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This page was generated on 2021-10-16 15:58:39 -0400 (Sat, 16 Oct 2021).

CHECK results for ChAMPdata on malbec2

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 58/406HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.24.0  (landing page)
Yuan Tian
Snapshot Date: 2021-10-16 09:30:07 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: RELEASE_3_13
git_last_commit: ed64648
git_last_commit_date: 2021-05-19 11:44:15 -0400 (Wed, 19 May 2021)
malbec2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChAMPdata
Version: 2.24.0
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_2.24.0.tar.gz
StartedAt: 2021-10-16 12:55:47 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 13:00:38 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 290.7 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_2.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.24.0’
* 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 31.396  0.535  31.934
testDataSet        9.245  0.104   9.350
* 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
Anno450K2.7390.0442.784
AnnoEPIC4.1150.0324.147
CellTypeMeans27K0.0020.0000.002
CellTypeMeans450K0.0010.0000.002
ChAMPdata-package31.396 0.53531.934
ControlProbes450K0.0000.0000.001
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg194.6170.1324.749
EPIC.manifest.pop.hg192.6240.0042.629
EPICSimData2.9770.0323.009
MatchGeneName0.0190.0000.019
PathwayList0.4180.0000.418
bloodCtl0.0010.0000.001
hm450.manifest.hg191.7400.0081.749
hm450.manifest.pop.hg191.0810.0041.085
hprdAsigH2.5400.2082.748
illumina450Gr2.2050.0442.249
illuminaEPICGr2.5590.0082.567
multi.hit0.7850.0000.785
probe.features0.6510.0040.655
probe.features.epic1.6270.0041.630
probeInfoALL.epic.lv0.6870.0040.690
probeInfoALL.lv0.4920.0040.495
snp.hit0.8180.0000.818
testDataSet9.2450.1049.350