BioC 3.4: CHECK report for SLGI on zin1

Package: SLGI

Version: 1.33.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.33.0.tar.gz

StartedAt: 2016-09-20 12:41:50 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:44:32 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 162.6 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.33.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SLGI.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.33.0’
* 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       17.688  0.060  17.745
siResult-class  9.400  0.008   9.409
compare         9.284  0.024   9.307
plot            8.780  0.004   8.786
modelSLGI       8.116  0.016   8.132
* 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-3.4-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	0.028	0.000	0.030
AtongFnDomain	3.436	0.152	3.587
AtongPair	0.448	0.012	0.461
SDL	0.004	0.004	0.006
SGA	0.008	0.000	0.006
SGD.SL	0.120	0.000	0.122
TFmat	0.072	0.004	0.078
byComplex	0.216	0.040	0.255
comemberIn	0.608	0.084	0.693
compare	9.284	0.024	9.307
congruence	0.004	0.000	0.002
createSquareMatrix	0.244	0.032	0.278
domainDist	2.412	0.044	2.456
essglist	0.008	0.000	0.009
getInteraction	0.004	0.000	0.002
getSharedDomains	0.008	0.004	0.010
getSharedInteraction	0.004	0.000	0.002
getTestedPairs	0.008	0.004	0.010
getUniquePairs	0.016	0.000	0.017
gi2005	0.044	0.000	0.042
gi2007	0.112	0.004	0.114
gi2Interactome	0.000	0.000	0.001
hyperG	0.008	0.000	0.005
iSummary	17.688	0.060	17.745
modelSLGI	8.116	0.016	8.132
normInteraction	3.316	0.008	3.326
plot	8.780	0.004	8.786
seqMatcherAlign	0.000	0.000	0.001
sharedBy	2.208	0.008	2.215
sharedInt	0.004	0.000	0.003
siResult-class	9.400	0.008	9.409
test2Interact	0.000	0.000	0.003
topInteraction	4.936	0.008	4.946
twoWayTable	4.828	0.020	4.845
withinComplex	0.760	0.008	0.770