Back to Build/check report for BioC 3.16 experimental data
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This page was generated on 2023-04-11 14:50:26 -0400 (Tue, 11 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
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 53/416HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.30.0  (landing page)
Yuan Tian
Snapshot Date: 2023-04-11 07:30:01 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: RELEASE_3_16
git_last_commit: 6e05b8f
git_last_commit_date: 2022-11-01 10:58:28 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChAMPdata
Version: 2.30.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ChAMPdata_2.30.0.tar.gz
StartedAt: 2023-04-11 11:32:49 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 11:36:52 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 242.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ChAMPdata.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ChAMPdata_2.30.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.30.0’
* 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 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 loading without being on the library search path ... 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 25.337  0.658  25.997
testDataSet        7.790  0.171   7.962
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.



Installation output

ChAMPdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL ChAMPdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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
Anno450K1.8870.0361.923
AnnoEPIC4.2420.0484.290
CellTypeMeans27K0.0010.0000.001
CellTypeMeans450K0.0010.0000.001
ChAMPdata-package25.337 0.65825.997
ControlProbes450K0.0000.0000.001
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg193.6530.1793.833
EPIC.manifest.pop.hg192.3750.0522.427
EPICSimData1.5890.0481.636
MatchGeneName0.0140.0000.014
PathwayList0.2870.0010.287
bloodCtl0.0010.0000.001
hm450.manifest.hg191.3580.0191.378
hm450.manifest.pop.hg190.8540.0130.866
hprdAsigH1.8540.2112.066
illumina450Gr2.6880.0562.744
illuminaEPICGr3.1020.0243.126
multi.hit0.6670.0000.668
probe.features0.5340.0130.547
probe.features.epic1.2700.0151.287
probeInfoALL.epic.lv0.5680.0000.568
probeInfoALL.lv0.3990.0150.414
snp.hit0.6570.0010.657
testDataSet7.7900.1717.962