Eugenia Galeota
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/Onassis |
| Branch: RELEASE_3_12 |
| Last Commit: f8644e7 |
| Last Changed Date: 2020-10-27 11:26:32 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:37 -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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Onassis.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Onassis_1.12.0.tar.gz |
| StartedAt: 2021-05-06 05:13:50 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:17:31 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 220.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Onassis.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Onassis.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Onassis_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Onassis.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 16.39 1.58 33.14
compare 10.03 0.45 16.23
collapse 7.72 0.72 6.30
annotate 6.14 0.60 5.11
sim 5.68 0.44 6.66
multisim 2.31 0.32 6.67
mergeonassis 1.99 0.29 6.23
* 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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/Onassis.Rcheck/00check.log'
for details.
Onassis.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Onassis
###
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* installing to library 'C:/Users/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
converting help for package 'Onassis'
finding HTML links ... done
CMdictionary-class html
CMdictionary html
CMoptions-class html
CMoptions html
CaseMatch html
EntityFinder-class html
EntityFinder html
FindAllMatches html
GEOHandler-functions html
Onassis-class html
Onassis html
OrderIndependentLookup html
SearchStrategy html
Similarity-class html
Similarity html
Stemmer html
StopWords html
SynonymType html
annotate html
annotateDF html
collapse html
compare html
dictInfo html
dictRef html
dictTypes html
dict_location html
dictionary html
entities html
experiment_types html
filterTerms html
filterconcepts html
findEntities html
findHealthy html
getGEOMetadata html
groupConfig html
groupsim html
groupwiseConfigRef html
icConfig html
listCMOptions html
listSimilarities html
mergeonassis html
multisim html
ontology html
organism_types html
pairsim html
pairwiseConfig html
pairwiseConfigRef html
paramValueIndex html
samplesim html
scores html
sim html
simil html
similarityInstance html
typeSystemRef html
** 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)
Making 'packages.html' ... done
Onassis.Rcheck/Onassis-Ex.timings
| name | user | system | elapsed | |
| CMdictionary-class | 0 | 0 | 0 | |
| CMdictionary | 0 | 0 | 0 | |
| CMoptions-class | 0.01 | 0.00 | 0.02 | |
| CMoptions | 0 | 0 | 0 | |
| CaseMatch | 0.02 | 0.00 | 0.01 | |
| EntityFinder-class | 0.06 | 0.01 | 2.19 | |
| EntityFinder | 16.39 | 1.58 | 33.14 | |
| FindAllMatches | 0.02 | 0.00 | 0.02 | |
| GEOHandler-functions | 0 | 0 | 0 | |
| Onassis | 0 | 0 | 0 | |
| OrderIndependentLookup | 0.02 | 0.00 | 0.01 | |
| SearchStrategy | 0.01 | 0.00 | 0.02 | |
| Similarity-class | 0.06 | 0.00 | 0.12 | |
| Similarity | 1.14 | 0.12 | 3.60 | |
| Stemmer | 0.04 | 0.00 | 0.01 | |
| StopWords | 0.03 | 0.00 | 0.02 | |
| SynonymType | 0.03 | 0.00 | 0.03 | |
| annotate | 6.14 | 0.60 | 5.11 | |
| annotateDF | 1.76 | 0.31 | 3.48 | |
| collapse | 7.72 | 0.72 | 6.30 | |
| compare | 10.03 | 0.45 | 16.23 | |
| dictInfo | 0 | 0 | 0 | |
| dictRef | 0 | 0 | 0 | |
| dictTypes | 0 | 0 | 0 | |
| dict_location | 0 | 0 | 0 | |
| dictionary | 0 | 0 | 0 | |
| entities | 0 | 0 | 0 | |
| experiment_types | 0 | 0 | 0 | |
| filterTerms | 0.05 | 0.00 | 0.05 | |
| filterconcepts | 1.06 | 0.17 | 3.31 | |
| findEntities | 1.30 | 0.18 | 3.23 | |
| findHealthy | 0.07 | 0.01 | 0.05 | |
| getGEOMetadata | 0 | 0 | 0 | |
| groupConfig | 0.18 | 0.00 | 0.06 | |
| groupsim | 0.37 | 0.02 | 0.24 | |
| groupwiseConfigRef | 0.06 | 0.00 | 0.06 | |
| icConfig | 0 | 0 | 0 | |
| listCMOptions | 0 | 0 | 0 | |
| listSimilarities | 0.08 | 0.00 | 0.08 | |
| mergeonassis | 1.99 | 0.29 | 6.23 | |
| multisim | 2.31 | 0.32 | 6.67 | |
| ontology | 0.11 | 0.00 | 0.03 | |
| organism_types | 0 | 0 | 0 | |
| pairsim | 0.17 | 0.00 | 0.11 | |
| pairwiseConfig | 0.44 | 0.01 | 0.11 | |
| pairwiseConfigRef | 0.11 | 0.00 | 0.05 | |
| paramValueIndex | 0.01 | 0.00 | 0.02 | |
| samplesim | 1.49 | 0.17 | 3.59 | |
| scores | 0 | 0 | 0 | |
| sim | 5.68 | 0.44 | 6.66 | |
| simil | 0 | 0 | 0 | |
| similarityInstance | 0 | 0 | 0 | |
| typeSystemRef | 0 | 0 | 0 | |