BioC 3.2: CHECK report for SLGI on oaxaca

Package: SLGI

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.30.0.tar.gz

StartedAt: 2015-10-27 08:03:10 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:07:41 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 270.8 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_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SLGI.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.30.0’
* 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 ... [10s/10s] 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 ... [141s/142s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        26.583  2.101  28.754
plot            12.245  5.932  18.196
siResult-class  12.313  5.853  18.194
modelSLGI       11.286  6.117  17.439
compare         11.152  5.476  16.648
topInteraction   6.226  2.883   9.123
normInteraction  5.220  3.336   8.561
twoWayTable      5.385  0.138   5.530
* 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	0.009	0.005	0.012
AtongFnDomain	4.379	0.105	4.487
AtongPair	0.063	0.023	0.086
SDL	0.007	0.001	0.008
SGA	0.007	0.020	0.026
SGD.SL	0.193	0.026	0.220
TFmat	0.061	0.023	0.083
byComplex	0.638	0.083	0.769
comemberIn	0.547	0.083	0.632
compare	11.152	5.476	16.648
congruence	0.003	0.000	0.003
createSquareMatrix	0.162	0.030	0.192
domainDist	2.658	0.082	2.745
essglist	0.013	0.004	0.018
getInteraction	0.004	0.001	0.006
getSharedDomains	0.029	0.001	0.030
getSharedInteraction	0.003	0.000	0.002
getTestedPairs	0.014	0.002	0.015
getUniquePairs	0.023	0.001	0.024
gi2005	0.049	0.022	0.069
gi2007	0.137	0.023	0.161
gi2Interactome	0.001	0.001	0.002
hyperG	0.005	0.001	0.006
iSummary	26.583	2.101	28.754
modelSLGI	11.286	6.117	17.439
normInteraction	5.220	3.336	8.561
plot	12.245	5.932	18.196
seqMatcherAlign	0.001	0.000	0.001
sharedBy	3.132	0.088	3.220
sharedInt	0.005	0.000	0.005
siResult-class	12.313	5.853	18.194
test2Interact	0.005	0.001	0.005
topInteraction	6.226	2.883	9.123
twoWayTable	5.385	0.138	5.530
withinComplex	0.928	0.058	0.986