Package: SLGI

Version: 1.46.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SLGI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SLGI_1.46.0.tar.gz

StartedAt: 2020-04-15 05:47:34 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:52:38 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 304.1 seconds

RetCode: 0

Status:  OK

CheckDir: SLGI.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SLGI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SLGI_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/SLGI.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.46.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iSummary        21.151  3.499  24.915
siResult-class  15.345  7.617  23.179
plot            13.898  8.112  22.228
modelSLGI       14.279  7.641  22.154
compare         13.332  6.661  20.238
topInteraction   6.797  3.508  10.443
normInteraction  6.105  4.043  10.249
* 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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/SLGI.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SLGI
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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	0.020	0.008	0.029
AtongFnDomain	3.216	0.113	3.356
AtongPair	0.641	0.038	0.688
SDL	0.004	0.002	0.005
SGA	0.006	0.029	0.039
SGD.SL	0.140	0.035	0.175
TFmat	0.099	0.036	0.135
byComplex	0.334	0.100	0.433
comemberIn	0.643	0.110	0.759
compare	13.332	6.661	20.238
congruence	0.002	0.000	0.002
createSquareMatrix	0.329	0.040	0.370
domainDist	2.752	0.091	2.874
essglist	0.011	0.004	0.016
getInteraction	0.002	0.000	0.002
getSharedDomains	0.009	0.000	0.010
getSharedInteraction	0.002	0.000	0.002
getTestedPairs	0.012	0.001	0.012
getUniquePairs	0.023	0.002	0.024
gi2005	0.237	0.039	0.278
gi2007	0.132	0.034	0.166
gi2Interactome	0.000	0.001	0.001
hyperG	0.005	0.000	0.005
iSummary	21.151	3.499	24.915
modelSLGI	14.279	7.641	22.154
normInteraction	6.105	4.043	10.249
plot	13.898	8.112	22.228
seqMatcherAlign	0.000	0.000	0.001
sharedBy	2.839	0.108	2.978
sharedInt	0.005	0.000	0.005
siResult-class	15.345	7.617	23.179
test2Interact	0.004	0.001	0.003
topInteraction	6.797	3.508	10.443
twoWayTable	3.899	0.155	4.088
withinComplex	0.806	0.059	0.876