BioC 2.14: CHECK report for SLGI on morelia

Package: SLGI

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SLGI_1.24.0.tar.gz

StartedAt: 2014-10-08 01:37:47 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:42:47 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 300.2 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 --no-multiarch SLGI_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/SLGI.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ... [14s/14s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [152s/152s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        25.794  1.604  27.530
plot            14.785  4.826  19.637
siResult-class  13.948  4.965  18.929
compare         15.606  3.126  18.747
modelSLGI       12.366  4.777  17.162
twoWayTable      9.691  0.176   9.874
topInteraction   7.370  2.086   9.480
normInteraction  5.518  2.342   7.881
AtongFnDomain    5.819  0.135   5.959
* 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
  ‘/Users/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	0.010	0.010	0.021
AtongFnDomain	5.819	0.135	5.959
AtongPair	0.411	0.032	0.444
SDL	0.005	0.000	0.006
SGA	0.007	0.022	0.029
SGD.SL	0.147	0.028	0.175
TFmat	0.091	0.027	0.117
byComplex	0.407	0.087	0.495
comemberIn	0.763	0.103	0.875
compare	15.606	3.126	18.747
congruence	0.002	0.000	0.003
createSquareMatrix	0.353	0.032	0.383
domainDist	2.761	0.084	2.851
essglist	0.013	0.004	0.018
getInteraction	0.005	0.000	0.005
getSharedDomains	0.227	0.014	0.285
getSharedInteraction	0.003	0.000	0.003
getTestedPairs	0.015	0.000	0.015
getUniquePairs	0.203	0.002	0.204
gi2005	0.048	0.023	0.071
gi2007	0.385	0.034	0.419
gi2Interactome	0.002	0.000	0.002
hyperG	0.008	0.000	0.009
iSummary	25.794	1.604	27.530
modelSLGI	12.366	4.777	17.162
normInteraction	5.518	2.342	7.881
plot	14.785	4.826	19.637
seqMatcherAlign	0.002	0.000	0.002
sharedBy	3.226	0.076	3.303
sharedInt	0.003	0.000	0.003
siResult-class	13.948	4.965	18.929
test2Interact	0.004	0.000	0.004
topInteraction	7.370	2.086	9.480
twoWayTable	9.691	0.176	9.874
withinComplex	0.941	0.108	1.048