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This page was generated on 2024-03-26 14:51:27 -0400 (Tue, 26 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
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 409/425HostnameOS / ArchINSTALLBUILDCHECK
TumourMethData 1.1.0  (landing page)
Richard Heery
Snapshot Date: 2024-03-26 07:30:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/TumourMethData
git_branch: devel
git_last_commit: e97bd72
git_last_commit_date: 2023-10-24 16:36:48 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

CHECK results for TumourMethData on nebbiolo1


To the developers/maintainers of the TumourMethData 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: TumourMethData
Version: 1.1.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TumourMethData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TumourMethData_1.1.0.tar.gz
StartedAt: 2024-03-26 12:30:27 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 12:33:48 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 201.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TumourMethData.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:TumourMethData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TumourMethData_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/TumourMethData.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘TumourMethData/DESCRIPTION’ ... OK
* this is package ‘TumourMethData’ version ‘1.1.0’
* 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 ‘TumourMethData’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘HDF5Array::h5ls’ by ‘rhdf5::h5ls’ when loading ‘TumourMethData’
See ‘/home/biocbuild/bbs-3.19-data-experiment/meat/TumourMethData.Rcheck/00install.out’ for details.
* 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 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 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 ... NOTE
download_meth_dataset: no visible global function definition for ‘data’
download_meth_dataset: no visible binding for global variable
  ‘TumourMethDatasets’
download_rnaseq_dataset: no visible global function definition for
  ‘data’
download_rnaseq_dataset: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  TumourMethDatasets data read.csv
Consider adding
  importFrom("utils", "data", "read.csv")
to your NAMESPACE file.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
download_meth_dataset 2.946  0.612   6.941
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/TumourMethData.Rcheck/00check.log’
for details.


Installation output

TumourMethData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL TumourMethData
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘TumourMethData’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘HDF5Array::h5ls’ by ‘rhdf5::h5ls’ when loading ‘TumourMethData’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘HDF5Array::h5ls’ by ‘rhdf5::h5ls’ when loading ‘TumourMethData’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘HDF5Array::h5ls’ by ‘rhdf5::h5ls’ when loading ‘TumourMethData’
** testing if installed package keeps a record of temporary installation path
* DONE (TumourMethData)

Tests output


Example timings

TumourMethData.Rcheck/TumourMethData-Ex.timings

nameusersystemelapsed
download_meth_dataset2.9460.6126.941