Nolwenn Le Meur
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SLGI |
| Branch: RELEASE_3_8 |
| Last Commit: 78f38a7 |
| Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:54:46 -0400 (Tue, 16 Apr 2019).
| Package 1464/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SLGI 1.42.0 Nolwenn Le Meur
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: SLGI |
| Version: 1.42.0 |
| 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_1.42.0.tar.gz |
| StartedAt: 2019-04-16 02:51:56 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:56:43 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 287.2 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_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SLGI.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.42.0’
* 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 25.963 3.681 30.017
siResult-class 15.631 7.533 23.376
plot 14.259 8.168 22.621
compare 13.730 7.354 21.319
modelSLGI 13.156 7.878 21.221
topInteraction 7.166 3.560 10.819
normInteraction 5.777 3.796 9.671
* 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-3.8-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 | 0.048 | 0.010 | 0.060 | |
| AtongFnDomain | 3.546 | 0.121 | 3.715 | |
| AtongPair | 0.064 | 0.044 | 0.108 | |
| SDL | 0.004 | 0.002 | 0.006 | |
| SGA | 0.006 | 0.039 | 0.045 | |
| SGD.SL | 0.317 | 0.042 | 0.361 | |
| TFmat | 0.081 | 0.044 | 0.125 | |
| byComplex | 0.670 | 0.099 | 0.775 | |
| comemberIn | 0.472 | 0.102 | 0.576 | |
| compare | 13.730 | 7.354 | 21.319 | |
| congruence | 0.003 | 0.000 | 0.003 | |
| createSquareMatrix | 0.103 | 0.033 | 0.139 | |
| domainDist | 3.110 | 0.092 | 3.246 | |
| essglist | 0.017 | 0.009 | 0.026 | |
| getInteraction | 0.004 | 0.000 | 0.004 | |
| getSharedDomains | 0.016 | 0.001 | 0.016 | |
| getSharedInteraction | 0.002 | 0.001 | 0.003 | |
| getTestedPairs | 0.016 | 0.001 | 0.017 | |
| getUniquePairs | 0.027 | 0.001 | 0.029 | |
| gi2005 | 0.055 | 0.033 | 0.088 | |
| gi2007 | 0.137 | 0.035 | 0.174 | |
| gi2Interactome | 0.001 | 0.000 | 0.000 | |
| hyperG | 0.005 | 0.000 | 0.006 | |
| iSummary | 25.963 | 3.681 | 30.017 | |
| modelSLGI | 13.156 | 7.878 | 21.221 | |
| normInteraction | 5.777 | 3.796 | 9.671 | |
| plot | 14.259 | 8.168 | 22.621 | |
| seqMatcherAlign | 0.000 | 0.000 | 0.001 | |
| sharedBy | 2.691 | 0.095 | 2.817 | |
| sharedInt | 0.003 | 0.001 | 0.003 | |
| siResult-class | 15.631 | 7.533 | 23.376 | |
| test2Interact | 0.002 | 0.000 | 0.003 | |
| topInteraction | 7.166 | 3.560 | 10.819 | |
| twoWayTable | 3.905 | 0.152 | 4.085 | |
| withinComplex | 0.817 | 0.064 | 0.893 | |