  5.298  16.650
compare         10.159  4.985  15.165
topInteraction   6.157  2.743   8.911
normInteraction  5.137  3.064   8.214
twoWayTable      5.690  0.141   5.836
* 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	0.010	0.005	0.015
AtongFnDomain	4.646	0.110	4.762
AtongPair	0.066	0.026	0.091
SDL	0.007	0.002	0.010
SGA	0.008	0.023	0.030
SGD.SL	0.227	0.029	0.256
TFmat	0.089	0.027	0.114
byComplex	0.610	0.085	0.739
comemberIn	0.531	0.092	0.624
compare	10.159	4.985	15.165
congruence	0.002	0.000	0.002
createSquareMatrix	0.185	0.035	0.222
domainDist	2.748	0.084	2.839
essglist	0.013	0.005	0.018
getInteraction	0.004	0.001	0.004
getSharedDomains	0.025	0.001	0.027
getSharedInteraction	0.003	0.001	0.003
getTestedPairs	0.014	0.000	0.014
getUniquePairs	0.022	0.002	0.025
gi2005	0.056	0.026	0.083
gi2007	0.152	0.030	0.183
gi2Interactome	0.002	0.000	0.002
hyperG	0.008	0.001	0.009
iSummary	26.897	2.208	31.136
modelSLGI	11.375	6.092	17.554
normInteraction	5.137	3.064	8.214
plot	11.292	5.298	16.650
seqMatcherAlign	0.001	0.001	0.001
sharedBy	3.212	0.081	3.297
sharedInt	0.004	0.001	0.005
siResult-class	12.452	5.715	18.188
test2Interact	0.003	0.000	0.004
topInteraction	6.157	2.743	8.911
twoWayTable	5.690	0.141	5.836
withinComplex	0.954	0.055	1.009