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CHECK report for SLGI on celaya2

This page was generated on 2019-10-16 12:46:47 -0400 (Wed, 16 Oct 2019).

Package 1539/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SLGI 1.44.0
Nolwenn Le Meur
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/SLGI
Branch: RELEASE_3_9
Last Commit: 02bddcc
Last Changed Date: 2019-05-02 11:53:09 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SLGI
Version: 1.44.0
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_1.44.0.tar.gz
StartedAt: 2019-10-16 06:58:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:05:26 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 427.7 seconds
RetCode: 0
Status:  OK 
CheckDir: SLGI.Rcheck
Warnings: 0

Command output

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### Running 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_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SLGI.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.44.0’
* 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  20.796 14.959  35.756
plot            19.916 14.906  34.823
iSummary        27.735  6.745  34.483
modelSLGI       19.109 15.055  34.163
compare         20.524 13.287  33.867
topInteraction   9.861  6.241  16.103
normInteraction  8.629  7.255  15.885
twoWayTable      5.283  0.267   5.550
* 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

SLGI.Rcheck/00install.out

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### Running command:
###
###   /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

SLGI.Rcheck/SLGI-Ex.timings

nameusersystemelapsed
Atong0.0350.0140.049
AtongFnDomain4.1940.2434.437
AtongPair0.7690.0660.835
SDL0.0080.0030.012
SGA0.0090.0530.062
SGD.SL0.1690.0630.231
TFmat0.0840.0520.135
byComplex0.3700.1680.540
comemberIn0.7230.2070.933
compare20.52413.28733.867
congruence0.0040.0000.004
createSquareMatrix0.2160.0670.284
domainDist2.8810.1763.056
essglist0.0250.0190.044
getInteraction0.0040.0010.005
getSharedDomains0.0190.0020.021
getSharedInteraction0.0030.0000.002
getTestedPairs0.0180.0010.019
getUniquePairs0.0350.0030.038
gi20050.0430.0550.099
gi20070.8360.0680.903
gi2Interactome0.0000.0000.001
hyperG0.0090.0000.009
iSummary27.735 6.74534.483
modelSLGI19.10915.05534.163
normInteraction 8.629 7.25515.885
plot19.91614.90634.823
seqMatcherAlign0.0010.0010.001
sharedBy3.6050.1973.803
sharedInt0.0060.0000.006
siResult-class20.79614.95935.756
test2Interact0.0060.0010.006
topInteraction 9.861 6.24116.103
twoWayTable5.2830.2675.550
withinComplex0.6280.1890.818