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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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

Package 2260/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Xeva 1.23.1  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/Xeva
git_branch: devel
git_last_commit: 54c191f
git_last_commit_date: 2024-11-27 14:03:04 -0500 (Wed, 27 Nov 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for Xeva on nebbiolo1

To the developers/maintainers of the Xeva package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Xeva.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Xeva
Version: 1.23.1
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Xeva.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Xeva_1.23.1.tar.gz
StartedAt: 2024-12-24 03:20:27 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 03:24:53 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 266.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Xeva.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Xeva.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Xeva_1.23.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Xeva.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Xeva/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Xeva’ version ‘1.23.1’
* 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 ‘Xeva’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    The datasets previously available have been deprecated.
    `downloadXevaSet` will no longer work.
* checking code 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 ... NOTE
checkRd: (-1) drugInform.Rd:7: Lost braces; missing escapes or markup?
     7 | Get the drug information slot from a {XevaSet} object.}
       |                                      ^
checkRd: (-1) drugInform.Rd:21: Lost braces; missing escapes or markup?
    21 | Get the drug information slot from a {XevaSet} object.
       |                                      ^
* 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 ... INFO
  Note: found 31 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Xeva-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: downloadXevaSet
> ### Title: Download a XevaSet object or table of available XevaSet objects
> ### Aliases: downloadXevaSet
> 
> ### ** Examples
> 
> downloadXevaSet()
Warning in file(file, "rt") :
  cannot open URL 'https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/XevaSets/XevaSet.csv': HTTP status was '503 Service Unavailable'
Error in file(file, "rt") : 
  cannot open the connection to 'https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/XevaSets/XevaSet.csv'
Calls: downloadXevaSet -> availableXevaSet -> read.csv -> read.table -> file
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Xeva.Rcheck/00check.log’
for details.


Installation output

Xeva.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Xeva
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Xeva’ ...
** using staged installation
** R
** data
** 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 (Xeva)

Tests output


Example timings

Xeva.Rcheck/Xeva-Ex.timings

nameusersystemelapsed
ABC0.0040.0000.005
AUC0.0130.0060.019
TGI0.0000.0000.001
addExperimentalDesign0.0950.0050.101
angle0.0060.0020.008
batchInfo0.1330.0210.153
createXevaSet0.0710.0250.097
dosePlot0.3010.0110.312