BioC 3.3: CHECK report for SLGI on oaxaca

Package: SLGI

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.32.0.tar.gz

StartedAt: 2016-10-13 06:26:31 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:30:44 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 253.8 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_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SLGI.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.32.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        24.562  2.651  27.240
plot            12.935  5.748  18.696
siResult-class  12.680  5.644  18.349
modelSLGI       11.471  5.666  17.145
compare         12.401  4.589  17.003
topInteraction   6.459  2.590   9.065
normInteraction  5.198  2.902   8.101
twoWayTable      5.868  0.118   6.023
* 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-3.3-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	0.025	0.006	0.031
AtongFnDomain	4.058	0.113	4.176
AtongPair	0.455	0.039	0.494
SDL	0.006	0.001	0.008
SGA	0.007	0.026	0.033
SGD.SL	0.153	0.022	0.174
TFmat	0.087	0.025	0.112
byComplex	0.300	0.072	0.373
comemberIn	0.712	0.113	0.826
compare	12.401	4.589	17.003
congruence	0.003	0.000	0.003
createSquareMatrix	0.313	0.034	0.348
domainDist	3.101	0.076	3.179
essglist	0.014	0.006	0.019
getInteraction	0.004	0.000	0.004
getSharedDomains	0.015	0.000	0.016
getSharedInteraction	0.002	0.000	0.003
getTestedPairs	0.014	0.001	0.015
getUniquePairs	0.023	0.001	0.024
gi2005	0.049	0.023	0.073
gi2007	0.131	0.026	0.157
gi2Interactome	0.002	0.000	0.001
hyperG	0.008	0.001	0.009
iSummary	24.562	2.651	27.240
modelSLGI	11.471	5.666	17.145
normInteraction	5.198	2.902	8.101
plot	12.935	5.748	18.696
seqMatcherAlign	0.001	0.000	0.002
sharedBy	2.843	0.080	2.925
sharedInt	0.004	0.001	0.004
siResult-class	12.680	5.644	18.349
test2Interact	0.004	0.000	0.004
topInteraction	6.459	2.590	9.065
twoWayTable	5.868	0.118	6.023
withinComplex	0.930	0.105	1.036