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CHECK report for SLGI on malbec2

This page was generated on 2018-10-17 08:22:16 -0400 (Wed, 17 Oct 2018).

Package 1388/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SLGI 1.40.0
Nolwenn Le Meur
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SLGI
Branch: RELEASE_3_7
Last Commit: 52bd395
Last Changed Date: 2018-04-30 10:35:08 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SLGI
Version: 1.40.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SLGI_1.40.0.tar.gz
StartedAt: 2018-10-16 03:50:24 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 03:53:03 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 158.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SLGI.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SLGI_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/SLGI.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.40.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary       14.584  0.080  14.675
siResult-class  9.664  0.056   9.727
compare         8.724  0.072   8.801
modelSLGI       8.664  0.048   8.718
plot            7.772  0.000   7.781
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/SLGI.Rcheck/00check.log’
for details.



Installation output

SLGI.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL SLGI
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘SLGI’ ...
** 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
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’
* DONE (SLGI)

Tests output


Example timings

SLGI.Rcheck/SLGI-Ex.timings

nameusersystemelapsed
Atong0.0320.0000.035
AtongFnDomain2.7320.0442.776
AtongPair0.1280.0080.136
SDL0.3880.0040.395
SGA0.0000.0040.006
SGD.SL0.1120.0040.115
TFmat0.0600.0080.067
byComplex0.1480.0120.159
comemberIn0.4960.0240.517
compare8.7240.0728.801
congruence0.0000.0000.002
createSquareMatrix0.0520.0120.065
domainDist1.7920.0281.820
essglist0.0080.0000.008
getInteraction0.0040.0000.002
getSharedDomains0.0120.0000.011
getSharedInteraction0.0040.0000.001
getTestedPairs0.0080.0000.010
getUniquePairs0.0080.0040.014
gi20050.0400.0040.042
gi20070.2280.0040.232
gi2Interactome0.0040.0000.001
hyperG0.0040.0000.006
iSummary14.584 0.08014.675
modelSLGI8.6640.0488.718
normInteraction3.9960.0003.999
plot7.7720.0007.781
seqMatcherAlign0.0000.0000.001
sharedBy1.7640.0281.794
sharedInt0.0000.0000.003
siResult-class9.6640.0569.727
test2Interact0.0040.0000.003
topInteraction4.3040.0044.312
twoWayTable2.6160.0282.642
withinComplex0.4440.0080.453