Back to Build/check report for BioC 3.17 annotations
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This page was generated on 2023-10-11 08:30:04 -0400 (Wed, 11 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
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 30/37HostnameOS / ArchINSTALLBUILDCHECK
phastCons30way.UCSC.hg38 3.13.0  (landing page)
Robert Castelo
Snapshot Date: 2023-10-11 05:00:01 -0400 (Wed, 11 Oct 2023)
git_url: https://git.bioconductor.org/packages/phastCons30way.UCSC.hg38
git_branch: RELEASE_3_17
git_last_commit: c114273
git_last_commit_date: 2020-12-22 10:39:25 -0400 (Tue, 22 Dec 2020)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  

CHECK results for phastCons30way.UCSC.hg38 on nebbiolo1


To the developers/maintainers of the phastCons30way.UCSC.hg38 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: phastCons30way.UCSC.hg38
Version: 3.13.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:phastCons30way.UCSC.hg38.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings phastCons30way.UCSC.hg38_3.13.0.tar.gz
StartedAt: 2023-10-11 05:33:29 -0400 (Wed, 11 Oct 2023)
EndedAt: 2023-10-11 05:34:27 -0400 (Wed, 11 Oct 2023)
EllapsedTime: 58.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: phastCons30way.UCSC.hg38.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:phastCons30way.UCSC.hg38.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings phastCons30way.UCSC.hg38_3.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-data-annotation/meat/phastCons30way.UCSC.hg38.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘phastCons30way.UCSC.hg38/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phastCons30way.UCSC.hg38’ version ‘3.13.0’
* 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 ‘phastCons30way.UCSC.hg38’ 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 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 Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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 ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘phastCons30way.UCSC.hg38.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘phastCons30way.UCSC.hg38.Rmd’ using rmarkdown
Error: processing vignette 'phastCons30way.UCSC.hg38.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘phastCons30way.UCSC.hg38.Rmd’

SUMMARY: processing the following file failed:
  ‘phastCons30way.UCSC.hg38.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.17-data-annotation/meat/phastCons30way.UCSC.hg38.Rcheck/00check.log’
for details.


Installation output

phastCons30way.UCSC.hg38.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL phastCons30way.UCSC.hg38
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘phastCons30way.UCSC.hg38’ ...
** using staged installation
** inst
** 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 (phastCons30way.UCSC.hg38)

Tests output


Example timings

phastCons30way.UCSC.hg38.Rcheck/phastCons30way.UCSC.hg38-Ex.timings

nameusersystemelapsed
package000