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CHECK report for SLGI on machv2

This page was generated on 2020-10-17 11:59:39 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SLGI PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1681/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SLGI 1.48.0
Nolwenn Le Meur
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SLGI
Branch: RELEASE_3_11
Last Commit: d220637
Last Changed Date: 2020-04-27 14:16:18 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SLGI
Version: 1.48.0
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_1.48.0.tar.gz
StartedAt: 2020-10-17 05:26:30 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:31:12 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 281.1 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_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SLGI.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.48.0’
* 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        21.761  1.265  23.123
siResult-class   9.473  2.479  11.970
plot             8.972  2.377  11.372
compare          9.050  2.285  11.356
modelSLGI        8.640  2.664  11.327
normInteraction  4.972  1.201   6.180
topInteraction   4.289  1.282   5.583
* 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.



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/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)

Tests output


Example timings

SLGI.Rcheck/SLGI-Ex.timings

nameusersystemelapsed
Atong0.0350.0100.045
AtongFnDomain3.6390.1023.743
AtongPair0.7200.0160.737
SDL0.0060.0030.011
SGA0.0070.0030.010
SGD.SL0.1500.0050.155
TFmat0.1090.0050.114
byComplex0.3680.0460.415
comemberIn0.6270.0560.686
compare 9.050 2.28511.356
congruence0.0020.0000.002
createSquareMatrix0.0650.0130.077
domainDist2.9430.0282.972
essglist0.0170.0180.036
getInteraction0.0030.0010.004
getSharedDomains0.0180.0020.020
getSharedInteraction0.0030.0010.003
getTestedPairs0.0160.0020.018
getUniquePairs0.0210.0030.024
gi20050.2870.0150.303
gi20070.3790.0260.406
gi2Interactome0.0010.0000.001
hyperG0.0080.0010.009
iSummary21.761 1.26523.123
modelSLGI 8.640 2.66411.327
normInteraction4.9721.2016.180
plot 8.972 2.37711.372
seqMatcherAlign0.0000.0010.001
sharedBy3.0520.0293.083
sharedInt0.0040.0010.005
siResult-class 9.473 2.47911.970
test2Interact0.0040.0010.005
topInteraction4.2891.2825.583
twoWayTable4.4850.0454.542
withinComplex0.4220.0310.452