BioC 2.14: CHECK report for SLGI on zin2

Package: SLGI

Version: 1.24.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.24.0.tar.gz

StartedAt: 2014-10-08 02:51:59 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:55:39 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 220.3 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/SLGI.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.24.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [99s/101s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary       21.381  0.072  21.694
compare        11.501  0.040  11.723
plot           10.573  0.012  10.729
siResult-class 10.109  0.004  10.314
modelSLGI       8.985  0.020   9.099
twoWayTable     8.373  0.048   8.475
topInteraction  5.272  0.012   5.395
AtongFnDomain   4.944  0.092   5.086
* 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 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-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	0.010
AtongFnDomain	4.944	0.092	5.086
AtongPair	0.356	0.004	0.360
SDL	0.008	0.000	0.006
SGA	0.008	0.000	0.007
SGD.SL	0.136	0.004	0.137
TFmat	0.076	0.004	0.079
byComplex	0.360	0.012	0.371
comemberIn	0.592	0.028	0.621
compare	11.501	0.040	11.723
congruence	0.000	0.000	0.003
createSquareMatrix	0.272	0.008	0.277
domainDist	2.296	0.040	2.383
essglist	0.000	0.008	0.011
getInteraction	0.000	0.000	0.004
getSharedDomains	0.196	0.004	0.209
getSharedInteraction	0.000	0.000	0.002
getTestedPairs	0.016	0.000	0.014
getUniquePairs	0.156	0.004	0.161
gi2005	0.044	0.004	0.051
gi2007	0.336	0.008	0.347
gi2Interactome	0.000	0.000	0.002
hyperG	0.008	0.000	0.006
iSummary	21.381	0.072	21.694
modelSLGI	8.985	0.020	9.099
normInteraction	3.884	0.012	3.996
plot	10.573	0.012	10.729
seqMatcherAlign	0.000	0.000	0.002
sharedBy	2.812	0.036	2.860
sharedInt	0.004	0.000	0.004
siResult-class	10.109	0.004	10.314
test2Interact	0.004	0.000	0.005
topInteraction	5.272	0.012	5.395
twoWayTable	8.373	0.048	8.475
withinComplex	0.952	0.016	0.971