Nolwenn Le Meur
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/SLGI |
| git_branch: RELEASE_3_15 |
| git_last_commit: 9112980 |
| git_last_commit_date: 2022-04-26 11:00:40 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:45 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
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. |
| Package 1866/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Nolwenn Le Meur
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: SLGI |
| Version: 1.56.0 |
| 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_1.56.0.tar.gz |
| StartedAt: 2022-10-19 08:11:31 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 08:17:29 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 358.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SLGI.Rcheck |
| Warnings: 1 |
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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_1.56.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/SLGI.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.56.0’
* 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 ... 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 25.965 1.523 27.545
plot 10.716 2.584 13.318
siResult-class 10.228 2.669 12.912
modelSLGI 9.523 2.793 12.329
compare 8.692 3.114 11.849
topInteraction 5.768 1.198 6.976
normInteraction 5.348 1.054 6.408
twoWayTable 5.422 0.068 5.496
* 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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.15-bioc/meat/SLGI.Rcheck/00check.log’
for details.
SLGI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
SLGI.Rcheck/SLGI-Ex.timings
| name | user | system | elapsed | |
| Atong | 0.016 | 0.004 | 0.020 | |
| AtongFnDomain | 4.667 | 0.120 | 4.793 | |
| AtongPair | 0.107 | 0.010 | 0.118 | |
| SDL | 0.007 | 0.003 | 0.010 | |
| SGA | 0.009 | 0.003 | 0.013 | |
| SGD.SL | 0.209 | 0.010 | 0.219 | |
| TFmat | 0.117 | 0.008 | 0.125 | |
| byComplex | 1.062 | 0.041 | 1.104 | |
| comemberIn | 0.732 | 0.047 | 0.781 | |
| compare | 8.692 | 3.114 | 11.849 | |
| congruence | 0.004 | 0.001 | 0.004 | |
| createSquareMatrix | 0.084 | 0.009 | 0.094 | |
| domainDist | 3.219 | 0.053 | 3.279 | |
| essglist | 0.009 | 0.008 | 0.017 | |
| getInteraction | 0.003 | 0.000 | 0.003 | |
| getSharedDomains | 0.020 | 0.001 | 0.021 | |
| getSharedInteraction | 0.003 | 0.000 | 0.003 | |
| getTestedPairs | 0.014 | 0.001 | 0.016 | |
| getUniquePairs | 0.021 | 0.002 | 0.023 | |
| gi2005 | 0.064 | 0.020 | 0.084 | |
| gi2007 | 0.174 | 0.020 | 0.195 | |
| gi2Interactome | 0.001 | 0.001 | 0.001 | |
| hyperG | 0.006 | 0.001 | 0.007 | |
| iSummary | 25.965 | 1.523 | 27.545 | |
| modelSLGI | 9.523 | 2.793 | 12.329 | |
| normInteraction | 5.348 | 1.054 | 6.408 | |
| plot | 10.716 | 2.584 | 13.318 | |
| seqMatcherAlign | 0 | 0 | 0 | |
| sharedBy | 3.412 | 0.031 | 3.447 | |
| sharedInt | 0.004 | 0.000 | 0.005 | |
| siResult-class | 10.228 | 2.669 | 12.912 | |
| test2Interact | 0.003 | 0.000 | 0.004 | |
| topInteraction | 5.768 | 1.198 | 6.976 | |
| twoWayTable | 5.422 | 0.068 | 5.496 | |
| withinComplex | 0.325 | 0.028 | 0.353 | |