Multiple platform build/check report for BioC 3.19 - CHECK results for RITAN on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4753
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4487
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4518
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*

CHECK results for RITAN on nebbiolo1

To the developers/maintainers of the RITAN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RITAN.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: RITAN

Version: 1.28.0

Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RITAN.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RITAN_1.28.0.tar.gz

StartedAt: 2024-06-03 10:19:01 -0400 (Mon, 03 Jun 2024)

EndedAt: 2024-06-03 10:19:13 -0400 (Mon, 03 Jun 2024)

EllapsedTime: 12.1 seconds

RetCode: 1

Status: ERROR

CheckDir: RITAN.Rcheck

Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RITAN.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RITAN_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RITAN.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘RITAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RITAN’ version ‘1.28.0’
* 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 ‘RITAN’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
  Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
See ‘/home/biocbuild/bbs-3.19-bioc/meat/RITAN.Rcheck/00install.out’ for details.
* 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:
  ‘BgeeDB’
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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... ERROR
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for ‘RITAN’ in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘GenomicAlignments’
Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/RITAN.Rcheck/00check.log’
for details.

Installation output

RITAN.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RITAN
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘RITAN’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** testing if installed package keeps a record of temporary installation path
* DONE (RITAN)

CHECK results for RITAN on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings