BioC 2.13: CHECK report for SLGI on zin1

Package: SLGI

Version: 1.22.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.22.0.tar.gz

StartedAt: 2014-04-05 04:01:24 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:05:05 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 221.7 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/SLGI.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.22.0’
* 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 ... [11s/11s] 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 ... OK
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘SLGI.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [103s/104s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary       23.350  0.048  23.453
plot           11.013  0.008  11.036
siResult-class 10.829  0.088  10.933
compare         9.873  0.012   9.970
twoWayTable     9.309  0.068   9.403
modelSLGI       9.340  0.016   9.371
topInteraction  5.428  0.004   5.442
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.012	0.000	0.012
AtongFnDomain	4.912	0.064	4.984
AtongPair	0.056	0.004	0.061
SDL	0.012	0.000	0.014
SGA	0.004	0.000	0.007
SGD.SL	0.120	0.004	0.122
TFmat	0.088	0.004	0.091
byComplex	0.488	0.016	0.506
comemberIn	0.888	0.020	0.912
compare	9.873	0.012	9.970
congruence	0.016	0.000	0.016
createSquareMatrix	0.292	0.008	0.300
domainDist	2.544	0.016	2.564
essglist	0.112	0.000	0.112
getInteraction	0.004	0.000	0.005
getSharedDomains	0.096	0.004	0.113
getSharedInteraction	0.000	0.004	0.002
getTestedPairs	0.012	0.000	0.011
getUniquePairs	0.024	0.000	0.027
gi2005	0.044	0.000	0.044
gi2007	0.124	0.000	0.125
gi2Interactome	0.000	0.000	0.002
hyperG	0.008	0.000	0.006
iSummary	23.350	0.048	23.453
modelSLGI	9.340	0.016	9.371
normInteraction	4.244	0.008	4.256
plot	11.013	0.008	11.036
seqMatcherAlign	0.052	0.000	0.050
sharedBy	2.820	0.052	2.876
sharedInt	0.084	0.000	0.086
siResult-class	10.829	0.088	10.933
test2Interact	0.020	0.000	0.018
topInteraction	5.428	0.004	5.442
twoWayTable	9.309	0.068	9.403
withinComplex	0.852	0.012	0.863