Package: SLGI

Version: 1.43.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SLGI_1.43.0.tar.gz

StartedAt: 2019-04-09 03:43:42 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:47:21 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 218.2 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SLGI_1.43.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SLGI.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.43.0’
* 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 15.8Mb
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary       16.552  0.236  17.349
siResult-class 11.240  0.008  11.247
compare        10.986  0.008  11.038
modelSLGI      10.369  0.020  10.392
plot            9.483  0.000   9.495
topInteraction  5.149  0.016   5.176
* 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-3.9-bioc/meat/SLGI.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SLGI
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘SLGI’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
** testing if installed package can be loaded from final location
No methods found in package ‘Biobase’ for request: ‘listlen’ when loading ‘RpsiXML’
No methods found in package ‘annotate’ for requests: ‘pubmed’, ‘buildPubMedAbst’ when loading ‘RpsiXML’
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
** testing if installed package keeps a record of temporary installation path
* DONE (SLGI)

name	user	system	elapsed
Atong	0.021	0.008	0.029
AtongFnDomain	3.708	0.064	3.772
AtongPair	0.063	0.016	0.079
SDL	0.004	0.000	0.005
SGA	0.006	0.000	0.006
SGD.SL	0.252	0.000	0.252
TFmat	0.065	0.000	0.065
byComplex	0.718	0.019	0.739
comemberIn	0.485	0.004	0.489
compare	10.986	0.008	11.038
congruence	0.003	0.000	0.003
createSquareMatrix	0.389	0.008	0.397
domainDist	3.268	0.036	3.356
essglist	0.004	0.008	0.013
getInteraction	0.003	0.000	0.003
getSharedDomains	0.017	0.000	0.016
getSharedInteraction	0.001	0.002	0.002
getTestedPairs	0.015	0.000	0.015
getUniquePairs	0.023	0.000	0.022
gi2005	0.056	0.004	0.060
gi2007	0.391	0.000	0.398
gi2Interactome	0.000	0.000	0.001
hyperG	0.007	0.000	0.006
iSummary	16.552	0.236	17.349
modelSLGI	10.369	0.020	10.392
normInteraction	4.858	0.000	4.862
plot	9.483	0.000	9.495
seqMatcherAlign	0	0	0
sharedBy	2.245	0.044	2.288
sharedInt	0.003	0.000	0.002
siResult-class	11.240	0.008	11.247
test2Interact	0.003	0.000	0.004
topInteraction	5.149	0.016	5.176
twoWayTable	3.152	0.016	3.172
withinComplex	0.662	0.004	0.667