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20 hours ago •
r-lib
r-lib
installation of package 'pak' had non-zero exit status
I have a problem installing pak on a certain machine, for which I get:
installation of package 'pak' had non-zero exit status
It is worth noting that the machine is remote, and I don't have admin privileges. Furthermore, the only mirror the firewall permits downloading from is https://cran.microsoft.com/.
Whereas pak fails to install, many other packages get installed just fine.
Here's the call to install.packages():
> install.packages("pak")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/***/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
pak 0.2.0 0.2.1 FALSE
installing the source package ‘pak’
trying URL 'https://cran.microsoft.com/src/contrib/pak_0.2.1.tar.gz'
Content type 'application/octet-stream' length 68695 bytes (67 KB)
downloaded 67 KB
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'pak' ...
** package 'pak' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** building pak dependency data, this can take several minutes
** deps data (37): ..........10..........20..........30.......37
** pak dependency data is embedded
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'pak'
finding HTML links ... done
cache html
handle_package_not_found html
lib_status html
local_deps html
local_deps_explain html
local_install html
local_install_deps html
local_install_dev_deps html
local_package_trees html
local_system_requirements html
lockfile_create html
lockfile_install html
metadata html
pak html
pak_cleanup html
pak_install_extra html
pak_package_sources html
pak_setup html
pak_sitrep html
pak_update html
pkg_deps html
pkg_deps_explain html
pkg_deps_tree html
pkg_download html
pkg_history html
pkg_install html
pkg_name_check html
pkg_remove html
pkg_search html
pkg_status html
repo_add html
repo_get html
repo_status html
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/sp360/Documents/R/win-library/4.1/pak'
Warning in install.packages :
installation of package ‘pak’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\***\AppData\Local\Temp\RtmpiYhNvm\downloaded_packages’
and my session info:
- Session info ------------------------------------------------------------------------------------------------------------------------------------------------
hash: man: medium-light skin tone, red hair, dvd, eject button
setting value
version R version 4.1.0 (2021-05-18)
os Windows Server x64 (build 17763)
system x86_64, mingw32
ui RStudio
language (EN)
date 2021-12-21
rstudio 1.4.1106 Tiger Daylily (desktop)
pandoc 2.12 @ C:/PROGRA~3/ANACON~1/Scripts/ (via rmarkdown)
- Packages -----------------------------------------------------------------------------------------------------------------------------------------------------
package * version date (UTC) lib source
assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.1.0)
backports 1.3.0 2021-10-27 [1] CRAN (R 4.1.1)
callr 3.7.0 2021-04-20 [2] CRAN (R 4.1.0)
cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.1)
clipr 0.7.1 2020-10-08 [2] CRAN (R 4.1.0)
crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.1)
DBI 1.1.1 2021-01-15 [2] CRAN (R 4.1.0)
digest 0.6.28 2021-09-23 [1] CRAN (R 4.1.1)
dplyr 1.0.7 2021-06-18 [1] CRAN (R 4.1.1)
ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.1.0)
evaluate 0.14 2019-05-28 [2] CRAN (R 4.1.0)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.1)
fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.1.0)
fs 1.5.0 2020-07-31 [2] CRAN (R 4.1.0)
generics 0.1.1 2021-10-25 [1] CRAN (R 4.1.1)
glue 1.5.0 2021-11-07 [1] CRAN (R 4.1.2)
highr 0.9 2021-04-16 [2] CRAN (R 4.1.0)
htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.1)
knitr 1.36 2021-09-29 [1] CRAN (R 4.1.1)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1)
magrittr 2.0.1 2020-11-17 [2] CRAN (R 4.1.0)
pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.1)
pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.1.0)
plyr 1.8.6 2020-03-03 [2] CRAN (R 4.1.0)
pROC 1.18.0 2021-09-03 [1] CRAN (R 4.1.1)
processx 3.5.2 2021-04-30 [2] CRAN (R 4.1.0)
ps 1.6.0 2021-02-28 [2] CRAN (R 4.1.0)
purrr 0.3.4 2020-04-17 [2] CRAN (R 4.1.0)
R.cache 0.15.0 2021-04-30 [1] CRAN (R 4.1.1)
R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.1.1)
R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.1.1)
R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.1.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.1)
reprex * 2.0.1 2021-08-05 [1] CRAN (R 4.1.1)
rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.1)
rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.1)
rstudioapi 0.13 2020-11-12 [2] CRAN (R 4.1.0)
sessioninfo 1.2.1 2021-11-02 [1] CRAN (R 4.1.2)
styler 1.6.2 2021-09-23 [1] CRAN (R 4.1.1)
tibble 3.1.5 2021-09-30 [1] CRAN (R 4.1.1)
tidyselect 1.1.1 2021-04-30 [2] CRAN (R 4.1.0)
tinytex 0.35 2021-11-04 [1] CRAN (R 4.1.2)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.1)
vctrs 0.3.8 2021-04-29 [2] CRAN (R 4.1.0)
withr 2.4.2 2021-04-18 [2] CRAN (R 4.1.0)
xfun 0.27 2021-10-18 [1] CRAN (R 4.1.1)
yaml 2.2.1 2020-02-01 [2] CRAN (R 4.1.0)
yardstick 0.0.9 2021-11-22 [1] CRAN (R 4.1.2)
[1] C:/Users/***/Documents/R/win-library/4.1
[2] C:/Program Files/R/R-4.1.0/library
I am not sure why the 32 bit installation fails, but you probably don't need that, anyway, so maybe this works:
install.packages("pak", INSTALL_opts="--no-test-load")
Alternatively you can install the development version, that is a binary, like this:
install.packages("pak", repos = "https://r-lib.github.io/p/pak/devel/")
See https://github.com/r-lib/pak#installation
Thanks @gaborcsardi !
I successfully installed pak via
install.packages("pak", INSTALL_opts="--no-test-load")
However, pak::pkg_install() doesn't work for me. For example, I tried to install here package:
> library(pak)
>
> pkg_install("here")
v Loading metadata database ... done
Error: Cannot install packages:
* here: Can't subset columns that don't exist.
x Columns `license` and `md5sum` don't exist.
Type .Last.error.trace to see where the error occurred
>
> .Last.error.trace
Stack trace:
12. (function (...) ...
13. base:::withCallingHandlers(cli_message = function(msg) { ...
14. get("pkg_install_make_plan", asNamespace("pak"))(...)
15. prop$stop_for_solution_error()
16. private$plan$stop_for_solve_error()
17. pkgdepends:::pkgplan_stop_for_solve_error(self, private)
18. base:::stop("Cannot install packages:\n", msg, call. = FALSE)
19. base:::.handleSimpleError(function (e) ...
20. h(simpleError(msg, call))
21. base:::stop(e)
22. (function (e) ...
x Cannot install packages:
* here: Can't subset columns that don't exist.
x Columns `license` and `md5sum` don't exist.
By contrast, install.packages("here") does work.
Try running pak::cache_clean() first. What does pak::repo_get() show? What does pak::meta_list() show?
Unfortunately pak::cache_clean() doesn't make any difference.
pak::meta_list() gives an empty table.
> pak::cache_clean()
> library(pak)
> pkg_install("here")
v Loading metadata database ... done
Error: Cannot install packages:
* here: Can't subset columns that don't exist.
x Columns `license` and `md5sum` don't exist.
Type .Last.error.trace to see where the error occurred
> pak::repo_get()
# A tibble: 5 x 5
name url type r_version bioc_version
<chr> <chr> <chr> <chr> <chr>
1 CRAN https://cran.microsoft.com cran * NA
2 BioCsoft https://bioconductor.org/packages/3.14/bioc bioc 4.1.0 3.14
3 BioCann https://bioconductor.org/packages/3.14/data/annotation bioc 4.1.0 3.14
4 BioCexp https://bioconductor.org/packages/3.14/data/experiment bioc 4.1.0 3.14
5 BioCworkflows https://bioconductor.org/packages/3.14/workflows bioc 4.1.0 3.14
> pak::meta_list()
# A tibble: 0 x 20
# ... with 20 variables: repodir <chr>, rversion <chr>, platform <chr>, needscompilation <chr>, priority <chr>, package <chr>, version <chr>, ref <chr>, type <chr>, direct <lgl>, status <chr>, target <chr>,
# mirror <chr>, sources <list>, filesize <int>, published <chr>, built <chr>, sysreqs <chr>, sha256 <chr>, deps <list>
>
Sorry, I should have said this, after a restart:
pak::meta_clean()
pak::meta_summary()
pak::meta_list()
And also this:
download.file("https://cran2.r-pkg.org/metadata/bin/windows/contrib/4.1/METADATA2.gz", tempfile())
I guess this fails for you?
Thanks.
So pak::meta_clean() and pak::meta_summary() run with no problem.
However, pak::meta_list() is still hanging (after several minutes).
See below.
As of
download.file("https://cran2.r-pkg.org/metadata/bin/windows/contrib/4.1/METADATA2.gz", tempfile())
I assume it won't run because of the firewall. Only microsoft.com domain is allowed.
> pak::meta_clean()
? Do you want to delete all package metadata (Y/n) Y
i Cleaning up cache directory C:\Users\***\AppData\Local\R\cache\R\pkgcache/_metadata.
> pak::meta_summary()
$cachepath
[1] "C:\\Users\\***\\AppData\\Local\\R\\cache\\R\\pkgcache/_metadata"
$current_db
[1] "C:\\Users\\***\\AppData\\Local\\R\\cache\\R\\pkgcache/_metadata/pkgs-9b1db897d6.rds"
$raw_files
character(0)
$db_files
character(0)
$size
[1] 0
> pak::meta_list()
- Updating metadata database [0/12] | Downloading [0 B / 0 B]
EDIT
After 15 minutes or so, pak::meta_list() finished:
> pak::meta_list()
v Updated metadata database: 0 B in 12 files.
i R 4.1 x86_64-w64-mingw32 packages are missing from CRAN and Bioconductor
i source packages are missing from CRAN and Bioconductor
v Updating metadata database ... done
# A tibble: 0 x 20
# ... with 20 variables: repodir <chr>, rversion <chr>, platform <chr>, needscompilation <chr>, priority <chr>, package <chr>, version <chr>, ref <chr>, type <chr>, direct <lgl>, status <chr>, target <chr>,
# mirror <chr>, sources <list>, filesize <int>, published <chr>, built <chr>, sysreqs <chr>, sha256 <chr>, deps <list>
EDIT 2
As predicted, the firewall blocks downloading https://cran2.r-pkg.org/metadata/bin/windows/contrib/4.1/METADATA2.gz:
> download.file("https://cran2.r-pkg.org/metadata/bin/windows/contrib/4.1/METADATA2.gz", tempfile())
trying URL 'https://cran2.r-pkg.org/metadata/bin/windows/contrib/4.1/METADATA2.gz'
Error in download.file("https://cran2.r-pkg.org/metadata/bin/windows/contrib/4.1/METADATA2.gz", :
cannot open URL 'https://cran2.r-pkg.org/metadata/bin/windows/contrib/4.1/METADATA2.gz'
In addition: Warning message:
In download.file("https://cran2.r-pkg.org/metadata/bin/windows/contrib/4.1/METADATA2.gz", :
cannot open URL 'https://cran2.r-pkg.org/metadata/bin/windows/contrib/4.1/METADATA2.gz': HTTP status was '403 URLBlocked'