Error(s) in re-building vignettes:
  ...
--- re-building ‘NACHO-analysis.Rmd’ using rmarkdown
trying URL ‘https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/matrix/GSE70970_series_matrix.txt.gz’
Content type 'application/x-gzip' length 351607 bytes (343 KB)
==================================================
downloaded 343 KB

trying URL ‘https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/suppl//GSE70970_RAW.tar?tool=geoquery’
Content type 'application/x-tar' length 1986560 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL ‘https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/suppl//GSE70970_characteristics_readme.txt.gz?tool=geoquery’
Content type 'application/x-gzip' length 672 bytes
==================================================
downloaded 672 bytes

pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'NACHO-analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘NACHO-analysis.Rmd’

--- re-building ‘NACHO.Rmd’ using rmarkdown

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Found 1 file(s)
GSE70970_series_matrix.txt.gz
trying URL ‘https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/matrix/GSE70970_series_matrix.txt.gz’
Content type 'application/x-gzip' length 351607 bytes (343 KB)
==================================================
downloaded 343 KB

Parsed with column specification:
cols(
  .default = col_double(),
  ID_REF = col_character()
)
See spec(...) for full column specifications.
File stored at: 
/home/hornik/tmp/scratch/RtmpQkiqV4/GPL20699.soft
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:NACHO':

    normalize

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, 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, which.max, which.min

Welcome to Bioconductor

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

Found 1 file(s)
GSE70970_series_matrix.txt.gz
Using locally cached version: /home/hornik/tmp/scratch/RtmpQkiqV4/GSE70970_series_matrix.txt.gz
Parsed with column specification:
cols(
  .default = col_double(),
  ID_REF = col_character()
)
See spec(...) for full column specifications.
Using locally cached version of GPL20699 found here:
/home/hornik/tmp/scratch/RtmpQkiqV4/GPL20699.soft 
trying URL ‘https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/suppl//GSE70970_RAW.tar?tool=geoquery’
Content type 'application/x-tar' length 1986560 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL ‘https://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70970/suppl//GSE70970_characteristics_readme.txt.gz?tool=geoquery’
Content type 'application/x-gzip' length 672 bytes
==================================================
downloaded 672 bytes

pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
CallStack (from HasCallStack):
  error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4-5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
Error running filter /usr/bin/pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'NACHO.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘NACHO.Rmd’

SUMMARY: processing the following files failed:
  ‘NACHO-analysis.Rmd’ ‘NACHO.Rmd’

Error: Vignette re-building failed.
Execution halted