Eugenia Galeota
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Onassis |
| Branch: RELEASE_3_8 |
| Last Commit: da9876b |
| Last Changed Date: 2018-11-28 04:18:07 -0400 (Wed, 28 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:57 -0400 (Tue, 16 Apr 2019).
| Package 1087/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Onassis 1.4.5 Eugenia Galeota
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Onassis |
| Version: 1.4.5 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Onassis_1.4.5.tar.gz |
| StartedAt: 2019-04-16 01:52:11 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:54:56 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 165.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Onassis.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Onassis.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Onassis_1.4.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Onassis.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.5’
* 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’
All declared Imports should be used.
':::' call which should be '::': ‘tools:::file_path_as_absolute’
See the note in ?`:::` about the use of this operator.
* 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’
compare,Onassis: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
ID NEW p.adjust sample_id
Consider adding
importFrom("stats", "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
semanticdifference 34.312 0.828 35.149
EntityFinder 16.536 0.568 7.103
compare 9.064 0.224 6.140
sim 6.204 0.124 3.986
collapse 6.000 0.168 2.950
annotate 5.964 0.136 2.032
* 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-3.8-bioc/meat/Onassis.Rcheck/00check.log’
for details.
Onassis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Onassis ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘Onassis’ ... ** 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 * DONE (Onassis)
Onassis.Rcheck/Onassis-Ex.timings
| name | user | system | elapsed | |
| CMdictionary-class | 0.000 | 0.000 | 0.001 | |
| CMdictionary | 0.000 | 0.000 | 0.001 | |
| CMoptions-class | 0.008 | 0.000 | 0.023 | |
| CMoptions | 0.004 | 0.000 | 0.006 | |
| CaseMatch | 0.024 | 0.000 | 0.021 | |
| EntityFinder-class | 0.088 | 0.000 | 0.160 | |
| EntityFinder | 16.536 | 0.568 | 7.103 | |
| FindAllMatches | 0.036 | 0.004 | 0.019 | |
| GEOHandler-functions | 0.004 | 0.000 | 0.001 | |
| Onassis | 0.004 | 0.000 | 0.001 | |
| OrderIndependentLookup | 0.04 | 0.00 | 0.02 | |
| SearchStrategy | 0.036 | 0.004 | 0.020 | |
| Similarity-class | 0.092 | 0.004 | 0.125 | |
| Similarity | 2.632 | 0.072 | 1.042 | |
| Stemmer | 0.036 | 0.004 | 0.019 | |
| StopWords | 0.036 | 0.004 | 0.019 | |
| SynonymType | 0.040 | 0.000 | 0.019 | |
| annotate | 5.964 | 0.136 | 2.032 | |
| annotateDF | 2.168 | 0.088 | 0.757 | |
| annotateTissueDisease | 0.008 | 0.000 | 0.001 | |
| collapse | 6.000 | 0.168 | 2.950 | |
| compare | 9.064 | 0.224 | 6.140 | |
| createScoreMatrix | 3.636 | 0.016 | 3.665 | |
| dictInfo | 0.004 | 0.000 | 0.003 | |
| dictRef | 0.000 | 0.004 | 0.004 | |
| dictTypes | 0.004 | 0.000 | 0.003 | |
| dict_location | 0.004 | 0.000 | 0.002 | |
| dictionary | 0.000 | 0.000 | 0.001 | |
| entities | 0.000 | 0.000 | 0.003 | |
| experiment_types | 0.000 | 0.000 | 0.001 | |
| filterTerms | 0.096 | 0.004 | 0.101 | |
| filterconcepts | 1.712 | 0.080 | 0.656 | |
| findEntities | 1.604 | 0.060 | 0.563 | |
| findHealthy | 0.232 | 0.000 | 0.096 | |
| getGEOMetadata | 0.004 | 0.000 | 0.001 | |
| groupConfig | 0.224 | 0.000 | 0.077 | |
| groupsim | 0.916 | 0.004 | 0.515 | |
| groupwiseConfigRef | 0.068 | 0.000 | 0.067 | |
| icConfig | 0.000 | 0.000 | 0.001 | |
| listCMOptions | 0.000 | 0.000 | 0.002 | |
| listSimilarities | 0.060 | 0.004 | 0.061 | |
| mergeonassis | 3.180 | 0.140 | 1.271 | |
| multisim | 2.452 | 0.116 | 1.604 | |
| ontology | 0.048 | 0.004 | 0.013 | |
| organism_types | 0.000 | 0.000 | 0.001 | |
| pairsim | 0.240 | 0.000 | 0.178 | |
| pairwiseConfig | 0.364 | 0.000 | 0.163 | |
| pairwiseConfigRef | 0.076 | 0.000 | 0.073 | |
| paramValueIndex | 0.02 | 0.00 | 0.02 | |
| samplesim | 1.688 | 0.076 | 0.905 | |
| scores | 0.000 | 0.000 | 0.001 | |
| semanticdifference | 34.312 | 0.828 | 35.149 | |
| sim | 6.204 | 0.124 | 3.986 | |
| simil | 0 | 0 | 0 | |
| similarityInstance | 0.000 | 0.000 | 0.002 | |
| typeSystemRef | 0.016 | 0.000 | 0.016 | |