Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:28:27 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the Onassis package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1261/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Onassis 1.12.0 (landing page) Eugenia Galeota
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: Onassis |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Onassis_1.12.0.tar.gz |
StartedAt: 2021-05-06 04:10:36 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 04:13:03 -0400 (Thu, 06 May 2021) |
EllapsedTime: 146.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Onassis.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Onassis_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/Onassis.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Onassis/DESCRIPTION’ ... OK * this is package ‘Onassis’ version ‘1.12.0’ * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Onassis’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘data.table’ 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 Namespaces in Imports field not imported from: ‘DT’ ‘Rtsne’ ‘clusteval’ ‘dendextend’ ‘ggfortify’ ‘ggplot2’ ‘knitr’ ‘stats’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE annotate,data.frame-character-character: no visible binding for global variable ‘sample_id’ annotateDF,EntityFinder-data.frame-character-CMoptions: no visible binding for global variable ‘ID’ annotateDF,EntityFinder-data.frame-character-CMoptions: no visible binding for global variable ‘NEW’ collapse,Onassis: no visible global function definition for ‘as.dist’ collapse,Onassis: no visible global function definition for ‘hclust’ collapse,Onassis: no visible global function definition for ‘cutree’ compare,Onassis: no visible global function definition for ‘p.adjust’ Undefined global functions or variables: ID NEW as.dist cutree hclust p.adjust sample_id Consider adding importFrom("stats", "as.dist", "cutree", "hclust", "p.adjust") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed EntityFinder 17.116 0.564 6.078 compare 11.056 0.264 8.986 sim 5.740 0.140 3.901 annotate 5.556 0.164 2.324 collapse 5.188 0.144 3.321 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.12-bioc/meat/Onassis.Rcheck/00check.log’ for details.
Onassis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Onassis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘Onassis’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Onassis)
Onassis.Rcheck/Onassis-Ex.timings
name | user | system | elapsed | |
CMdictionary-class | 0.000 | 0.000 | 0.001 | |
CMdictionary | 0 | 0 | 0 | |
CMoptions-class | 0.004 | 0.004 | 0.017 | |
CMoptions | 0.000 | 0.004 | 0.004 | |
CaseMatch | 0.012 | 0.000 | 0.012 | |
EntityFinder-class | 0.068 | 0.016 | 0.166 | |
EntityFinder | 17.116 | 0.564 | 6.078 | |
FindAllMatches | 0.036 | 0.000 | 0.018 | |
GEOHandler-functions | 0.000 | 0.000 | 0.001 | |
Onassis | 0.004 | 0.000 | 0.001 | |
OrderIndependentLookup | 0.040 | 0.000 | 0.019 | |
SearchStrategy | 0.040 | 0.000 | 0.018 | |
Similarity-class | 0.204 | 0.008 | 0.188 | |
Similarity | 1.132 | 0.056 | 0.833 | |
Stemmer | 0.02 | 0.00 | 0.02 | |
StopWords | 0.020 | 0.000 | 0.019 | |
SynonymType | 0.02 | 0.00 | 0.02 | |
annotate | 5.556 | 0.164 | 2.324 | |
annotateDF | 1.984 | 0.084 | 0.673 | |
collapse | 5.188 | 0.144 | 3.321 | |
compare | 11.056 | 0.264 | 8.986 | |
dictInfo | 0.000 | 0.000 | 0.001 | |
dictRef | 0.004 | 0.000 | 0.003 | |
dictTypes | 0.000 | 0.000 | 0.002 | |
dict_location | 0.004 | 0.000 | 0.000 | |
dictionary | 0.000 | 0.000 | 0.001 | |
entities | 0.004 | 0.000 | 0.001 | |
experiment_types | 0 | 0 | 0 | |
filterTerms | 0.044 | 0.000 | 0.047 | |
filterconcepts | 0.964 | 0.064 | 0.544 | |
findEntities | 1.112 | 0.056 | 0.471 | |
findHealthy | 0.084 | 0.000 | 0.056 | |
getGEOMetadata | 0.000 | 0.000 | 0.001 | |
groupConfig | 0.164 | 0.000 | 0.084 | |
groupsim | 0.412 | 0.000 | 0.329 | |
groupwiseConfigRef | 0.068 | 0.000 | 0.046 | |
icConfig | 0.000 | 0.000 | 0.001 | |
listCMOptions | 0.000 | 0.000 | 0.002 | |
listSimilarities | 0.064 | 0.000 | 0.065 | |
mergeonassis | 2.392 | 0.104 | 0.911 | |
multisim | 2.376 | 0.112 | 1.188 | |
ontology | 0.048 | 0.000 | 0.014 | |
organism_types | 0 | 0 | 0 | |
pairsim | 0.228 | 0.004 | 0.147 | |
pairwiseConfig | 0.328 | 0.000 | 0.150 | |
pairwiseConfigRef | 0.056 | 0.000 | 0.057 | |
paramValueIndex | 0.012 | 0.000 | 0.011 | |
samplesim | 1.176 | 0.048 | 0.661 | |
scores | 0 | 0 | 0 | |
sim | 5.740 | 0.140 | 3.901 | |
simil | 0.004 | 0.000 | 0.001 | |
similarityInstance | 0.000 | 0.000 | 0.002 | |
typeSystemRef | 0.012 | 0.000 | 0.012 | |