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CHECK report for ChAMPdata on malbec2

This page was generated on 2018-10-16 14:18:34 -0400 (Tue, 16 Oct 2018).

Package 47/342HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMPdata 2.12.0
Yuan Tian
Snapshot Date: 2018-10-16 07:35:22 -0400 (Tue, 16 Oct 2018)
URL: https://git.bioconductor.org/packages/ChAMPdata
Branch: RELEASE_3_7
Last Commit: ddf3bd2
Last Changed Date: 2018-04-30 10:31:28 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ChAMPdata
Version: 2.12.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ChAMPdata_2.12.0.tar.gz
StartedAt: 2018-10-16 10:42:29 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 10:45:59 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 209.9 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-3.7-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ChAMPdata_2.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.12.0’
* 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 712.9Mb
  sub-directories of 1Mb or more:
    data     589.2Mb
    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 in nrow(x@elementMetadata) : 
    no slot of name "elementMetadata" for this object of class "RGChannelSetExtended"
  Calls: <Anonymous> ... check_one -> lapply -> FUN -> length -> length -> nrow
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ChAMPdata-package  30.484  0.528  32.332
testDataSet        10.144  0.092  10.246
AnnoEPIC            6.280  0.032   6.409
EPIC.manifest.hg38  5.076  0.100   5.558
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-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-3.7-bioc/R/bin/R CMD INSTALL ChAMPdata
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ChAMPdata’ ...
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (ChAMPdata)

Tests output


Example timings

ChAMPdata.Rcheck/ChAMPdata-Ex.timings

nameusersystemelapsed
Anno450K2.0960.0442.156
AnnoEPIC6.2800.0326.409
CellTypeMeans27K0.0040.0000.013
CellTypeMeans450K0.0000.0000.012
ChAMPdata-package30.484 0.52832.332
ControlProbes450K0.0000.0000.001
ControlProbesEPIC0.0040.0000.001
EPIC.manifest.hg385.0760.1005.558
EPIC.manifest.pop.hg381.7560.0201.931
EPICSimData2.1280.0842.212
MatchGeneName0.0320.0000.299
PathwayList0.5000.0000.599
bloodCtl0.0040.0000.003
hm450.manifest.hg382.6680.0083.241
hm450.manifest.pop.hg380.8240.0041.021
hprdAsigH2.7840.1722.976
illumina450Gr2.3720.0362.416
illuminaEPICGr2.6840.0042.693
multi.hit0.8840.0000.915
probe.features0.7120.0040.719
probe.features.epic1.6600.0041.666
probeInfoALL.epic.lv0.7160.0000.718
probeInfoALL.lv0.5480.0000.549
snp.hit0.9560.0120.993
testDataSet10.144 0.09210.246