rmarkdown updated version in posit cloud

R Markdown
, , ,
#1

While trying to knit a markdown file in the posit cloud workspace, it says it requires an updated version of the markdown package. When I tried to update the package, I was getting " installation of package ‘markdown’ had non-zero exit status." I'm still not able to knit the file. Every time I try, it says I need to update rmarkdown.

install.packages("rmarkdown")
Installing package into ‘/cloud/lib/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'http://rspm/default/__linux__/focal/latest/src/contrib/rmarkdown_2.24.tar.gz'
Content type 'application/x-gzip' length 2192010 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

  • installing source package ‘rmarkdown’ ...
    ** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
    number of columns of matrices must match (see arg 2)
    ERROR: lazy loading failed for package ‘rmarkdown’
  • removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/3.5/rmarkdown’
  • restoring previous ‘/cloud/lib/x86_64-pc-linux-gnu-library/3.5/rmarkdown’
    Warning in install.packages :
    installation of package ‘rmarkdown’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmpr4Qc8k/downloaded_packages’

#2

It seems like your package library contains packages that are not compatible with this version of R. I am not sure how that happened, but you could try to load the dependencies of rmarkdown to see which package it is, and then try to reinstall it, first from rspm, and then from a CRAN mirror.

These are the dependencies of rmarkdown:

❯ pak::pkg_deps_tree("rmarkdown")
rmarkdown 2.24 ✨ ⬇ (2.61 MB)
├─bslib 0.5.1 ✨ ⬇ (5.90 MB)
│ ├─base64enc 0.1-3 ✨
│ ├─cachem 1.0.8 ✨
│ │ ├─rlang 1.1.1 ✨
│ │ └─fastmap 1.1.1 ✨
│ ├─htmltools 0.5.6 ✨ ⬇ (355.96 kB)
│ │ ├─digest 0.6.33 ✨
│ │ ├─base64enc
│ │ ├─rlang
│ │ ├─fastmap
│ │ └─ellipsis 0.3.2 ✨
│ │   └─rlang
│ ├─jquerylib 0.1.4 ✨
│ │ └─htmltools
│ ├─jsonlite 1.8.7 ✨
│ ├─memoise 2.0.1 ✨
│ │ ├─rlang
│ │ └─cachem
│ ├─mime 0.12 ✨
│ ├─rlang
│ └─sass 0.4.7 ✨
│   ├─fs 1.6.3 ✨
│   ├─rlang
│   ├─htmltools
│   ├─R6 2.5.1 ✨
│   └─rappdirs 0.3.3 ✨
├─evaluate 0.21 ✨
├─fontawesome 0.5.2 ✨ ⬇ (1.36 MB)
│ ├─rlang
│ └─htmltools
├─htmltools
├─jquerylib
├─jsonlite
├─knitr 1.43 ✨
│ ├─evaluate
│ ├─highr 0.10 ✨
│ │ └─xfun 0.40 ✨ ⬇ (437.23 kB)
│ ├─xfun
│ └─yaml 2.3.7 ✨
├─stringr 1.5.0 ✨
│ ├─cli 3.6.1 ✨
│ ├─glue 1.6.2 ✨
│ ├─lifecycle 1.0.3 ✨
│ │ ├─cli
│ │ ├─glue
│ │ └─rlang
│ ├─magrittr 2.0.3 ✨
│ ├─rlang
│ ├─stringi 1.7.12 ✨
│ └─vctrs 0.6.3 ✨
│   ├─cli
│   ├─glue
│   ├─lifecycle
│   └─rlang
├─tinytex 0.46 ✨ ⬇ (134.98 kB)
│ └─xfun
├─xfun
└─yaml
#3

If it says the markdown package, then it could be this one, different than rmarkdown

so install.packages("markdown")

I am thinking of this, because it is a known issue in the IDE and maybe it happens also in RStudio Cloud:

1 Like