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This page was generated on 2022-01-26 11:12:33 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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 merida1


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? here 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 1812/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SLGI 1.55.1  (landing page)
Nolwenn Le Meur
Snapshot Date: 2022-01-25 13:55:17 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/SLGI
git_branch: master
git_last_commit: dc93f14
git_last_commit_date: 2022-01-10 10:27:08 -0500 (Mon, 10 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  NO, package depends on 'ScISI' which is not available
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'ScISI' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'ScISI' which is not available

Summary

Package: SLGI
Version: 1.55.1
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_1.55.1.tar.gz
StartedAt: 2022-01-26 05:57:16 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 06:02:55 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 339.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SLGI.Rcheck
Warnings: 1

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_1.55.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/SLGI.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.55.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SLGI’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor
  Warning: Package 'ScISI' is deprecated and will be removed from Bioconductor
  Warning: Package 'SLGI' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/SLGI.Rcheck/00install.out’ for details.
* 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        25.580  1.640  27.313
compare         10.431  2.675  13.133
plot            10.326  2.491  12.840
siResult-class  10.113  2.559  12.706
modelSLGI        9.103  2.549  11.681
topInteraction   5.618  1.260   6.885
normInteraction  4.522  1.179   5.707
* 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘SLGI’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: Package 'RpsiXML' is deprecated and will be removed from Bioconductor
  version 3.16 
2: Package 'ScISI' is deprecated and will be removed from Bioconductor
  version 3.16 
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
Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor
  version 3.16
Warning: Package 'ScISI' is deprecated and will be removed from Bioconductor
  version 3.16
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
Warning: Package 'SLGI' is deprecated and will be removed from Bioconductor
  version 3.16
** testing if installed package can be loaded from final location
Warning: Package 'RpsiXML' is deprecated and will be removed from Bioconductor
  version 3.16
Warning: Package 'ScISI' is deprecated and will be removed from Bioconductor
  version 3.16
No methods found in package ‘BiocGenerics’ for request: ‘plot’ when loading ‘SLGI’
Warning: Package 'SLGI' is deprecated and will be removed from Bioconductor
  version 3.16
** testing if installed package keeps a record of temporary installation path
* DONE (SLGI)

Tests output


Example timings

SLGI.Rcheck/SLGI-Ex.timings

nameusersystemelapsed
Atong0.0120.0030.014
AtongFnDomain4.6660.1254.801
AtongPair0.1010.0070.108
SDL0.0060.0020.009
SGA0.0100.0040.013
SGD.SL0.1940.0110.206
TFmat0.1170.0080.125
byComplex1.1350.0421.179
comemberIn0.3270.0430.372
compare10.431 2.67513.133
congruence0.0020.0000.003
createSquareMatrix0.0550.0030.058
domainDist3.2710.0493.328
essglist0.0100.0080.019
getInteraction0.0030.0000.004
getSharedDomains0.0210.0010.024
getSharedInteraction0.0020.0000.002
getTestedPairs0.0150.0010.016
getUniquePairs0.0210.0020.023
gi20050.0660.0160.081
gi20070.1720.0190.192
gi2Interactome0.0000.0000.001
hyperG0.0070.0010.007
iSummary25.580 1.64027.313
modelSLGI 9.103 2.54911.681
normInteraction4.5221.1795.707
plot10.326 2.49112.840
seqMatcherAlign000
sharedBy3.1100.0263.140
sharedInt0.0040.0010.003
siResult-class10.113 2.55912.706
test2Interact0.0040.0000.004
topInteraction5.6181.2606.885
twoWayTable4.4270.0444.474
withinComplex0.9440.0661.011