Multiple platform build/check report for BioC 3.9 - CHECK report for SLGI on celaya2

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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_1.43.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SLGI.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.43.0’
* 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 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
siResult-class  23.921 14.882  38.807
iSummary        26.699  7.012  33.764
plot            17.700 14.508  32.208
modelSLGI       16.798 14.851  31.648
compare         18.055 13.511  31.566
topInteraction  10.176  7.435  17.612
normInteraction  8.147  7.432  15.579
* 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-3.9-bioc/meat/SLGI.Rcheck/00check.log’
for details.

Installation output

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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)

Tests output

Example timings

name	user	system	elapsed
Atong	0.031	0.013	0.045
AtongFnDomain	4.127	0.222	4.349
AtongPair	0.066	0.057	0.123
SDL	0.006	0.003	0.009
SGA	0.010	0.055	0.064
SGD.SL	0.364	0.068	0.433
TFmat	0.106	0.064	0.169
byComplex	1.019	0.148	1.169
comemberIn	0.754	0.221	0.978
compare	18.055	13.511	31.566
congruence	0.005	0.000	0.005
createSquareMatrix	0.589	0.082	0.671
domainDist	3.294	0.187	3.481
essglist	0.014	0.010	0.023
getInteraction	0.004	0.001	0.005
getSharedDomains	0.019	0.001	0.020
getSharedInteraction	0.002	0.001	0.003
getTestedPairs	0.012	0.001	0.013
getUniquePairs	0.023	0.001	0.025
gi2005	0.055	0.053	0.108
gi2007	0.482	0.055	0.537
gi2Interactome	0.001	0.000	0.001
hyperG	0.008	0.000	0.008
iSummary	26.699	7.012	33.764
modelSLGI	16.798	14.851	31.648
normInteraction	8.147	7.432	15.579
plot	17.700	14.508	32.208
seqMatcherAlign	0.000	0.000	0.001
sharedBy	2.418	0.141	2.558
sharedInt	0.003	0.000	0.004
siResult-class	23.921	14.882	38.807
test2Interact	0.005	0.001	0.006
topInteraction	10.176	7.435	17.612
twoWayTable	3.314	0.229	3.543
withinComplex	0.904	0.271	1.175

CHECK report for SLGI on celaya2

Summary

Command output

Installation output

Tests output

Example timings