BioC 3.0: CHECK report for SLGI on zin1

Package: SLGI

Version: 1.26.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.26.0.tar.gz

StartedAt: 2015-04-10 04:27:24 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:31:27 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 243.0 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/SLGI.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.26.0’
* 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 ... [13s/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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [103s/105s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary       23.382  0.040  23.840
compare        11.937  0.016  12.040
plot           10.744  0.016  10.988
siResult-class  9.537  0.020   9.643
modelSLGI       8.996  0.012   9.053
twoWayTable     8.509  0.076   8.633
topInteraction  5.228  0.004   5.509
AtongFnDomain   5.044  0.044   5.111
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/SLGI.Rcheck/00check.log’
for details.

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing package for lazy loading
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 "BiocGenerics" for requests: plot
* DONE (SLGI)

name	user	system	elapsed
Atong	0.008	0.000	0.009
AtongFnDomain	5.044	0.044	5.111
AtongPair	0.364	0.012	0.386
SDL	0.004	0.000	0.006
SGA	0.004	0.000	0.007
SGD.SL	0.136	0.000	0.139
TFmat	0.076	0.008	0.083
byComplex	0.340	0.044	0.404
comemberIn	0.636	0.056	0.713
compare	11.937	0.016	12.040
congruence	0.004	0.000	0.003
createSquareMatrix	0.304	0.004	0.307
domainDist	2.288	0.028	2.334
essglist	0.008	0.000	0.011
getInteraction	0.004	0.000	0.003
getSharedDomains	0.024	0.000	0.024
getSharedInteraction	0.000	0.000	0.002
getTestedPairs	0.012	0.000	0.012
getUniquePairs	0.024	0.000	0.023
gi2005	0.048	0.000	0.049
gi2007	0.212	0.004	0.217
gi2Interactome	0.000	0.004	0.001
hyperG	0.328	0.000	0.331
iSummary	23.382	0.040	23.840
modelSLGI	8.996	0.012	9.053
normInteraction	4.089	0.004	4.104
plot	10.744	0.016	10.988
seqMatcherAlign	0.000	0.000	0.001
sharedBy	2.908	0.044	2.982
sharedInt	0.004	0.000	0.004
siResult-class	9.537	0.020	9.643
test2Interact	0.004	0.000	0.004
topInteraction	5.228	0.004	5.509
twoWayTable	8.509	0.076	8.633
withinComplex	0.868	0.008	0.875