Back to Build/check report for BioC 3.15 experimental data
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This page was generated on 2022-02-17 08:36:51 -0500 (Thu, 17 Feb 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 1362
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 52/406HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.27.1  (landing page)
Yuan Tian
Snapshot Date: 2022-02-17 04:00:02 -0500 (Thu, 17 Feb 2022)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: master
git_last_commit: 765eaa8
git_last_commit_date: 2021-11-22 03:15:09 -0500 (Mon, 22 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChAMPdata
Version: 2.27.1
Command: /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.15-data-experiment/R/library --no-vignettes --timings ChAMPdata_2.27.1.tar.gz
StartedAt: 2022-02-17 07:09:20 -0500 (Thu, 17 Feb 2022)
EndedAt: 2022-02-17 07:15:48 -0500 (Thu, 17 Feb 2022)
EllapsedTime: 387.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ChAMPdata.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.15-data-experiment/R/library --no-vignettes --timings ChAMPdata_2.27.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/ChAMPdata.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘2.27.1’
* 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 730.0Mb
  sub-directories of 1Mb or more:
    data     606.3Mb
    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  47.257  1.355  48.615
testDataSet        10.699  0.147  10.847
AnnoEPIC            7.192  0.323   7.516
EPIC.manifest.hg19  5.540  0.200   5.740
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.



Installation output

ChAMPdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD INSTALL ChAMPdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-data-experiment/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
Anno450K4.2830.0994.383
AnnoEPIC7.1920.3237.516
CellTypeMeans27K0.0030.0000.004
CellTypeMeans450K0.0030.0000.003
ChAMPdata-package47.257 1.35548.615
ControlProbes450K0.0010.0000.001
ControlProbesEPIC0.0010.0010.001
EPIC.manifest.hg195.540.205.74
EPIC.manifest.pop.hg193.4790.0153.494
EPICSimData2.7500.1282.877
MatchGeneName0.020.000.02
PathwayList0.4340.0000.434
bloodCtl0.0010.0000.002
hm450.manifest.hg191.8950.0001.895
hm450.manifest.pop.hg192.3250.0602.384
hprdAsigH2.1930.2092.400
illumina450Gr3.5250.0073.532
illuminaEPICGr4.2350.0084.242
multi.hit1.3640.0561.420
probe.features0.6870.0040.690
probe.features.epic1.7780.0041.783
probeInfoALL.epic.lv0.7380.0000.739
probeInfoALL.lv0.5120.0000.512
snp.hit0.8680.0090.875
testDataSet10.699 0.14710.847