Installing knitr 1.37 from CRAN in R 4.1.2 failed

[jlduan]

Hi,

Thanks for this wonderful package. I have some difficulties installing the latest 1.37 version. Tried remotes::install_github('yihui/knitr'), the same error.

Best

> install.packages('knitr')
Installing package into ‘/opt/homebrew/lib/R/4.1/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.37.tar.gz'
Content type 'application/x-gzip' length 895567 bytes (874 KB)
==================================================
downloaded 874 KB

* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'glue', details:
  call: NULL
  error: 'knit_engines' is not an exported object from 'namespace:knitr'
Error: unable to load R code in package ‘knitr’
Execution halted
ERROR: lazy loading failed for package ‘knitr’
* removing ‘/opt/homebrew/lib/R/4.1/site-library/knitr’
* restoring previous ‘/opt/homebrew/lib/R/4.1/site-library/knitr’

The downloaded source packages are in
        ‘/private/var/folders/yr/vrcclyl91kd_dg97yrqtwqz40000gn/T/RtmpcwyqsX/downloaded_packages’
Warning message:
In install.packages("knitr") :
  installation of package ‘knitr’ had non-zero exit status
>

R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20.6.0 (64-bit)
Running under: macOS Monterey 12.1

Matrix products: default
BLAS:   /opt/homebrew/Cellar/openblas/0.3.18/lib/libopenblasp-r0.3.18.dylib
LAPACK: /opt/homebrew/Cellar/r/4.1.2/lib/R/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2
>

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[yihui]

I have no idea why that happens, but I strongly recommend that you install R via brew install --cask r instead of brew install r. Currently you seem to have installed R in the latter way.

[jlduan]

Thanks for the reply and suggestion!
I'm probably going to migrate to cask at next R version release.

[cderv]

Error : .onLoad failed in loadNamespace() for 'glue', details:
 call: NULL
 error: 'knit_engines' is not an exported object from 'namespace:knitr'

This could also be related to glue. There was an update the same day of the last knitr release. You could try

1. uninstalling glue
2. installing knitr
3. reinstalling glue

It may work if this is indeed the issue.

[jlduan]

Error : .onLoad failed in loadNamespace() for 'glue', details:
 call: NULL
 error: 'knit_engines' is not an exported object from 'namespace:knitr'

This could also be related to glue. There was an update the same day of the last knitr release. You could try

1. uninstalling glue
2. installing knitr
3. reinstalling glue

It may work if this is indeed the issue.

Hi,

Thanks for the suggestion. I have tried uninstalling glue. It's the same error.

Uninstall glue & install knitr

> remove.packages('glue')
Removing package from ‘/opt/homebrew/lib/R/4.1/site-library’
(as ‘lib’ is unspecified)
> install.packages('knitr')
Installing package into ‘/opt/homebrew/lib/R/4.1/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.37.tar.gz'
Content type 'application/x-gzip' length 895567 bytes (874 KB)
==================================================
downloaded 874 KB

* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  there is no package called ‘glue’
Error: unable to load R code in package ‘knitr’
Execution halted
ERROR: lazy loading failed for package ‘knitr’
* removing ‘/opt/homebrew/lib/R/4.1/site-library/knitr’
* restoring previous ‘/opt/homebrew/lib/R/4.1/site-library/knitr’

The downloaded source packages are in
        ‘/private/var/folders/yr/vrcclyl91kd_dg97yrqtwqz40000gn/T/Rtmp2ZuLCx/downloaded_packages’
Warning message:
In install.packages("knitr") :
  installation of package ‘knitr’ had non-zero exit status
>

install glue and install knitr

> install.packages('glue')
Installing package into ‘/opt/homebrew/lib/R/4.1/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/glue_1.6.0.tar.gz'
Content type 'application/x-gzip' length 110320 bytes (107 KB)
==================================================
downloaded 107 KB

* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/opt/homebrew/Cellar/r/4.1.2/lib/R/include" -DNDEBUG   -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include   -fPIC  -Wno-implicit-function-declaration  -c glue.c -o glue.o
clang -I"/opt/homebrew/Cellar/r/4.1.2/lib/R/include" -DNDEBUG   -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include   -fPIC  -Wno-implicit-function-declaration  -c init.c -o init.o
clang -I"/opt/homebrew/Cellar/r/4.1.2/lib/R/include" -DNDEBUG   -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/opt/xz/include -I/opt/homebrew/include   -fPIC  -Wno-implicit-function-declaration  -c trim.c -o trim.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/homebrew/Cellar/r/4.1.2/lib/R/lib -L/opt/homebrew/opt/gettext/lib -L/opt/homebrew/opt/readline/lib -L/opt/homebrew/opt/xz/lib -L/opt/homebrew/lib -o glue.so glue.o init.o trim.o -L/opt/homebrew/Cellar/r/4.1.2/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /opt/homebrew/lib/R/4.1/site-library/00LOCK-glue/00new/glue/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (glue)

The downloaded source packages are in
        ‘/private/var/folders/yr/vrcclyl91kd_dg97yrqtwqz40000gn/T/Rtmp2ZuLCx/downloaded_packages’
> install.packages('knitr')
Installing package into ‘/opt/homebrew/lib/R/4.1/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.37.tar.gz'
Content type 'application/x-gzip' length 895567 bytes (874 KB)
==================================================
downloaded 874 KB

* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'glue', details:
  call: NULL
  error: 'knit_engines' is not an exported object from 'namespace:knitr'
Error: unable to load R code in package ‘knitr’
Execution halted
ERROR: lazy loading failed for package ‘knitr’
* removing ‘/opt/homebrew/lib/R/4.1/site-library/knitr’
* restoring previous ‘/opt/homebrew/lib/R/4.1/site-library/knitr’

The downloaded source packages are in
        ‘/private/var/folders/yr/vrcclyl91kd_dg97yrqtwqz40000gn/T/Rtmp2ZuLCx/downloaded_packages’
Warning message:
In install.packages("knitr") :
  installation of package ‘knitr’ had non-zero exit status
>

Best,

[yihui]

That's really weird. knitr doesn't use glue. I don't know why your R is always trying to load glue. Do you have anything in your ~/.Rprofile that uses glue?

BTW, again, as I mentioned in my first reply, I strongly recommend that you install the cask r instead (brew remove r && brew install --cask r).

[cderv]

Recent change in glue was to export the knitr engine
https://github.com/tidyverse/glue/blob/e9b08dd8aee6e0d5c5ab57520e219592ded849fb/R/zzz.R#L14-L20

but knitr::knit_engines is an exported object so I don't understand this issue

Error : .onLoad failed in loadNamespace() for 'glue', details:
call: NULL
error: 'knit_engines' is not an exported object from 'namespace:knitr'

knitr has glue as dependency through stringr, but again it should not be an issue during installation

> pak::pkg_deps_explain("knitr", "glue")
knitr -> stringr -> glue                                                   

Unless this creates somehow a weird conflicting loop but I can't reproduce.

Also when you are uninstalling, uninstalling packages don't forget to restart your R session.

You should retry all that with correct R version also - I don't use Mac so I don't know about that but I would trust the above ☝️

[jlduan]

Hi @yihui and @cderv

Thanks for all your suggestions.

I reinstalled stringi & stringr. And after that, I was able to get knitr installed.

Thanks! Happy holidays.

[yihui]

knitr has glue as dependency through stringr, but again it should not be an issue during installation

Oh I didn't notice that. I just looked at https://github.com/tidyverse/stringr/blob/5f48256b/DESCRIPTION#L21-L30 and I was impressed (although not surprised)... Now I tend to work on #1549 earlier next year.

[cderv]

glue has been a dependency since a few years now (tidyverse/stringr@d2a0233), mainly for str_glue() and str_glue_data(). Could have been made a Suggest probably if not using this function.

But glue is part of base tidyverse and quite low level so it is expected to be in most packages from tidyverse and related.

stringr is really painful to install from source so I would just try to remove it for this purpose. If we don't have issue on performance.

Anyway, glad it works now @jlduan. I'll close this issue.

[cderv]

😓 and... it was already closed 😅

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