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CHECK report for ChAMPdata on malbec1

This page was generated on 2020-04-14 17:46:21 -0400 (Tue, 14 Apr 2020).

Package 56/384HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.18.0
Yuan Tian
Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/ChAMPdata
Branch: RELEASE_3_10
Last Commit: 828d233
Last Changed Date: 2019-10-29 13:29:41 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ChAMPdata
Version: 2.18.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChAMPdata_2.18.0.tar.gz
StartedAt: 2020-04-14 13:18:03 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 13:23:02 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 299.0 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-3.10-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ChAMPdata_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.18.0’
* 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 nrow(x@elementMetadata) : 
    no slot of name "elementMetadata" for this object of class "RGChannelSetExtended"
  
  Error loading dataset 'myLoad':
   Error in nrow(x@elementMetadata) : 
    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 or elapsed time > 5s
                    user system elapsed
ChAMPdata-package 32.388  0.464  32.876
testDataSet       10.568  0.088  10.661
AnnoEPIC           5.712  0.044   5.756
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.



Installation output

ChAMPdata.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ChAMPdata
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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
Anno450K2.3200.0642.383
AnnoEPIC5.7120.0445.756
CellTypeMeans27K0.0000.0000.002
CellTypeMeans450K0.0040.0000.002
ChAMPdata-package32.388 0.46432.876
ControlProbes450K0.0000.0000.001
ControlProbesEPIC000
EPIC.manifest.hg194.8440.1404.985
EPIC.manifest.pop.hg193.1960.0203.215
EPICSimData2.2720.0842.359
MatchGeneName0.0240.0000.020
PathwayList0.4400.0120.453
bloodCtl0.0000.0000.002
hm450.manifest.hg191.9000.0081.906
hm450.manifest.pop.hg191.1920.0001.193
hprdAsigH2.7280.1602.888
illumina450Gr2.2920.0522.347
illuminaEPICGr2.8200.0082.829
multi.hit0.880.000.88
probe.features0.7360.0040.738
probe.features.epic1.6840.0081.694
probeInfoALL.epic.lv0.7480.0040.751
probeInfoALL.lv0.5240.0000.522
snp.hit0.9120.0040.916
testDataSet10.568 0.08810.661