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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings REMP_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/REMP.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘REMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘REMP’ version ‘1.23.0’
* package encoding: UTF-8
* 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 ‘REMP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... 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 ... WARNING
Killed
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
  ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initREMP: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
initREMP: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’
remprofile: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
remprofile: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’
Undefined global functions or variables:
  IlluminaHumanMethylation450kanno.ilmn12.hg19
  IlluminaHumanMethylationEPICanno.ilm10b2.hg19
* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘REMP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fetchRMSK
> ### Title: Get RE database from RepeatMasker
> ### Aliases: fetchRMSK
> 
> ### ** Examples
> 
> L1 <- fetchRMSK(REtype = "L1", 
+                 annotation.source = "AH",
+                 genome = "hg19", 
+                 verbose = TRUE)
Loading L1 annotation data from RepeatMasker (hg19) database from AnnotationHub: AH99002
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘REMP.Rnw’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘REMP.Rnw’
  ...
  Zheng Y, Joyce BT, Liu L, Zhang Z, Kibbe WA, Zhang W, Hou L.
  Prediction of genome-wide DNA methylation in repetitive elements.
  Nucleic Acids Research. 2017;45(15):8697-711.
  PubMed PMID: 28911103; PMCID: PMC5587781. http://dx.doi.org/10.1093/nar/gkx587
********************************************************************************

> GM12878_450k <- getGM12878("450k")
Killed

... incomplete output.  Crash?

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘REMP.Rnw’ using Sweave
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins,
    colOrderStats, colProds, colQuantiles, colRanges, colRanks,
    colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs,
    colVars, colWeightedMads, colWeightedMeans,
    colWeightedMedians, colWeightedSds, colWeightedVars,
    rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse,
    rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums,
    rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs,
    rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs,
    rowVars, rowWeightedMads, rowWeightedMeans,
    rowWeightedMedians, rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages
    'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: minfi
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.7 	 2023-01-02
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

********************************************************************************
REMP version 1.23.0 (Devel)
To access full functionality of REMP, please make sure this version is current.

Citation:
  Zheng Y, Joyce BT, Liu L, Zhang Z, Kibbe WA, Zhang W, Hou L.
  Prediction of genome-wide DNA methylation in repetitive elements.
  Nucleic Acids Research. 2017;45(15):8697-711.
  PubMed PMID: 28911103; PMCID: PMC5587781. http://dx.doi.org/10.1093/nar/gkx587
********************************************************************************
Killed

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/REMP.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL REMP
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘REMP’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (REMP)