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CHECK report for ChAMPdata on malbec1

This page was generated on 2019-04-16 15:26:09 -0400 (Tue, 16 Apr 2019).

Package 52/360HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMPdata 2.14.1
Yuan Tian
Snapshot Date: 2019-04-16 11:00:05 -0400 (Tue, 16 Apr 2019)
URL: https://git.bioconductor.org/packages/ChAMPdata
Branch: RELEASE_3_8
Last Commit: a75d97a
Last Changed Date: 2019-01-27 15:31:20 -0400 (Sun, 27 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ChAMPdata
Version: 2.14.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ChAMPdata_2.14.1.tar.gz
StartedAt: 2019-04-16 13:32:18 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 13:36:11 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 232.7 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-3.8-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ChAMPdata_2.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.14.1’
* 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 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 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  33.008  0.580  40.354
testDataSet        10.656  0.108  10.767
AnnoEPIC            5.652  0.060   5.737
EPIC.manifest.hg19  4.976  0.104   5.646
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-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-3.8-bioc/R/bin/R CMD INSTALL ChAMPdata
###
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* installing to library ‘/home/biocbuild/bbs-3.8-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
Anno450K2.3720.0402.625
AnnoEPIC5.6520.0605.737
CellTypeMeans27K0.0040.0000.012
CellTypeMeans450K0.0040.0000.002
ChAMPdata-package33.008 0.58040.354
ControlProbes450K0.0040.0000.001
ControlProbesEPIC0.0000.0000.001
EPIC.manifest.hg194.9760.1045.646
EPIC.manifest.pop.hg193.6160.0403.995
EPICSimData2.3080.0722.382
MatchGeneName0.0200.0000.141
PathwayList0.5160.0120.660
bloodCtl0.0000.0000.002
hm450.manifest.hg191.9120.0202.017
hm450.manifest.pop.hg191.2160.0041.282
hprdAsigH2.7240.1842.933
illumina450Gr2.2880.0442.331
illuminaEPICGr2.7160.0122.732
multi.hit1.0000.0041.145
probe.features0.80.00.8
probe.features.epic1.8360.0161.857
probeInfoALL.epic.lv0.8440.0080.851
probeInfoALL.lv0.5360.0040.540
snp.hit0.8920.0041.530
testDataSet10.656 0.10810.767