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This page was generated on 2021-10-23 15:51:46 -0400 (Sat, 23 Oct 2021).

CHECK results for ChAMPdata on nebbiolo2

To the developers/maintainers of the ChAMPdata package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 54/408HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.25.0  (landing page)
Yuan Tian
Snapshot Date: 2021-10-23 09:30:01 -0400 (Sat, 23 Oct 2021)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: master
git_last_commit: 1aba2b9
git_last_commit_date: 2021-05-19 11:44:15 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChAMPdata
Version: 2.25.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ChAMPdata_2.25.0.tar.gz
StartedAt: 2021-10-23 12:12:56 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 12:17:14 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 257.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ChAMPdata.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ChAMPdata_2.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.25.0’
* 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 ... NOTE
  installed size is 743.0Mb
  sub-directories of 1Mb or more:
    data     619.3Mb
    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 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 ... NOTE
  Error loading dataset 'bloodCtl':
   Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'nrow': no slot of name "elementMetadata" for this object of class "RGChannelSetExtended"
  
  Error loading dataset 'myLoad':
   Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'x' in selecting a method for function 'nrow': no slot of name "elementMetadata" for this object of class "MethylSet"
  
* 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 26.779  0.660  27.439
testDataSet        7.795  0.191   7.987
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.



Installation output

ChAMPdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ChAMPdata
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
Anno450K2.1770.0202.197
AnnoEPIC3.4230.0673.490
CellTypeMeans27K0.0020.0000.002
CellTypeMeans450K0.0020.0000.002
ChAMPdata-package26.779 0.66027.439
ControlProbes450K0.0010.0000.001
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg193.8980.1924.090
EPIC.manifest.pop.hg192.2530.0402.292
EPICSimData2.1350.0642.198
MatchGeneName0.0160.0000.015
PathwayList0.3300.0120.342
bloodCtl0.0010.0000.001
hm450.manifest.hg191.4720.0161.487
hm450.manifest.pop.hg191.7110.0401.750
hprdAsigH1.7260.2311.958
illumina450Gr1.3700.0161.387
illuminaEPICGr2.1050.0362.142
multi.hit0.9690.0361.005
probe.features0.5310.0000.531
probe.features.epic1.3090.0161.325
probeInfoALL.epic.lv0.5370.0040.540
probeInfoALL.lv0.3780.0080.386
snp.hit0.6330.0000.633
testDataSet7.7950.1917.987