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 13:20:54 -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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SLGI_1.56.0.tar.gz |
| StartedAt: 2022-10-18 21:53:39 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 21:56:50 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 191.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SLGI.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SLGI_1.56.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/SLGI.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.56.0’
* 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 ‘/home/biocbuild/bbs-3.15-bioc/meat/SLGI.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 10.4Mb
sub-directories of 1Mb or more:
data 4.3Mb
extdata 5.7Mb
* 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 (user + system) or elapsed time > 5s
user system elapsed
iSummary 11.605 0.304 11.909
siResult-class 7.818 0.049 7.868
plot 7.028 0.084 7.111
modelSLGI 6.626 0.176 6.802
compare 6.207 0.180 6.387
* 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
‘/home/biocbuild/bbs-3.15-bioc/meat/SLGI.Rcheck/00check.log’
for details.
SLGI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL SLGI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 | 0.009 | 0.000 | 0.009 | |
| AtongFnDomain | 3.051 | 0.120 | 3.171 | |
| AtongPair | 0.037 | 0.020 | 0.058 | |
| SDL | 0.005 | 0.000 | 0.005 | |
| SGA | 0.006 | 0.000 | 0.006 | |
| SGD.SL | 0.129 | 0.000 | 0.129 | |
| TFmat | 0.048 | 0.016 | 0.064 | |
| byComplex | 0.810 | 0.052 | 0.862 | |
| comemberIn | 0.566 | 0.024 | 0.591 | |
| compare | 6.207 | 0.180 | 6.387 | |
| congruence | 0.003 | 0.000 | 0.003 | |
| createSquareMatrix | 0.044 | 0.028 | 0.071 | |
| domainDist | 1.749 | 0.080 | 1.829 | |
| essglist | 0.013 | 0.004 | 0.016 | |
| getInteraction | 0.000 | 0.003 | 0.003 | |
| getSharedDomains | 0.016 | 0.000 | 0.016 | |
| getSharedInteraction | 0.002 | 0.000 | 0.002 | |
| getTestedPairs | 0.009 | 0.000 | 0.009 | |
| getUniquePairs | 0.010 | 0.003 | 0.013 | |
| gi2005 | 0.036 | 0.004 | 0.040 | |
| gi2007 | 0.100 | 0.008 | 0.108 | |
| gi2Interactome | 0.000 | 0.000 | 0.001 | |
| hyperG | 0.002 | 0.004 | 0.006 | |
| iSummary | 11.605 | 0.304 | 11.909 | |
| modelSLGI | 6.626 | 0.176 | 6.802 | |
| normInteraction | 4.146 | 0.040 | 4.187 | |
| plot | 7.028 | 0.084 | 7.111 | |
| seqMatcherAlign | 0.001 | 0.000 | 0.000 | |
| sharedBy | 1.96 | 0.04 | 2.00 | |
| sharedInt | 0.002 | 0.002 | 0.003 | |
| siResult-class | 7.818 | 0.049 | 7.868 | |
| test2Interact | 0.002 | 0.000 | 0.003 | |
| topInteraction | 3.637 | 0.052 | 3.689 | |
| twoWayTable | 3.207 | 0.048 | 3.255 | |
| withinComplex | 0.272 | 0.016 | 0.289 | |