BioC 3.6: CHECK report for SLGI on veracruz1

Package: SLGI

Version: 1.37.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SLGI_1.37.0.tar.gz

StartedAt: 2017-08-16 08:40:07 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:44:05 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 238.1 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_1.37.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SLGI.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.37.0’
* 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        20.739  1.963  23.527
siResult-class  11.885  5.025  17.379
plot            11.557  5.223  17.270
modelSLGI        9.621  5.822  15.980
compare         10.624  4.372  15.468
topInteraction   6.103  2.034   8.444
normInteraction  4.453  2.387   7.097
twoWayTable      5.337  0.108   5.593
* 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-3.6-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	0.030
AtongFnDomain	3.329	0.094	3.523
AtongPair	0.456	0.032	0.495
SDL	0.006	0.001	0.006
SGA	0.005	0.025	0.033
SGD.SL	0.132	0.028	0.164
TFmat	0.071	0.028	0.105
byComplex	0.232	0.069	0.312
comemberIn	0.537	0.088	0.643
compare	10.624	4.372	15.468
congruence	0.003	0.000	0.003
createSquareMatrix	0.321	0.025	0.365
domainDist	2.876	0.065	3.052
essglist	0.012	0.005	0.017
getInteraction	0.003	0.001	0.003
getSharedDomains	0.012	0.000	0.013
getSharedInteraction	0.022	0.000	0.023
getTestedPairs	0.012	0.002	0.013
getUniquePairs	0.090	0.007	0.098
gi2005	0.046	0.027	0.072
gi2007	0.107	0.030	0.140
gi2Interactome	0.002	0.000	0.001
hyperG	0.007	0.001	0.007
iSummary	20.739	1.963	23.527
modelSLGI	9.621	5.822	15.980
normInteraction	4.453	2.387	7.097
plot	11.557	5.223	17.270
seqMatcherAlign	0.001	0.001	0.001
sharedBy	2.387	0.067	2.536
sharedInt	0.004	0.000	0.004
siResult-class	11.885	5.025	17.379
test2Interact	0.003	0.001	0.004
topInteraction	6.103	2.034	8.444
twoWayTable	5.337	0.108	5.593
withinComplex	0.531	0.095	0.649