BioC 3.5: CHECK report for SLGI on oaxaca

Package: SLGI

Version: 1.35.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.35.0.tar.gz

StartedAt: 2017-03-04 09:18:51 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:22:53 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 241.8 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_1.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SLGI.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.35.0’
* 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        22.258  2.431  24.921
siResult-class  11.001  5.553  16.559
plot            10.571  5.326  15.902
compare         11.886  3.856  15.750
modelSLGI        8.998  5.386  14.391
topInteraction   5.972  2.897   8.873
normInteraction  4.937  3.194   8.136
* 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-3.5-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	0.005	0.028
AtongFnDomain	3.092	0.095	3.189
AtongPair	0.339	0.022	0.361
SDL	0.004	0.001	0.005
SGA	0.005	0.017	0.022
SGD.SL	0.100	0.020	0.121
TFmat	0.059	0.021	0.079
byComplex	0.435	0.072	0.533
comemberIn	0.599	0.078	0.700
compare	11.886	3.856	15.750
congruence	0.003	0.000	0.004
createSquareMatrix	0.365	0.037	0.402
domainDist	2.554	0.080	2.634
essglist	0.011	0.005	0.015
getInteraction	0.005	0.000	0.005
getSharedDomains	0.018	0.001	0.041
getSharedInteraction	0.027	0.001	0.028
getTestedPairs	0.015	0.001	0.015
getUniquePairs	0.109	0.013	0.121
gi2005	0.050	0.029	0.079
gi2007	0.130	0.030	0.159
gi2Interactome	0.001	0.000	0.001
hyperG	0.007	0.001	0.009
iSummary	22.258	2.431	24.921
modelSLGI	8.998	5.386	14.391
normInteraction	4.937	3.194	8.136
plot	10.571	5.326	15.902
seqMatcherAlign	0.002	0.000	0.001
sharedBy	2.281	0.072	2.353
sharedInt	0.003	0.001	0.002
siResult-class	11.001	5.553	16.559
test2Interact	0.004	0.000	0.005
topInteraction	5.972	2.897	8.873
twoWayTable	4.624	0.124	4.749
withinComplex	1.021	0.119	1.140