Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:49 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SLGI on machv2


To the developers/maintainers of the SLGI package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SLGI.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1817/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SLGI 1.54.0  (landing page)
Nolwenn Le Meur
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/SLGI
git_branch: RELEASE_3_14
git_last_commit: b4f5841
git_last_commit_date: 2021-10-26 11:51:49 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SLGI
Version: 1.54.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SLGI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SLGI_1.54.0.tar.gz
StartedAt: 2022-04-12 18:41:28 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:46:36 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 308.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SLGI.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SLGI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SLGI_1.54.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/SLGI.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.54.0’
* 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 16.0Mb
  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       22.445  1.597  24.071
siResult-class  9.706  2.603  12.315
plot            8.759  2.398  11.166
modelSLGI       7.932  2.803  10.741
compare         7.534  2.723  10.269
topInteraction  5.005  1.096   6.106
* 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-3.14-bioc/meat/SLGI.Rcheck/00check.log’
for details.



Installation output

SLGI.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SLGI
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 ‘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 ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
** testing if installed package can be loaded from final location
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
Atong0.0350.0040.039
AtongFnDomain4.2730.1094.391
AtongPair0.1030.0100.113
SDL0.0040.0030.006
SGA0.0080.0030.010
SGD.SL0.1990.0090.209
TFmat0.1190.0090.129
byComplex1.0850.0461.133
comemberIn0.7140.0450.761
compare 7.534 2.72310.269
congruence0.0020.0000.002
createSquareMatrix0.0630.0120.076
domainDist3.1560.0263.183
essglist0.0110.0150.026
getInteraction0.0030.0000.004
getSharedDomains0.0200.0010.022
getSharedInteraction0.0010.0000.002
getTestedPairs0.0140.0020.017
getUniquePairs0.0160.0030.018
gi20050.0600.0170.076
gi20070.1650.0180.184
gi2Interactome0.0010.0010.001
hyperG0.0070.0010.008
iSummary22.445 1.59724.071
modelSLGI 7.932 2.80310.741
normInteraction3.4231.3884.816
plot 8.759 2.39811.166
seqMatcherAlign0.0010.0010.000
sharedBy3.1290.0343.169
sharedInt0.0020.0000.003
siResult-class 9.706 2.60312.315
test2Interact0.0030.0000.003
topInteraction5.0051.0966.106
twoWayTable4.6390.0404.688
withinComplex0.3340.0370.371