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BioC experimental data: CHECK report for ChAMPdata on malbec2

This page was generated on 2017-10-18 15:09:40 -0400 (Wed, 18 Oct 2017).

Package 44/314HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMPdata 2.8.1
Yuan Tian
Snapshot Date: 2017-10-18 09:00:07 -0400 (Wed, 18 Oct 2017)
URL: https://git.bioconductor.org/packages/ChAMPdata
Branch: RELEASE_3_5
Last Commit: 7c77533
Last Changed Date: 2017-08-16 15:05:21 -0400 (Wed, 16 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ChAMPdata
Version: 2.8.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ChAMPdata_2.8.1.tar.gz
StartedAt: 2017-10-18 10:35:08 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 10:39:02 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 234.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ChAMPdata.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ChAMPdata_2.8.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘2.8.1’
* 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 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  34.900  0.344  35.266
testDataSet        11.132  0.332  11.471
AnnoEPIC            6.684  0.040   6.727
EPIC.manifest.hg38  4.940  0.056   5.002
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.


ChAMPdata.Rcheck/00install.out:

* installing *source* package ‘ChAMPdata’ ...
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (ChAMPdata)

ChAMPdata.Rcheck/ChAMPdata-Ex.timings:

nameusersystemelapsed
Anno450K3.5240.0563.580
AnnoEPIC6.6840.0406.727
CellTypeMeans27K0.0040.0000.002
CellTypeMeans450K0.0040.0000.002
ChAMPdata-package34.900 0.34435.266
ControlProbes450K0.0000.0000.002
ControlProbesEPIC0.0000.0000.001
EPIC.manifest.hg384.9400.0565.002
EPIC.manifest.pop.hg380.8640.0560.924
EPICSimData2.9400.0282.968
MatchGeneName0.0240.0000.024
PathwayList0.6040.0000.603
bloodCtl0.0000.0000.002
hm450.manifest.hg382.6320.0002.635
hm450.manifest.pop.hg381.2120.0201.229
hprdAsigH3.4360.2203.661
illumina450Gr1.7880.0001.790
illuminaEPICGr2.6280.0162.642
multi.hit0.8240.0000.826
probe.features0.7120.0120.724
probe.features.epic1.7080.0041.711
probeInfoALL.epic.lv0.7400.0040.747
probeInfoALL.lv0.5360.0000.538
snp.hit0.8680.0000.866
testDataSet11.132 0.33211.471