BioC 3.4: CHECK report for SLGI on morelia

Package: SLGI

Version: 1.33.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.33.0.tar.gz

StartedAt: 2016-09-20 13:13:27 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:16:40 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 193.0 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_1.33.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘1.33.0’
* 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        18.748  1.329  20.134
siResult-class   9.881  4.377  14.262
compare         11.659  2.296  13.958
plot             9.523  4.405  13.933
modelSLGI        8.822  4.423  13.248
topInteraction   5.223  2.138   7.366
normInteraction  4.004  2.394   6.401
* 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-3.4-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	0.023	0.007	0.030
AtongFnDomain	3.075	0.092	3.169
AtongPair	0.312	0.023	0.335
SDL	0.004	0.001	0.005
SGA	0.005	0.016	0.021
SGD.SL	0.142	0.025	0.167
TFmat	0.061	0.021	0.083
byComplex	0.236	0.057	0.293
comemberIn	0.576	0.093	0.670
compare	11.659	2.296	13.958
congruence	0.001	0.000	0.002
createSquareMatrix	0.221	0.024	0.245
domainDist	1.726	0.057	1.782
essglist	0.016	0.007	0.023
getInteraction	0.005	0.001	0.005
getSharedDomains	0.016	0.001	0.018
getSharedInteraction	0.003	0.000	0.003
getTestedPairs	0.011	0.001	0.012
getUniquePairs	0.018	0.003	0.021
gi2005	0.037	0.017	0.053
gi2007	0.528	0.029	0.558
gi2Interactome	0.002	0.000	0.002
hyperG	0.007	0.000	0.008
iSummary	18.748	1.329	20.134
modelSLGI	8.822	4.423	13.248
normInteraction	4.004	2.394	6.401
plot	9.523	4.405	13.933
seqMatcherAlign	0.001	0.000	0.002
sharedBy	2.072	0.077	2.148
sharedInt	0.002	0.000	0.003
siResult-class	9.881	4.377	14.262
test2Interact	0.003	0.000	0.003
topInteraction	5.223	2.138	7.366
twoWayTable	4.413	0.113	4.527
withinComplex	0.672	0.105	0.778