Back to Build/check report for BioC 3.22 experimental data
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-07-10 15:41 -0400 (Thu, 10 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4781
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 52/429HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.41.0  (landing page)
Yuan Tian
Snapshot Date: 2025-07-10 07:30 -0400 (Thu, 10 Jul 2025)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: devel
git_last_commit: 7fc7530
git_last_commit_date: 2025-04-15 09:24:28 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published


CHECK results for ChAMPdata on nebbiolo2

To the developers/maintainers of the ChAMPdata 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: ChAMPdata
Version: 2.41.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChAMPdata_2.41.0.tar.gz
StartedAt: 2025-07-10 12:06:05 -0400 (Thu, 10 Jul 2025)
EndedAt: 2025-07-10 12:10:38 -0400 (Thu, 10 Jul 2025)
EllapsedTime: 273.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChAMPdata.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChAMPdata_2.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.41.0’
* 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 ‘ChAMPdata’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 730.0Mb
  sub-directories of 1Mb or more:
    data     606.3Mb
    extdata  123.6Mb
* 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 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 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:  'there is no package called 'minfi''
  Error loading dataset 'bloodCtl':
   Error in .requirePackage(package) : 
    unable to load required package 'minfi'
  
  Failed with error:  'there is no package called 'minfi''
  Error loading dataset 'myLoad':
   Error in .requirePackage(package) : 
    unable to load required package 'minfi'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
ChAMPdata-package 32.343  0.647  32.991
testDataSet        9.265  0.100   9.368
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.


Installation output

ChAMPdata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ChAMPdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ChAMPdata’ ...
** this is package ‘ChAMPdata’ version ‘2.41.0’
** using staged installation
** data
** inst
** 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 (ChAMPdata)

Tests output


Example timings

ChAMPdata.Rcheck/ChAMPdata-Ex.timings

nameusersystemelapsed
Anno450K2.6640.0632.728
AnnoEPIC3.8700.0453.916
CellTypeMeans27K0.1610.0010.162
CellTypeMeans450K0.0020.0000.001
ChAMPdata-package32.343 0.64732.991
ControlProbes450K0.0000.0000.001
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg194.5210.1814.702
EPIC.manifest.pop.hg192.4670.0202.488
EPICSimData2.8550.0352.891
MatchGeneName0.0180.0000.019
PathwayList0.3930.0010.395
bloodCtl0.0000.0010.001
hm450.manifest.hg191.7420.0061.748
hm450.manifest.pop.hg190.9850.0020.987
hprdAsigH2.0400.2592.299
illumina450Gr3.4290.0583.486
illuminaEPICGr4.0420.0014.044
multi.hit0.7920.0040.796
probe.features0.6550.0000.655
probe.features.epic1.5990.0051.605
probeInfoALL.epic.lv0.6870.0010.689
probeInfoALL.lv0.4760.0000.476
snp.hit0.7910.0020.793
testDataSet9.2650.1009.368