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 11:56:45 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SLGI_1.44.0.tar.gz |
| StartedAt: 2019-10-16 05:06:31 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:10:15 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 223.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SLGI.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SLGI.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SLGI_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SLGI.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.44.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
iSummary 19.082 0.227 19.448
siResult-class 12.232 0.008 12.239
compare 11.753 0.096 11.848
modelSLGI 11.214 0.020 11.258
plot 9.196 0.012 9.209
topInteraction 6.529 0.008 6.537
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/SLGI.Rcheck/00check.log’
for details.
SLGI.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SLGI ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 | 0.023 | 0.008 | 0.031 | |
| AtongFnDomain | 3.696 | 0.060 | 3.760 | |
| AtongPair | 0.508 | 0.004 | 0.512 | |
| SDL | 0.000 | 0.004 | 0.004 | |
| SGA | 0.005 | 0.000 | 0.006 | |
| SGD.SL | 0.111 | 0.000 | 0.111 | |
| TFmat | 0.067 | 0.004 | 0.072 | |
| byComplex | 0.181 | 0.024 | 0.204 | |
| comemberIn | 0.534 | 0.024 | 0.558 | |
| compare | 11.753 | 0.096 | 11.848 | |
| congruence | 0.002 | 0.000 | 0.002 | |
| createSquareMatrix | 0.302 | 0.000 | 0.301 | |
| domainDist | 2.011 | 0.048 | 2.059 | |
| essglist | 0.005 | 0.004 | 0.008 | |
| getInteraction | 0.001 | 0.000 | 0.002 | |
| getSharedDomains | 0.011 | 0.000 | 0.011 | |
| getSharedInteraction | 0.001 | 0.000 | 0.002 | |
| getTestedPairs | 0.009 | 0.000 | 0.010 | |
| getUniquePairs | 0.014 | 0.000 | 0.014 | |
| gi2005 | 0.264 | 0.004 | 0.267 | |
| gi2007 | 0.112 | 0.000 | 0.112 | |
| gi2Interactome | 0 | 0 | 0 | |
| hyperG | 0.002 | 0.004 | 0.005 | |
| iSummary | 19.082 | 0.227 | 19.448 | |
| modelSLGI | 11.214 | 0.020 | 11.258 | |
| normInteraction | 4.536 | 0.004 | 4.540 | |
| plot | 9.196 | 0.012 | 9.209 | |
| seqMatcherAlign | 0.001 | 0.000 | 0.000 | |
| sharedBy | 2.973 | 0.056 | 3.030 | |
| sharedInt | 0.003 | 0.000 | 0.002 | |
| siResult-class | 12.232 | 0.008 | 12.239 | |
| test2Interact | 0.004 | 0.000 | 0.003 | |
| topInteraction | 6.529 | 0.008 | 6.537 | |
| twoWayTable | 4.360 | 0.048 | 4.423 | |
| withinComplex | 1.121 | 0.004 | 1.124 | |