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: 2017-10-18 02:34:35 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:37:36 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 180.9 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SLGI.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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       16.532  0.052  16.704
siResult-class 10.508  0.008  10.520
compare         9.800  0.012   9.818
plot            9.136  0.008   9.149
modelSLGI       8.604  0.004   8.612
topInteraction  5.816  0.012   5.832
* 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	0.020	0.000	0.021
AtongFnDomain	3.332	0.016	3.350
AtongPair	0.456	0.008	0.468
SDL	0.004	0.000	0.005
SGA	0.004	0.000	0.006
SGD.SL	0.108	0.000	0.109
TFmat	0.064	0.000	0.063
byComplex	0.160	0.012	0.171
comemberIn	0.448	0.012	0.462
compare	9.800	0.012	9.818
congruence	0.004	0.000	0.002
createSquareMatrix	0.108	0.004	0.110
domainDist	2.620	0.004	2.624
essglist	0.008	0.000	0.008
getInteraction	0.004	0.000	0.002
getSharedDomains	0.008	0.000	0.009
getSharedInteraction	0.012	0.000	0.015
getTestedPairs	0.008	0.000	0.009
getUniquePairs	0.056	0.000	0.057
gi2005	0.036	0.004	0.042
gi2007	0.116	0.000	0.115
gi2Interactome	0.004	0.000	0.001
hyperG	0.008	0.000	0.007
iSummary	16.532	0.052	16.704
modelSLGI	8.604	0.004	8.612
normInteraction	3.956	0.000	3.961
plot	9.136	0.008	9.149
seqMatcherAlign	0.000	0.000	0.001
sharedBy	2.288	0.008	2.295
sharedInt	0.008	0.000	0.005
siResult-class	10.508	0.008	10.520
test2Interact	0.004	0.000	0.003
topInteraction	5.816	0.012	5.832
twoWayTable	3.544	0.000	3.545
withinComplex	0.736	0.004	0.739