Eugenia Galeota
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Onassis |
| Branch: RELEASE_3_9 |
| Last Commit: 8f2beb2 |
| Last Changed Date: 2019-10-01 06:15:22 -0400 (Tue, 01 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:11:44 -0400 (Wed, 16 Oct 2019).
| Package 1136/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Onassis 1.6.1 Eugenia Galeota
| 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: Onassis |
| Version: 1.6.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Onassis_1.6.1.tar.gz |
| StartedAt: 2019-10-16 03:39:38 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:41:59 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 140.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Onassis.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Onassis_1.6.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Onassis.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 ‘Onassis/DESCRIPTION’ ... OK
* this is package ‘Onassis’ version ‘1.6.1’
* 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 ... OK
* 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’ ‘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 or elapsed time > 5s
user system elapsed
EntityFinder 16.910 0.646 7.360
compare 11.935 0.220 9.003
collapse 7.370 0.213 2.863
annotate 6.746 0.194 2.151
sim 6.136 0.126 3.576
* 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/Onassis.Rcheck/00check.log’
for details.
Onassis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Onassis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 | 0.001 | 0.000 | 0.001 | |
| CMdictionary | 0 | 0 | 0 | |
| CMoptions-class | 0.002 | 0.004 | 0.017 | |
| CMoptions | 0.003 | 0.000 | 0.003 | |
| CaseMatch | 0.01 | 0.00 | 0.01 | |
| EntityFinder-class | 0.073 | 0.012 | 0.175 | |
| EntityFinder | 16.910 | 0.646 | 7.360 | |
| FindAllMatches | 0.045 | 0.004 | 0.017 | |
| GEOHandler-functions | 0.001 | 0.000 | 0.000 | |
| Onassis | 0.001 | 0.000 | 0.001 | |
| OrderIndependentLookup | 0.048 | 0.004 | 0.020 | |
| SearchStrategy | 0.033 | 0.000 | 0.017 | |
| Similarity-class | 0.060 | 0.001 | 0.029 | |
| Similarity | 2.230 | 0.076 | 0.785 | |
| Stemmer | 0.018 | 0.000 | 0.018 | |
| StopWords | 0.018 | 0.000 | 0.017 | |
| SynonymType | 0.018 | 0.000 | 0.018 | |
| annotate | 6.746 | 0.194 | 2.151 | |
| annotateDF | 2.011 | 0.127 | 0.709 | |
| collapse | 7.370 | 0.213 | 2.863 | |
| compare | 11.935 | 0.220 | 9.003 | |
| dictInfo | 0.001 | 0.000 | 0.002 | |
| dictRef | 0.004 | 0.000 | 0.004 | |
| dictTypes | 0.000 | 0.003 | 0.003 | |
| dict_location | 0.001 | 0.000 | 0.001 | |
| dictionary | 0.001 | 0.000 | 0.001 | |
| entities | 0.002 | 0.000 | 0.003 | |
| experiment_types | 0.001 | 0.000 | 0.000 | |
| filterTerms | 0.077 | 0.000 | 0.076 | |
| filterconcepts | 1.679 | 0.077 | 0.643 | |
| findEntities | 0.824 | 0.032 | 0.397 | |
| findHealthy | 0.092 | 0.000 | 0.046 | |
| getGEOMetadata | 0 | 0 | 0 | |
| groupConfig | 0.099 | 0.000 | 0.049 | |
| groupsim | 0.302 | 0.004 | 0.195 | |
| groupwiseConfigRef | 0.04 | 0.00 | 0.04 | |
| icConfig | 0.001 | 0.000 | 0.000 | |
| listCMOptions | 0.002 | 0.000 | 0.001 | |
| listSimilarities | 0.039 | 0.000 | 0.039 | |
| mergeonassis | 3.156 | 0.111 | 1.100 | |
| multisim | 2.503 | 0.132 | 1.489 | |
| ontology | 0.052 | 0.003 | 0.013 | |
| organism_types | 0.002 | 0.000 | 0.001 | |
| pairsim | 0.228 | 0.000 | 0.145 | |
| pairwiseConfig | 0.327 | 0.000 | 0.115 | |
| pairwiseConfigRef | 0.067 | 0.000 | 0.067 | |
| paramValueIndex | 0.013 | 0.000 | 0.013 | |
| samplesim | 1.626 | 0.082 | 0.776 | |
| scores | 0.001 | 0.000 | 0.001 | |
| sim | 6.136 | 0.126 | 3.576 | |
| simil | 0.000 | 0.000 | 0.001 | |
| similarityInstance | 0.002 | 0.000 | 0.002 | |
| typeSystemRef | 0.014 | 0.000 | 0.014 | |