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This page was generated on 2025-03-31 20:49 -0400 (Mon, 31 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 871
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Package 113/217HostnameOS / ArchINSTALLBUILDCHECK
HDF5Array 1.35.16  (landing page)
Hervé Pagès
Snapshot Date: 2025-03-31 18:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/HDF5Array
git_branch: devel
git_last_commit: 34b6219
git_last_commit_date: 2025-03-19 18:22:56 -0400 (Wed, 19 Mar 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  


CHECK results for HDF5Array on teran2

To the developers/maintainers of the HDF5Array package:
- 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: HDF5Array
Version: 1.35.16
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings HDF5Array_1.35.16.tar.gz
StartedAt: 2025-03-31 20:17:46 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 20:19:04 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 77.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: HDF5Array.Rcheck
Warnings: NA

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings HDF5Array_1.35.16.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/HDF5Array.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.35.16’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HDF5Array’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
* 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 ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking Rd metadata ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking Rd cross-references ... INFO
Fatal error: cannot create 'R_TempDir'
* checking for missing documentation entries ... WARNING
Fatal error: cannot create 'R_TempDir'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Fatal error: cannot create 'R_TempDir'
Fatal error: cannot create 'R_TempDir'
Fatal error: cannot create 'R_TempDir'
* checking Rd \usage sections ... WARNING
Fatal error: cannot create 'R_TempDir'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Fatal error: cannot create 'R_TempDir'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking for unstated dependencies in examples ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking files in ‘vignettes’ ...Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error: inferior call failed
Execution halted

Installation output

HDF5Array.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL HDF5Array
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘HDF5Array’ ...
** this is package ‘HDF5Array’ version ‘1.35.16’
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HDF5Array)

Tests output


Example timings