BioC experimental data: CHECK report for ChAMPdata on malbec2

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

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### Running command:
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###   /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.

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

name	user	system	elapsed
Anno450K	3.524	0.056	3.580
AnnoEPIC	6.684	0.040	6.727
CellTypeMeans27K	0.004	0.000	0.002
CellTypeMeans450K	0.004	0.000	0.002
ChAMPdata-package	34.900	0.344	35.266
ControlProbes450K	0.000	0.000	0.002
ControlProbesEPIC	0.000	0.000	0.001
EPIC.manifest.hg38	4.940	0.056	5.002
EPIC.manifest.pop.hg38	0.864	0.056	0.924
EPICSimData	2.940	0.028	2.968
MatchGeneName	0.024	0.000	0.024
PathwayList	0.604	0.000	0.603
bloodCtl	0.000	0.000	0.002
hm450.manifest.hg38	2.632	0.000	2.635
hm450.manifest.pop.hg38	1.212	0.020	1.229
hprdAsigH	3.436	0.220	3.661
illumina450Gr	1.788	0.000	1.790
illuminaEPICGr	2.628	0.016	2.642
multi.hit	0.824	0.000	0.826
probe.features	0.712	0.012	0.724
probe.features.epic	1.708	0.004	1.711
probeInfoALL.epic.lv	0.740	0.004	0.747
probeInfoALL.lv	0.536	0.000	0.538
snp.hit	0.868	0.000	0.866
testDataSet	11.132	0.332	11.471