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CHECK report for ChAMPdata on malbec2

This page was generated on 2020-10-15 20:45:45 -0400 (Thu, 15 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ChAMPdata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 55/391HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.20.0
Yuan Tian
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/ChAMPdata
Branch: RELEASE_3_11
Last Commit: 69dcc8c
Last Changed Date: 2020-04-27 15:23:32 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ChAMPdata
Version: 2.20.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ChAMPdata_2.20.0.tar.gz
StartedAt: 2020-10-15 13:03:50 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 13:10:56 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 425.0 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-3.11-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ChAMPdata_2.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.20.0’
* 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 31.164  0.477  31.642
testDataSet        9.337  0.105   9.441
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.



Installation output

ChAMPdata.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ChAMPdata
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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
Anno450K2.5980.0432.641
AnnoEPIC3.7700.0313.802
CellTypeMeans27K0.0020.0000.001
CellTypeMeans450K0.0020.0000.002
ChAMPdata-package31.164 0.47731.642
ControlProbes450K0.0000.0010.001
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg194.2930.1274.421
EPIC.manifest.pop.hg192.6430.0272.671
EPICSimData2.9290.0392.969
MatchGeneName0.0190.0010.019
PathwayList0.4010.0000.401
bloodCtl0.0010.0000.001
hm450.manifest.hg191.6700.0151.687
hm450.manifest.pop.hg191.0650.0001.065
hprdAsigH2.4740.1482.622
illumina450Gr2.1060.0472.153
illuminaEPICGr2.6530.0052.656
multi.hit0.7810.0000.781
probe.features0.6270.0040.631
probe.features.epic1.5350.0001.535
probeInfoALL.epic.lv0.7020.0000.702
probeInfoALL.lv0.4760.0000.476
snp.hit0.7390.0030.743
testDataSet9.3370.1059.441