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This page was generated on 2025-08-28 15:01 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
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 53/432HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.40.0  (landing page)
Yuan Tian
Snapshot Date: 2025-08-28 07:30 -0400 (Thu, 28 Aug 2025)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: RELEASE_3_21
git_last_commit: 2e76a6e
git_last_commit_date: 2025-04-15 09:24:28 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published


CHECK results for ChAMPdata on nebbiolo1

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: 2.40.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ChAMPdata_2.40.0.tar.gz
StartedAt: 2025-08-28 12:41:07 -0400 (Thu, 28 Aug 2025)
EndedAt: 2025-08-28 12:45:45 -0400 (Thu, 28 Aug 2025)
EllapsedTime: 278.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChAMPdata.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ChAMPdata_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.40.0’
* 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 730.2Mb
  sub-directories of 1Mb or more:
    data     606.3Mb
    extdata  123.7Mb
* 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 33.595  0.899  34.538
testDataSet        9.462  0.261   9.723
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.


Installation output

ChAMPdata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ChAMPdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ChAMPdata’ ...
** this is package ‘ChAMPdata’ version ‘2.40.0’
** 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
Anno450K2.6850.0622.746
AnnoEPIC3.8490.0673.916
CellTypeMeans27K0.0010.0010.002
CellTypeMeans450K0.1620.0000.163
ChAMPdata-package33.595 0.89934.538
ControlProbes450K0.0010.0000.001
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg194.5490.2024.751
EPIC.manifest.pop.hg192.4980.0352.533
EPICSimData2.9320.0813.013
MatchGeneName0.0180.0020.019
PathwayList0.4050.0030.407
bloodCtl0.0020.0000.001
hm450.manifest.hg191.7720.0231.796
hm450.manifest.pop.hg190.9900.0111.001
hprdAsigH2.0560.2762.333
illumina450Gr3.5560.0663.623
illuminaEPICGr4.1050.0134.120
multi.hit0.8060.0080.815
probe.features0.6610.0030.664
probe.features.epic1.6320.0111.643
probeInfoALL.epic.lv0.7070.0020.708
probeInfoALL.lv0.4700.0010.471
snp.hit0.7840.0060.791
testDataSet9.4620.2619.723