| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-11 11:38 -0400 (Thu, 11 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| 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 1726/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Chi-Lam Poon
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the ReactomeContentService4R package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReactomeContentService4R.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. |
| Package: ReactomeContentService4R |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReactomeContentService4R.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReactomeContentService4R_1.16.0.tar.gz |
| StartedAt: 2025-09-11 03:19:29 -0400 (Thu, 11 Sep 2025) |
| EndedAt: 2025-09-11 03:20:05 -0400 (Thu, 11 Sep 2025) |
| EllapsedTime: 36.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ReactomeContentService4R.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReactomeContentService4R.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReactomeContentService4R_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeContentService4R.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReactomeContentService4R/DESCRIPTION’ ... OK
* this is package ‘ReactomeContentService4R’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ReactomeContentService4R’ 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 ... OK
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
exportImage.Rd: magick
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... ERROR
Running examples in ‘ReactomeContentService4R-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exportImage
> ### Title: Image exporter
> ### Aliases: exportImage
>
> ### ** Examples
>
> # fireworks
> exportImage(species="9606", output="fireworks",
+ format="jpg", quality=7)
Warning in .matchSpecies(species, "taxId") :
This species is not unique, please use IDs or full name instead
Error in curl::curl_download(url, tmp, handle = h) :
URL using bad/illegal format or missing URL:
URL rejected: Malformed input to a URL function
Calls: exportImage ... paste0 -> download_url -> <Anonymous> -> raise_libcurl_error
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘ReactomeContentService4R.Rmd’ using rmarkdown
starting worker pid=1260203 on localhost:11877 at 03:19:49.378
starting worker pid=1260204 on localhost:11877 at 03:19:49.380
Loading required package: ReactomeContentService4R
loaded ReactomeContentService4R and set parent environment
Loading required package: ReactomeContentService4R
loaded ReactomeContentService4R and set parent environment
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|======================================================================| 100%Warning message:
Warning message:
In fun(libname, pkgname) :
In fun(libname, pkgname) : Package 'ReactomeContentService4R' is deprecated and will be removed
from Bioconductor version 3.22
Package 'ReactomeContentService4R' is deprecated and will be removed
from Bioconductor version 3.22
Quitting from ReactomeContentService4R.Rmd:158-162 [ref-all]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! SSL connect error [reactome.org]:
OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to reactome.org:443
---
Backtrace:
▆
1. └─ReactomeContentService4R::map2RefEntities("TP53")
2. └─ReactomeContentService4R:::.retrieveData(url, as = "text")
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ReactomeContentService4R.Rmd' failed with diagnostics:
SSL connect error [reactome.org]:
OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to reactome.org:443
--- failed re-building ‘ReactomeContentService4R.Rmd’
SUMMARY: processing the following file failed:
‘ReactomeContentService4R.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeContentService4R.Rcheck/00check.log’
for details.
ReactomeContentService4R.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReactomeContentService4R ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘ReactomeContentService4R’ ... ** this is package ‘ReactomeContentService4R’ version ‘1.16.0’ ** 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 Warning in fun(libname, pkgname) : Package 'ReactomeContentService4R' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'ReactomeContentService4R' is deprecated and will be removed from Bioconductor version 3.22 ** testing if installed package keeps a record of temporary installation path * DONE (ReactomeContentService4R)
ReactomeContentService4R.Rcheck/ReactomeContentService4R-Ex.timings
| name | user | system | elapsed | |
| discover | 0.103 | 0.008 | 0.327 | |
| exportEventFile | 0.010 | 0.000 | 0.058 | |