Back to Build/check report for BioC 3.14 experimental data
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This page was generated on 2022-04-13 14:50:22 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
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

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 2.26.0  (landing page)
Yuan Tian
Snapshot Date: 2022-04-13 07:30:01 -0400 (Wed, 13 Apr 2022)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: RELEASE_3_14
git_last_commit: ea78827
git_last_commit_date: 2021-10-26 12:05:27 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChAMPdata
Version: 2.26.0
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_2.26.0.tar.gz
StartedAt: 2022-04-13 11:16:46 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 11:20:51 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 244.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ChAMPdata.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running 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_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘2.26.0’
* 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 26.912   0.78  27.692
testDataSet        7.827   0.14   7.967
* 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
###
##############################################################################
##############################################################################


* 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
Anno450K2.4350.1362.571
AnnoEPIC4.1460.0724.219
CellTypeMeans27K0.0010.0000.001
CellTypeMeans450K0.0010.0000.001
ChAMPdata-package26.912 0.78027.692
ControlProbes450K0.0010.0000.001
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg193.6980.1763.874
EPIC.manifest.pop.hg192.2280.0042.232
EPICSimData2.0480.0802.128
MatchGeneName0.0160.0000.015
PathwayList0.3050.0000.306
bloodCtl0.0010.0000.001
hm450.manifest.hg191.4010.0041.405
hm450.manifest.pop.hg191.6310.0281.659
hprdAsigH1.6790.2721.951
illumina450Gr1.3270.0081.335
illuminaEPICGr1.9780.0161.995
multi.hit0.9400.0320.972
probe.features0.5520.0080.559
probe.features.epic1.2600.0081.267
probeInfoALL.epic.lv0.5420.0000.542
probeInfoALL.lv0.3610.0000.361
snp.hit0.6490.0000.648
testDataSet7.8270.1407.967