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: 2015-10-22 11:26:50 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 11:30:21 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 210.4 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 Under development (unstable) (2015-10-08 r69496)
* 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 ... [8s/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 ... [116s/117s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        20.010  1.706  21.873
plot            10.835  4.324  15.263
compare         11.433  3.522  15.031
siResult-class   9.774  4.965  14.843
modelSLGI       10.059  4.571  14.742
topInteraction   5.079  2.576   7.695
normInteraction  4.469  2.209   6.719
* 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	0.035	0.012	0.047
AtongFnDomain	4.005	0.111	4.150
AtongPair	0.054	0.024	0.077
SDL	0.004	0.000	0.006
SGA	0.005	0.016	0.021
SGD.SL	0.162	0.023	0.185
TFmat	0.071	0.025	0.097
byComplex	0.491	0.069	0.591
comemberIn	0.624	0.093	0.719
compare	11.433	3.522	15.031
congruence	0.001	0.000	0.002
createSquareMatrix	0.219	0.027	0.246
domainDist	2.027	0.054	2.086
essglist	0.008	0.003	0.010
getInteraction	0.002	0.000	0.003
getSharedDomains	0.009	0.001	0.010
getSharedInteraction	0.001	0.001	0.001
getTestedPairs	0.008	0.001	0.009
getUniquePairs	0.023	0.001	0.023
gi2005	0.045	0.020	0.065
gi2007	0.132	0.020	0.152
gi2Interactome	0.001	0.000	0.001
hyperG	0.005	0.000	0.005
iSummary	20.010	1.706	21.873
modelSLGI	10.059	4.571	14.742
normInteraction	4.469	2.209	6.719
plot	10.835	4.324	15.263
seqMatcherAlign	0.000	0.000	0.001
sharedBy	2.673	0.064	2.787
sharedInt	0.004	0.000	0.005
siResult-class	9.774	4.965	14.843
test2Interact	0.003	0.000	0.003
topInteraction	5.079	2.576	7.695
twoWayTable	4.162	0.128	4.322
withinComplex	0.786	0.127	0.914