Package: SLGI

Version: 1.47.0

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_1.47.0.tar.gz

StartedAt: 2020-01-16 09:01:32 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 09:07:47 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 374.6 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_1.47.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SLGI.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.47.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
iSummary        27.819  4.204  32.107
siResult-class  18.816  7.929  26.748
plot            13.700  8.444  22.146
modelSLGI       13.858  7.519  21.378
compare         10.828  7.073  17.901
topInteraction   6.565  3.588  10.153
normInteraction  6.221  3.798  10.019
twoWayTable      4.951  0.289   5.240
* 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-3.11-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/4.0/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	0.032	0.013	0.046
AtongFnDomain	4.325	0.271	4.597
AtongPair	0.919	0.062	0.980
SDL	0.008	0.006	0.014
SGA	0.010	0.052	0.062
SGD.SL	0.189	0.062	0.250
TFmat	0.071	0.054	0.125
byComplex	0.801	0.175	0.977
comemberIn	0.750	0.190	0.943
compare	10.828	7.073	17.901
congruence	0.004	0.000	0.004
createSquareMatrix	0.173	0.059	0.231
domainDist	3.116	0.213	3.329
essglist	0.024	0.021	0.044
getInteraction	0.004	0.001	0.005
getSharedDomains	0.028	0.002	0.029
getSharedInteraction	0.002	0.000	0.003
getTestedPairs	0.021	0.004	0.025
getUniquePairs	0.034	0.004	0.038
gi2005	0.062	0.058	0.121
gi2007	0.485	0.069	0.554
gi2Interactome	0.001	0.001	0.002
hyperG	0.009	0.001	0.009
iSummary	27.819	4.204	32.107
modelSLGI	13.858	7.519	21.378
normInteraction	6.221	3.798	10.019
plot	13.700	8.444	22.146
seqMatcherAlign	0.001	0.001	0.001
sharedBy	3.192	0.178	3.369
sharedInt	0.005	0.000	0.006
siResult-class	18.816	7.929	26.748
test2Interact	0.005	0.000	0.006
topInteraction	6.565	3.588	10.153
twoWayTable	4.951	0.289	5.240
withinComplex	0.395	0.123	0.518