BioC 3.2: CHECK report for SLGI on perceval

Package: SLGI

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.29.0.tar.gz

StartedAt: 2015-08-24 05:19:54 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 05:26:38 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 404.3 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_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘1.29.0’
* 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 ... [14s/15s] 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 ... [242s/243s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        38.421  4.318  42.849
siResult-class  22.372 11.958  34.350
plot            23.707 10.010  33.769
modelSLGI       19.746 12.584  32.394
compare         19.406 11.257  30.772
topInteraction  12.369  5.852  18.233
normInteraction 10.855  5.008  15.922
twoWayTable      8.274  0.259   8.536
AtongFnDomain    6.825  0.235   7.073
* 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	0.012	0.010	0.021
AtongFnDomain	6.825	0.235	7.073
AtongPair	0.069	0.054	0.122
SDL	0.007	0.002	0.009
SGA	0.008	0.041	0.049
SGD.SL	0.300	0.054	0.356
TFmat	0.081	0.048	0.130
byComplex	1.040	0.154	1.195
comemberIn	0.867	0.196	1.088
compare	19.406	11.257	30.772
congruence	0.006	0.001	0.006
createSquareMatrix	0.253	0.069	0.323
domainDist	2.957	0.139	3.113
essglist	0.014	0.005	0.019
getInteraction	0.004	0.000	0.004
getSharedDomains	0.059	0.001	0.059
getSharedInteraction	0.002	0.001	0.002
getTestedPairs	0.014	0.001	0.015
getUniquePairs	0.022	0.002	0.024
gi2005	0.048	0.048	0.096
gi2007	0.128	0.051	0.182
gi2Interactome	0.002	0.000	0.002
hyperG	0.008	0.001	0.009
iSummary	38.421	4.318	42.849
modelSLGI	19.746	12.584	32.394
normInteraction	10.855	5.008	15.922
plot	23.707	10.010	33.769
seqMatcherAlign	0.002	0.001	0.001
sharedBy	4.018	0.132	4.154
sharedInt	0.004	0.001	0.005
siResult-class	22.372	11.958	34.350
test2Interact	0.004	0.000	0.005
topInteraction	12.369	5.852	18.233
twoWayTable	8.274	0.259	8.536
withinComplex	0.805	0.170	0.975