Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for SLGI on malbec2

This page was generated on 2019-04-09 11:26:12 -0400 (Tue, 09 Apr 2019).

Package 1509/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SLGI 1.43.0
Nolwenn Le Meur
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/SLGI
Branch: master
Last Commit: b796d18
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: SLGI
Version: 1.43.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SLGI_1.43.0.tar.gz
StartedAt: 2019-04-09 03:43:42 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:47:21 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 218.2 seconds
RetCode: 0
Status:  OK 
CheckDir: SLGI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SLGI_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SLGI.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.43.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary       16.552  0.236  17.349
siResult-class 11.240  0.008  11.247
compare        10.986  0.008  11.038
modelSLGI      10.369  0.020  10.392
plot            9.483  0.000   9.495
topInteraction  5.149  0.016   5.176
* 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-3.9-bioc/meat/SLGI.Rcheck/00check.log’
for details.



Installation output

SLGI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SLGI
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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
Atong0.0210.0080.029
AtongFnDomain3.7080.0643.772
AtongPair0.0630.0160.079
SDL0.0040.0000.005
SGA0.0060.0000.006
SGD.SL0.2520.0000.252
TFmat0.0650.0000.065
byComplex0.7180.0190.739
comemberIn0.4850.0040.489
compare10.986 0.00811.038
congruence0.0030.0000.003
createSquareMatrix0.3890.0080.397
domainDist3.2680.0363.356
essglist0.0040.0080.013
getInteraction0.0030.0000.003
getSharedDomains0.0170.0000.016
getSharedInteraction0.0010.0020.002
getTestedPairs0.0150.0000.015
getUniquePairs0.0230.0000.022
gi20050.0560.0040.060
gi20070.3910.0000.398
gi2Interactome0.0000.0000.001
hyperG0.0070.0000.006
iSummary16.552 0.23617.349
modelSLGI10.369 0.02010.392
normInteraction4.8580.0004.862
plot9.4830.0009.495
seqMatcherAlign000
sharedBy2.2450.0442.288
sharedInt0.0030.0000.002
siResult-class11.240 0.00811.247
test2Interact0.0030.0000.004
topInteraction5.1490.0165.176
twoWayTable3.1520.0163.172
withinComplex0.6620.0040.667