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CHECK report for ChAMPdata on malbec1

This page was generated on 2021-05-06 14:10:06 -0400 (Thu, 06 May 2021).

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 56/398HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.22.0  (landing page)
Yuan Tian
Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021)
URL: https://git.bioconductor.org/packages/ChAMPdata
Branch: RELEASE_3_12
Last Commit: eeedd4c
Last Changed Date: 2020-10-27 10:05:58 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ChAMPdata
Version: 2.22.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ChAMPdata_2.22.0.tar.gz
StartedAt: 2021-05-06 11:44:28 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 11:49:25 -0400 (Thu, 06 May 2021)
EllapsedTime: 297.2 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-3.12-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ChAMPdata_2.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.22.0’
* 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 32.136  0.512  32.672
testDataSet        9.712  0.112   9.834
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.



Installation output

ChAMPdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ChAMPdata
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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
Anno450K2.8520.0442.900
AnnoEPIC4.3480.0364.388
CellTypeMeans27K0.0000.0000.003
CellTypeMeans450K0.0000.0040.002
ChAMPdata-package32.136 0.51232.672
ControlProbes450K0.0000.0000.001
ControlProbesEPIC0.0000.0000.001
EPIC.manifest.hg194.5840.1444.731
EPIC.manifest.pop.hg192.6880.0082.698
EPICSimData3.0840.0283.112
MatchGeneName0.0160.0000.018
PathwayList0.4080.0000.410
bloodCtl0.0000.0000.002
hm450.manifest.hg191.7720.0081.783
hm450.manifest.pop.hg191.0640.0081.071
hprdAsigH2.5240.1722.697
illumina450Gr2.1880.0362.228
illuminaEPICGr2.5960.0082.604
multi.hit0.7920.0000.792
probe.features0.6640.0080.672
probe.features.epic1.5600.0041.564
probeInfoALL.epic.lv0.6400.0080.648
probeInfoALL.lv0.4240.0000.425
snp.hit0.7600.0080.770
testDataSet9.7120.1129.834