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This page was generated on 2024-02-29 14:52:02 -0500 (Thu, 29 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
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 330/429HostnameOS / ArchINSTALLBUILDCHECK
RnBeads.hg19 1.34.0  (landing page)
RnBeadsAnnotationCreator
Snapshot Date: 2024-02-29 07:30:02 -0500 (Thu, 29 Feb 2024)
git_url: https://git.bioconductor.org/packages/RnBeads.hg19
git_branch: RELEASE_3_18
git_last_commit: 4d3f651
git_last_commit_date: 2023-10-24 09:10:24 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

CHECK results for RnBeads.hg19 on nebbiolo2


To the developers/maintainers of the RnBeads.hg19 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: RnBeads.hg19
Version: 1.34.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RnBeads.hg19.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RnBeads.hg19_1.34.0.tar.gz
StartedAt: 2024-02-29 11:59:55 -0500 (Thu, 29 Feb 2024)
EndedAt: 2024-02-29 12:01:53 -0500 (Thu, 29 Feb 2024)
EllapsedTime: 118.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RnBeads.hg19.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RnBeads.hg19.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RnBeads.hg19_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/RnBeads.hg19.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RnBeads.hg19/DESCRIPTION’ ... OK
* this is package ‘RnBeads.hg19’ version ‘1.34.0’
* 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 ‘RnBeads.hg19’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 100.4Mb
  sub-directories of 1Mb or more:
    data     89.2Mb
    extdata  11.1Mb
* checking package 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 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 ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘GenomicRanges’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
  Failed with error:  'package 'TxDb.Hsapiens.UCSC.hg19.knownGene' could not be loaded'
  Error loading dataset 'rnb.set.example':
   Error in .requirePackage(package) : 
    unable to find required package 'RnBeads'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-data-experiment/meat/RnBeads.hg19.Rcheck/00check.log’
for details.



Installation output

RnBeads.hg19.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL RnBeads.hg19
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘RnBeads.hg19’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (RnBeads.hg19)

Tests output


Example timings