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CHECK report for ChAMPdata on malbec2

This page was generated on 2021-01-14 15:58:58 -0500 (Thu, 14 Jan 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 56/385HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.23.0
Yuan Tian
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/ChAMPdata
Branch: master
Last Commit: 9095bbe
Last Changed Date: 2020-10-27 10:05:58 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: ChAMPdata
Version: 2.23.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChAMPdata_2.23.0.tar.gz
StartedAt: 2021-01-14 11:49:31 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:54:27 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 295.8 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-3.13-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChAMPdata_2.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/ChAMPdata.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘2.23.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 32.075  0.556  32.632
testDataSet        9.093  0.124   9.217
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.



Installation output

ChAMPdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ChAMPdata
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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
Anno450K2.6420.0482.690
AnnoEPIC4.2180.0604.278
CellTypeMeans27K0.0020.0000.002
CellTypeMeans450K0.0020.0000.002
ChAMPdata-package32.075 0.55632.632
ControlProbes450K0.0010.0000.000
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg194.3820.1284.510
EPIC.manifest.pop.hg192.5960.0202.616
EPICSimData2.9190.0402.960
MatchGeneName0.0180.0000.018
PathwayList0.4010.0040.406
bloodCtl0.0000.0010.002
hm450.manifest.hg191.7650.0071.772
hm450.manifest.pop.hg191.0830.0041.087
hprdAsigH2.5690.1602.729
illumina450Gr2.1280.0442.172
illuminaEPICGr2.5470.0082.556
multi.hit0.740.000.74
probe.features0.6330.0040.637
probe.features.epic1.5060.0041.510
probeInfoALL.epic.lv0.6720.0000.672
probeInfoALL.lv0.4510.0000.451
snp.hit0.7760.0000.776
testDataSet9.0930.1249.217