Nolwenn Le Meur
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SLGI |
| Branch: RELEASE_3_9 |
| Last Commit: 02bddcc |
| Last Changed Date: 2019-05-02 11:53:09 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:46:47 -0400 (Wed, 16 Oct 2019).
| Package 1539/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SLGI 1.44.0 Nolwenn Le Meur
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: SLGI |
| Version: 1.44.0 |
| 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_1.44.0.tar.gz |
| StartedAt: 2019-10-16 06:58:18 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:05:26 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 427.7 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_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SLGI.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.44.0’
* 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
siResult-class 20.796 14.959 35.756
plot 19.916 14.906 34.823
iSummary 27.735 6.745 34.483
modelSLGI 19.109 15.055 34.163
compare 20.524 13.287 33.867
topInteraction 9.861 6.241 16.103
normInteraction 8.629 7.255 15.885
twoWayTable 5.283 0.267 5.550
* 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-3.9-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/3.6/Resources/library’ * installing *source* package ‘SLGI’ ... ** using staged installation ** 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 from temporary location 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’ ** testing if installed package can be loaded from final location 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’ ** testing if installed package keeps a record of temporary installation path * DONE (SLGI)
SLGI.Rcheck/SLGI-Ex.timings
| name | user | system | elapsed | |
| Atong | 0.035 | 0.014 | 0.049 | |
| AtongFnDomain | 4.194 | 0.243 | 4.437 | |
| AtongPair | 0.769 | 0.066 | 0.835 | |
| SDL | 0.008 | 0.003 | 0.012 | |
| SGA | 0.009 | 0.053 | 0.062 | |
| SGD.SL | 0.169 | 0.063 | 0.231 | |
| TFmat | 0.084 | 0.052 | 0.135 | |
| byComplex | 0.370 | 0.168 | 0.540 | |
| comemberIn | 0.723 | 0.207 | 0.933 | |
| compare | 20.524 | 13.287 | 33.867 | |
| congruence | 0.004 | 0.000 | 0.004 | |
| createSquareMatrix | 0.216 | 0.067 | 0.284 | |
| domainDist | 2.881 | 0.176 | 3.056 | |
| essglist | 0.025 | 0.019 | 0.044 | |
| getInteraction | 0.004 | 0.001 | 0.005 | |
| getSharedDomains | 0.019 | 0.002 | 0.021 | |
| getSharedInteraction | 0.003 | 0.000 | 0.002 | |
| getTestedPairs | 0.018 | 0.001 | 0.019 | |
| getUniquePairs | 0.035 | 0.003 | 0.038 | |
| gi2005 | 0.043 | 0.055 | 0.099 | |
| gi2007 | 0.836 | 0.068 | 0.903 | |
| gi2Interactome | 0.000 | 0.000 | 0.001 | |
| hyperG | 0.009 | 0.000 | 0.009 | |
| iSummary | 27.735 | 6.745 | 34.483 | |
| modelSLGI | 19.109 | 15.055 | 34.163 | |
| normInteraction | 8.629 | 7.255 | 15.885 | |
| plot | 19.916 | 14.906 | 34.823 | |
| seqMatcherAlign | 0.001 | 0.001 | 0.001 | |
| sharedBy | 3.605 | 0.197 | 3.803 | |
| sharedInt | 0.006 | 0.000 | 0.006 | |
| siResult-class | 20.796 | 14.959 | 35.756 | |
| test2Interact | 0.006 | 0.001 | 0.006 | |
| topInteraction | 9.861 | 6.241 | 16.103 | |
| twoWayTable | 5.283 | 0.267 | 5.550 | |
| withinComplex | 0.628 | 0.189 | 0.818 | |