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This page was generated on 2024-11-21 15:01 -0500 (Thu, 21 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4742
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Package 53/429HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.39.0  (landing page)
Yuan Tian
Snapshot Date: 2024-11-21 07:30 -0500 (Thu, 21 Nov 2024)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: devel
git_last_commit: c9833d6
git_last_commit_date: 2024-10-29 09:37:50 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 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: 2.39.0
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_2.39.0.tar.gz
StartedAt: 2024-11-21 11:58:13 -0500 (Thu, 21 Nov 2024)
EndedAt: 2024-11-21 12:06:16 -0500 (Thu, 21 Nov 2024)
EllapsedTime: 483.0 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_2.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/ChAMPdata.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.39.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 30.776  0.803  31.584
testDataSet        8.742  0.209   8.952
* 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’ ...
** 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
Anno450K2.5280.0682.596
AnnoEPIC3.6470.0713.718
CellTypeMeans27K0.0020.0000.002
CellTypeMeans450K0.0000.0020.002
ChAMPdata-package30.776 0.80331.584
ControlProbes450K0.0010.0000.001
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg194.0930.1954.288
EPIC.manifest.pop.hg192.2040.0202.224
EPICSimData2.6820.0642.762
MatchGeneName0.0160.0020.018
PathwayList0.3630.0070.371
bloodCtl0.0000.0010.002
hm450.manifest.hg191.5750.0171.593
hm450.manifest.pop.hg190.8580.0060.865
hprdAsigH1.9270.2602.188
illumina450Gr3.1390.0613.201
illuminaEPICGr3.7430.0143.759
multi.hit0.7390.0040.744
probe.features0.6000.0100.611
probe.features.epic1.4700.0061.477
probeInfoALL.epic.lv0.6360.0010.638
probeInfoALL.lv0.4510.0020.454
snp.hit0.7470.0050.753
testDataSet8.7420.2098.952