BioC 3.5: CHECK report for SLGI on malbec2

Package: SLGI

Version: 1.36.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.36.0.tar.gz

StartedAt: 2017-08-16 02:21:24 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:24:21 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 176.2 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SLGI.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.36.0’
* 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 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       16.236  0.036  16.282
siResult-class 10.768  0.008  10.784
compare         9.464  0.008   9.479
plot            9.196  0.000   9.201
modelSLGI       8.692  0.020   8.713
topInteraction  5.336  0.004   5.345
* 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
  ‘/home/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	0.02	0.00	0.02
AtongFnDomain	3.452	0.040	3.495
AtongPair	0.496	0.008	0.501
SDL	0.004	0.000	0.005
SGA	0.008	0.000	0.006
SGD.SL	0.112	0.000	0.113
TFmat	0.060	0.004	0.067
byComplex	0.164	0.016	0.183
comemberIn	0.444	0.024	0.468
compare	9.464	0.008	9.479
congruence	0.004	0.000	0.002
createSquareMatrix	0.096	0.008	0.104
domainDist	2.004	0.012	2.018
essglist	0.000	0.004	0.007
getInteraction	0.000	0.000	0.002
getSharedDomains	0.016	0.000	0.013
getSharedInteraction	0.016	0.000	0.015
getTestedPairs	0.012	0.000	0.010
getUniquePairs	0.052	0.012	0.064
gi2005	0.040	0.000	0.041
gi2007	0.108	0.004	0.112
gi2Interactome	0.000	0.000	0.001
hyperG	0.008	0.000	0.006
iSummary	16.236	0.036	16.282
modelSLGI	8.692	0.020	8.713
normInteraction	4.000	0.004	4.007
plot	9.196	0.000	9.201
seqMatcherAlign	0.000	0.000	0.001
sharedBy	1.984	0.012	1.998
sharedInt	0.000	0.000	0.003
siResult-class	10.768	0.008	10.784
test2Interact	0.000	0.000	0.003
topInteraction	5.336	0.004	5.345
twoWayTable	4.564	0.012	4.576
withinComplex	0.352	0.004	0.356