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CHECK report for SLGI on malbec1

This page was generated on 2018-04-12 13:08:13 -0400 (Thu, 12 Apr 2018).

Package 1310/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SLGI 1.38.0
Nolwenn Le Meur
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/SLGI
Branch: RELEASE_3_6
Last Commit: 958ff28
Last Changed Date: 2017-10-30 12:39:22 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SLGI
Version: 1.38.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.38.0.tar.gz
StartedAt: 2018-04-12 03:00:23 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:03:19 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 176.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SLGI.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SLGI_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SLGI.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.38.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary       17.452  0.044  17.503
siResult-class 10.464  0.008  10.479
compare         9.712  0.040   9.756
plot            9.424  0.004   9.432
modelSLGI       8.012  0.152   8.167
topInteraction  5.504  0.008   5.515
* 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-3.6-bioc/meat/SLGI.Rcheck/00check.log’
for details.



Installation output

SLGI.Rcheck/00install.out

* installing *source* package ‘SLGI’ ...
** R
** data
** inst
** preparing 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
Atong0.0160.0040.020
AtongFnDomain3.4200.0723.493
AtongPair0.4920.0040.496
SDL0.0040.0000.004
SGA0.0080.0000.005
SGD.SL0.1080.0040.112
TFmat0.0640.0040.068
byComplex0.1680.0120.183
comemberIn0.4600.0360.498
compare9.7120.0409.756
congruence0.0000.0000.002
createSquareMatrix0.1120.0160.129
domainDist1.9560.0321.991
essglist0.0080.0000.008
getInteraction0.0000.0000.002
getSharedDomains0.0080.0000.010
getSharedInteraction0.0120.0040.016
getTestedPairs0.0040.0040.010
getUniquePairs0.0520.0080.061
gi20050.0440.0000.042
gi20070.1120.0040.117
gi2Interactome0.0040.0000.001
hyperG0.0040.0000.006
iSummary17.452 0.04417.503
modelSLGI8.0120.1528.167
normInteraction4.1160.0964.213
plot9.4240.0049.432
seqMatcherAlign0.0000.0000.001
sharedBy2.2160.0122.228
sharedInt0.0040.0000.002
siResult-class10.464 0.00810.479
test2Interact0.0040.0000.003
topInteraction5.5040.0085.515
twoWayTable3.4480.0083.459
withinComplex0.7760.0120.791