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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings REMP_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/REMP.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘REMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘REMP’ version ‘1.34.0’
* 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 code 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 ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Alu.hg19.demo.Rd: GRanges
  Alu.hg38.demo.Rd: GRanges
  GRannot.Rd: GRanges, GRangesList
  REMProduct-class.Rd: BiocParallelParam, org.Hs.eg.db
  fetchRMSK.Rd: GRanges
  fetchRefSeqGene.Rd: GRangesList, GRanges
  findRECpG.Rd: GRanges, BiocParallel
  getBackend.Rd: BiocParallel
  getGM12878.Rd: GenomicRatioSet, RatioSet
  grooMethy.Rd: RatioSet, GenomicRatioSet, DataFrame, GRanges,
    impute.knn
  initREMP.Rd: GRanges, AnnotationHub, BiocParallelParam
  remp.Rd: RatioSet, GenomicRatioSet, DataFrame, GRanges,
    BiocParallelParam, ranger
  rempTemplate.Rd: RatioSet, GenomicRatioSet, DataFrame, GRanges
  remprofile.Rd: RatioSet, GenomicRatioSet, DataFrame, GRanges,
    AnnotationHub
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
Warning: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/105748’
  local file path: ‘/home/biocbuild/.cache/R/AnnotationHub/29e746adcde29_105748’
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! SSL peer certificate or SSH remote key was not OK [functionalgenomics.upf.edu]:
server certificate verification failed. CAfile: none CRLfile: none
Warning: bfcadd() failed; resource removed
  rid: BFC85
  fpath: ‘https://annotationhub.bioconductor.org/fetch/105748’
  reason: download failed
Warning: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/105748’
  cache resource: ‘AH99002 : 105748’
  reason: bfcadd() failed; see warnings()
Warning: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/105748’
  local file path: ‘/home/biocbuild/.cache/R/AnnotationHub/29e74677c70378_105748’
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! SSL peer certificate or SSH remote key was not OK [functionalgenomics.upf.edu]:
server certificate verification failed. CAfile: none CRLfile: none
Warning: bfcadd() failed; resource removed
  rid: BFC86
  fpath: ‘https://annotationhub.bioconductor.org/fetch/105748’
  reason: download failed
Warning: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/105748’
  cache resource: ‘AH99002 : 105748’
  reason: bfcadd() failed; see warnings()
Error: failed to load resource
  name: AH99002
  title: UCSC RepeatMasker annotations (Mar2020) for Human (hg19)
  reason: 1 resources failed to download
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
GRannot 12.209  1.272  14.779
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/REMP.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL REMP
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘REMP’ ...
** this is package ‘REMP’ version ‘1.34.0’
** 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)