BioC 3.2: CHECK report for SLGI on linux1.bioconductor.org

Package: SLGI

Version: 1.30.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.30.0.tar.gz

StartedAt: 2015-10-27 08:14:40 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:17:48 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 188.0 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SLGI.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.30.0’
* 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 ... [9s/9s] 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 ... [93s/93s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary       21.782  0.052  21.846
plot           10.649  0.008  10.678
modelSLGI      10.401  0.104  10.526
siResult-class  9.654  0.008   9.676
compare         8.148  0.260   8.417
twoWayTable     5.331  0.060   5.396
AtongFnDomain   5.346  0.043   5.393
* 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-3.2-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	0.012	0.000	0.012
AtongFnDomain	5.346	0.043	5.393
AtongPair	0.072	0.004	0.077
SDL	0.005	0.000	0.007
SGA	0.008	0.000	0.009
SGD.SL	0.244	0.008	0.253
TFmat	0.096	0.000	0.097
byComplex	0.534	0.024	0.558
comemberIn	0.409	0.012	0.421
compare	8.148	0.260	8.417
congruence	0.003	0.000	0.003
createSquareMatrix	0.182	0.000	0.182
domainDist	2.194	0.020	2.217
essglist	0.012	0.000	0.012
getInteraction	0.004	0.000	0.004
getSharedDomains	0.025	0.000	0.025
getSharedInteraction	0.002	0.000	0.002
getTestedPairs	0.014	0.000	0.014
getUniquePairs	0.019	0.004	0.023
gi2005	0.059	0.000	0.059
gi2007	0.142	0.008	0.151
gi2Interactome	0.001	0.000	0.002
hyperG	0.007	0.000	0.007
iSummary	21.782	0.052	21.846
modelSLGI	10.401	0.104	10.526
normInteraction	4.392	0.000	4.401
plot	10.649	0.008	10.678
seqMatcherAlign	0.001	0.000	0.001
sharedBy	2.581	0.016	2.596
sharedInt	0.002	0.000	0.003
siResult-class	9.654	0.008	9.676
test2Interact	0.003	0.000	0.002
topInteraction	4.904	0.012	4.918
twoWayTable	5.331	0.060	5.396
withinComplex	0.755	0.008	0.764