BioC 3.5: CHECK report for SLGI on toluca2

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: 2017-04-23 10:04:29 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 10:08:54 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 264.1 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 r72187)
* 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        24.254  1.872  26.290
plot            12.851  6.548  19.545
siResult-class  12.330  6.349  18.782
compare         13.077  4.381  17.702
modelSLGI       10.325  6.583  16.987
topInteraction   6.146  2.838   9.034
normInteraction  4.832  3.071   7.930
twoWayTable      5.138  0.117   5.277
* 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	0.021	0.006	0.026
AtongFnDomain	3.393	0.108	3.514
AtongPair	0.380	0.026	0.407
SDL	0.005	0.001	0.007
SGA	0.008	0.020	0.026
SGD.SL	0.138	0.025	0.164
TFmat	0.079	0.027	0.108
byComplex	0.477	0.066	0.545
comemberIn	0.625	0.082	0.709
compare	13.077	4.381	17.702
congruence	0.003	0.000	0.004
createSquareMatrix	0.381	0.034	0.417
domainDist	2.894	0.079	3.008
essglist	0.011	0.004	0.016
getInteraction	0.004	0.000	0.004
getSharedDomains	0.017	0.000	0.018
getSharedInteraction	0.026	0.000	0.027
getTestedPairs	0.013	0.002	0.014
getUniquePairs	0.102	0.009	0.112
gi2005	0.048	0.022	0.072
gi2007	0.124	0.024	0.149
gi2Interactome	0.001	0.000	0.001
hyperG	0.006	0.000	0.007
iSummary	24.254	1.872	26.290
modelSLGI	10.325	6.583	16.987
normInteraction	4.832	3.071	7.930
plot	12.851	6.548	19.545
seqMatcherAlign	0.000	0.000	0.001
sharedBy	2.687	0.080	2.797
sharedInt	0.005	0.000	0.006
siResult-class	12.330	6.349	18.782
test2Interact	0.005	0.001	0.005
topInteraction	6.146	2.838	9.034
twoWayTable	5.138	0.117	5.277
withinComplex	1.108	0.086	1.203