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 13:00:41 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Onassis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Onassis_1.6.1.tar.gz |
| StartedAt: 2019-10-16 05:13:53 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:17:29 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 215.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Onassis.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:Onassis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Onassis_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Onassis.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 ‘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 23.948 6.752 10.019
compare 17.794 2.563 14.470
annotate 13.203 2.308 4.040
sim 8.167 1.121 5.627
collapse 7.433 1.493 5.991
mergeonassis 5.446 1.299 2.316
annotateDF 4.620 1.028 1.459
* 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/Onassis.Rcheck/00check.log’
for details.
Onassis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Onassis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 | 0.001 | 0.002 | |
| CMdictionary | 0.001 | 0.001 | 0.001 | |
| CMoptions-class | 0.010 | 0.002 | 0.012 | |
| CMoptions | 0.005 | 0.001 | 0.005 | |
| CaseMatch | 0.015 | 0.003 | 0.018 | |
| EntityFinder-class | 0.092 | 0.035 | 0.089 | |
| EntityFinder | 23.948 | 6.752 | 10.019 | |
| FindAllMatches | 0.040 | 0.005 | 0.025 | |
| GEOHandler-functions | 0.000 | 0.001 | 0.001 | |
| Onassis | 0.012 | 0.000 | 0.002 | |
| OrderIndependentLookup | 0.039 | 0.002 | 0.023 | |
| SearchStrategy | 0.038 | 0.002 | 0.020 | |
| Similarity-class | 0.051 | 0.004 | 0.018 | |
| Similarity | 2.704 | 0.478 | 1.159 | |
| Stemmer | 0.038 | 0.002 | 0.022 | |
| StopWords | 0.011 | 0.001 | 0.012 | |
| SynonymType | 0.012 | 0.001 | 0.013 | |
| annotate | 13.203 | 2.308 | 4.040 | |
| annotateDF | 4.620 | 1.028 | 1.459 | |
| collapse | 7.433 | 1.493 | 5.991 | |
| compare | 17.794 | 2.563 | 14.470 | |
| dictInfo | 0.002 | 0.001 | 0.003 | |
| dictRef | 0.005 | 0.001 | 0.006 | |
| dictTypes | 0.005 | 0.000 | 0.005 | |
| dict_location | 0.002 | 0.000 | 0.002 | |
| dictionary | 0.002 | 0.000 | 0.002 | |
| entities | 0.004 | 0.000 | 0.004 | |
| experiment_types | 0.001 | 0.000 | 0.002 | |
| filterTerms | 0.089 | 0.001 | 0.090 | |
| filterconcepts | 3.236 | 0.394 | 1.244 | |
| findEntities | 1.710 | 0.630 | 1.156 | |
| findHealthy | 0.121 | 0.001 | 0.088 | |
| getGEOMetadata | 0.001 | 0.000 | 0.002 | |
| groupConfig | 0.182 | 0.003 | 0.095 | |
| groupsim | 0.579 | 0.016 | 0.474 | |
| groupwiseConfigRef | 0.091 | 0.001 | 0.091 | |
| icConfig | 0.002 | 0.000 | 0.002 | |
| listCMOptions | 0.002 | 0.001 | 0.003 | |
| listSimilarities | 0.093 | 0.001 | 0.094 | |
| mergeonassis | 5.446 | 1.299 | 2.316 | |
| multisim | 3.854 | 1.045 | 2.966 | |
| ontology | 0.063 | 0.003 | 0.020 | |
| organism_types | 0.001 | 0.000 | 0.002 | |
| pairsim | 0.317 | 0.004 | 0.218 | |
| pairwiseConfig | 0.504 | 0.013 | 0.250 | |
| pairwiseConfigRef | 0.100 | 0.001 | 0.101 | |
| paramValueIndex | 0.023 | 0.003 | 0.025 | |
| samplesim | 2.250 | 0.582 | 1.609 | |
| scores | 0.002 | 0.000 | 0.001 | |
| sim | 8.167 | 1.121 | 5.627 | |
| simil | 0.000 | 0.001 | 0.001 | |
| similarityInstance | 0.002 | 0.001 | 0.003 | |
| typeSystemRef | 0.018 | 0.001 | 0.019 | |