Nolwenn Le Meur
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/SLGI |
| Branch: RELEASE_3_7 |
| Last Commit: 52bd395 |
| Last Changed Date: 2018-04-30 10:35:08 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:47:34 -0400 (Wed, 17 Oct 2018).
| Package 1388/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SLGI 1.40.0 Nolwenn Le Meur
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: SLGI |
| Version: 1.40.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SLGI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SLGI_1.40.0.tar.gz |
| StartedAt: 2018-10-17 00:08:38 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:13:12 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 273.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SLGI.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SLGI.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SLGI_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SLGI.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SLGI/DESCRIPTION’ ... OK
* this is package ‘SLGI’ version ‘1.40.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
iSummary 23.592 3.604 27.437
plot 14.687 7.878 22.802
siResult-class 14.624 7.663 22.499
modelSLGI 12.428 7.710 20.303
compare 12.560 6.782 19.501
topInteraction 6.994 3.531 10.597
normInteraction 5.939 3.781 9.809
* 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-3.7-bioc/meat/SLGI.Rcheck/00check.log’
for details.
SLGI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SLGI ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘SLGI’ ... ** 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 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’ * DONE (SLGI)
SLGI.Rcheck/SLGI-Ex.timings
| name | user | system | elapsed | |
| Atong | 0.019 | 0.005 | 0.025 | |
| AtongFnDomain | 2.948 | 0.099 | 3.063 | |
| AtongPair | 0.067 | 0.041 | 0.110 | |
| SDL | 0.006 | 0.002 | 0.007 | |
| SGA | 0.010 | 0.032 | 0.042 | |
| SGD.SL | 0.253 | 0.038 | 0.293 | |
| TFmat | 0.073 | 0.037 | 0.112 | |
| byComplex | 0.646 | 0.086 | 0.734 | |
| comemberIn | 0.459 | 0.096 | 0.555 | |
| compare | 12.560 | 6.782 | 19.501 | |
| congruence | 0.004 | 0.000 | 0.005 | |
| createSquareMatrix | 0.117 | 0.041 | 0.157 | |
| domainDist | 2.956 | 0.090 | 3.082 | |
| essglist | 0.016 | 0.007 | 0.023 | |
| getInteraction | 0.004 | 0.000 | 0.004 | |
| getSharedDomains | 0.020 | 0.001 | 0.022 | |
| getSharedInteraction | 0.004 | 0.000 | 0.004 | |
| getTestedPairs | 0.016 | 0.001 | 0.017 | |
| getUniquePairs | 0.027 | 0.002 | 0.029 | |
| gi2005 | 0.042 | 0.038 | 0.081 | |
| gi2007 | 0.140 | 0.039 | 0.178 | |
| gi2Interactome | 0.004 | 0.000 | 0.004 | |
| hyperG | 0.009 | 0.000 | 0.009 | |
| iSummary | 23.592 | 3.604 | 27.437 | |
| modelSLGI | 12.428 | 7.710 | 20.303 | |
| normInteraction | 5.939 | 3.781 | 9.809 | |
| plot | 14.687 | 7.878 | 22.802 | |
| seqMatcherAlign | 0.002 | 0.000 | 0.002 | |
| sharedBy | 2.765 | 0.087 | 2.866 | |
| sharedInt | 0.006 | 0.000 | 0.006 | |
| siResult-class | 14.624 | 7.663 | 22.499 | |
| test2Interact | 0.006 | 0.000 | 0.007 | |
| topInteraction | 6.994 | 3.531 | 10.597 | |
| twoWayTable | 4.186 | 0.144 | 4.354 | |
| withinComplex | 0.347 | 0.046 | 0.397 | |