Karim Mezhoud
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/bioCancer |
| git_branch: master |
| git_last_commit: 9e8b914 |
| git_last_commit_date: 2021-10-26 12:28:03 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:01 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the bioCancer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bioCancer.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 153/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bioCancer 1.23.0 (landing page) Karim Mezhoud
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: bioCancer |
| Version: 1.23.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bioCancer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings bioCancer_1.23.0.tar.gz |
| StartedAt: 2022-03-17 18:31:57 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:34:51 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 173.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bioCancer.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bioCancer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings bioCancer_1.23.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/bioCancer.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bioCancer/DESCRIPTION' ... OK
* this is package 'bioCancer' version '1.23.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'bioCancer' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
app 3.3Mb
extdata 1.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
'AlgDesign' 'GO.db' 'import' 'methods' 'org.Bt.eg.db' 'shinythemes'
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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* 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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/bioCancer.Rcheck/00check.log'
for details.
bioCancer.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL bioCancer
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'bioCancer' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'bioCancer'
finding HTML links ... done
AnnotationFuncs-package html
Edges_Diseases_obj html
Mutation_obj html
Node_Diseases_obj html
Node_df_FreqIn html
Node_obj_CNA_ProfData html
Node_obj_FreqIn html
Node_obj_Met_ProfData html
Node_obj_mRNA_Classifier html
Studies_obj html
UnifyRowNames html
attriColorGene html
attriColorValue html
attriColorVector html
attriShape2Gene html
attriShape2Node html
bioCancer html
checkDimensions html
coffeewheel html
coffeewheelOutput html
displayTable html
dot-dbEscapeString html
dot-getTableName html
dot-pickRef html
epiGenomics html
findPhantom html
getEvidenceCodes html
getFreqMutData html
getGenesClassification html
getListProfData html
getList_Cases html
getList_GenProfs html
getMegaProfData html
getOrthologs html
getSequensed_SampleSize html
grepRef html
mapLists html
metabologram html
metabologramOutput html
pickGO html
pickRefSeq html
reStrColorGene html
reStrDimension html
reStrDisease html
removeNAs html
renderCoffeewheel html
renderMetabologram html
returnTextAreaInput html
switchButton html
translate html
user_CNA html
user_MetHM27 html
user_MetHM450 html
user_Mut html
user_mRNA html
whichGeneList html
widgetThumbnail 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 (bioCancer)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RGMQL' is missing or broken
done
bioCancer.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(bioCancer)
Loading required package: radiant.data
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Loading required package: ggplot2
Loading required package: lubridate
Attaching package: 'lubridate'
The following objects are masked from 'package:base':
date, intersect, setdiff, union
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:magrittr':
extract
The following object is masked from 'package:testthat':
matches
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'radiant.data'
The following objects are masked from 'package:lubridate':
month, wday
The following object is masked from 'package:ggplot2':
diamonds
The following object is masked from 'package:magrittr':
set_attr
The following object is masked from 'package:testthat':
describe
The following object is masked from 'package:base':
date
Loading required package: cgdsr
Please send questions to cbioportal@googlegroups.com
Loading required package: XML
>
> test_check("bioCancer")
getCancerStudies... OK
getCaseLists (1/2) ... OK
getCaseLists (2/2) ... OK
getGeneticProfiles (1/2) ... OK
getGeneticProfiles (2/2) ... OK
getClinicalData (1/1) ... OK
getProfileData (1/6) ... OK
getProfileData (2/6) ... OK
getProfileData (3/6) ... OK
getProfileData (4/6) ... OK
getProfileData (5/6) ... OK
getProfileData (6/6) ... OK
ReactomeFI connection... OK
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
== Skipped tests ===============================================================
* empty test (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 0 ]
>
> proc.time()
user system elapsed
9.70 0.68 11.25
bioCancer.Rcheck/bioCancer-Ex.timings
| name | user | system | elapsed | |
| AnnotationFuncs-package | 0.41 | 0.04 | 0.52 | |
| Edges_Diseases_obj | 0 | 0 | 0 | |
| Mutation_obj | 0.01 | 0.00 | 0.01 | |
| Node_Diseases_obj | 0 | 0 | 0 | |
| Node_df_FreqIn | 0 | 0 | 0 | |
| Node_obj_CNA_ProfData | 0 | 0 | 0 | |
| Node_obj_FreqIn | 0 | 0 | 0 | |
| Node_obj_Met_ProfData | 0 | 0 | 0 | |
| Node_obj_mRNA_Classifier | 0 | 0 | 0 | |
| Studies_obj | 0 | 0 | 0 | |
| UnifyRowNames | 0 | 0 | 0 | |
| attriColorGene | 0.02 | 0.00 | 0.02 | |
| attriColorValue | 0 | 0 | 0 | |
| attriColorVector | 0 | 0 | 0 | |
| attriShape2Gene | 0 | 0 | 0 | |
| attriShape2Node | 0 | 0 | 0 | |
| bioCancer | 0 | 0 | 0 | |
| checkDimensions | 0 | 0 | 0 | |
| coffeewheel | 0 | 0 | 0 | |
| coffeewheelOutput | 0 | 0 | 0 | |
| displayTable | 0.07 | 0.01 | 0.23 | |
| findPhantom | 0 | 0 | 0 | |
| getEvidenceCodes | 0 | 0 | 0 | |
| getFreqMutData | 0 | 0 | 0 | |
| getGenesClassification | 0.02 | 0.00 | 0.06 | |
| getListProfData | 0 | 0 | 0 | |
| getList_Cases | 0.02 | 0.00 | 0.08 | |
| getList_GenProfs | 0.00 | 0.00 | 0.07 | |
| getMegaProfData | 0 | 0 | 0 | |
| getOrthologs | 0.01 | 0.00 | 0.01 | |
| getSequensed_SampleSize | 0 | 0 | 0 | |
| grepRef | 0 | 0 | 0 | |
| mapLists | 0 | 0 | 0 | |
| metabologram | 0 | 0 | 0 | |
| metabologramOutput | 0 | 0 | 0 | |
| pickGO | 0.11 | 0.02 | 0.13 | |
| pickRefSeq | 0.56 | 0.01 | 0.57 | |
| reStrColorGene | 0 | 0 | 0 | |
| reStrDimension | 0 | 0 | 0 | |
| reStrDisease | 0 | 0 | 0 | |
| removeNAs | 0 | 0 | 0 | |
| renderCoffeewheel | 0 | 0 | 0 | |
| renderMetabologram | 0 | 0 | 0 | |
| returnTextAreaInput | 0 | 0 | 0 | |
| translate | 0.14 | 0.00 | 0.14 | |
| whichGeneList | 0 | 0 | 0 | |
| widgetThumbnail | 0 | 0 | 0 | |