| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-29 16:33:43 -0000 (Sun, 29 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4021 |
| 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 | ||||
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To the developers/maintainers of the decoupleR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 484/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.5.0 (landing page) Pau Badia-i-Mompel
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: decoupleR |
| Version: 2.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings decoupleR_2.5.0.tar.gz |
| StartedAt: 2023-01-28 21:07:49 -0000 (Sat, 28 Jan 2023) |
| EndedAt: 2023-01-28 21:18:41 -0000 (Sat, 28 Jan 2023) |
| EllapsedTime: 651.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings decoupleR_2.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.5.0’
* 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 ‘decoupleR’ can be installed ... 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
Warning message:
In utils::packageDescription(basename(dir), dirname(dir)) :
no package 'decoupleR' was found
* 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 loading without being on the library search path ... WARNING
Error in library(decoupleR, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘decoupleR’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
[2023-01-28 21:08:23] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-01-28 21:08:23] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-01-28 21:08:23] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-01-28 21:08:23] [TRACE] [OmnipathR] Contains 6 files.
[2023-01-28 21:08:23] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-01-28 21:08:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-01-28 21:08:23] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-01-28 21:08:23] [TRACE] [OmnipathR] Cache locked: FALSE
* 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 files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘decoupleR.Rmd’ using ‘UTF-8’... OK
‘pw_bk.Rmd’ using ‘UTF-8’... OK
‘pw_sc.Rmd’ using ‘UTF-8’... OK
‘tf_bk.Rmd’ using ‘UTF-8’... OK
‘tf_sc.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘decoupleR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (decoupleR)
decoupleR.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(decoupleR)
>
> test_check("decoupleR")
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