BioC 3.3: CHECK report for SLGI on morelia

Package: SLGI

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.31.0.tar.gz

StartedAt: 2016-04-21 07:41:06 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:45:00 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 234.3 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_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SLGI.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.31.0’
* 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 ... [9s/9s] 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 ... [130s/130s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        22.629  1.946  24.693
plot            12.339  4.957  17.315
modelSLGI       11.688  5.218  16.926
siResult-class  11.084  5.603  16.701
compare         10.505  5.269  15.801
topInteraction   5.689  2.840   8.540
normInteraction  5.088  2.537   7.634
* 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-3.3-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	0.032	0.009	0.039
AtongFnDomain	4.326	0.119	4.449
AtongPair	0.063	0.028	0.091
SDL	0.006	0.002	0.008
SGA	0.005	0.018	0.023
SGD.SL	0.158	0.022	0.180
TFmat	0.082	0.027	0.109
byComplex	0.542	0.073	0.616
comemberIn	0.489	0.086	0.596
compare	10.505	5.269	15.801
congruence	0.003	0.000	0.003
createSquareMatrix	0.135	0.034	0.168
domainDist	2.328	0.074	2.402
essglist	0.011	0.005	0.015
getInteraction	0.003	0.000	0.003
getSharedDomains	0.019	0.001	0.020
getSharedInteraction	0.002	0.000	0.002
getTestedPairs	0.010	0.002	0.011
getUniquePairs	0.031	0.004	0.034
gi2005	0.048	0.026	0.075
gi2007	0.138	0.023	0.162
gi2Interactome	0.001	0.001	0.001
hyperG	0.005	0.000	0.006
iSummary	22.629	1.946	24.693
modelSLGI	11.688	5.218	16.926
normInteraction	5.088	2.537	7.634
plot	12.339	4.957	17.315
seqMatcherAlign	0.002	0.000	0.001
sharedBy	3.129	0.069	3.203
sharedInt	0.003	0.000	0.003
siResult-class	11.084	5.603	16.701
test2Interact	0.004	0.000	0.005
topInteraction	5.689	2.840	8.540
twoWayTable	4.595	0.132	4.736
withinComplex	1.054	0.093	1.150