pak
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Published
20 hours ago •
r-lib
r-lib
Newer version (0.2.0) does not work on windows os
Installation is okay, but using it will throw error:
install.packages("pak")
#> Installing package into 'C:/Users/liang/Documents/R/win-library/4.1'
#> (as 'lib' is unspecified)
#> package 'pak' successfully unpacked and MD5 sums checked
#>
#> The downloaded binary packages are in
#> C:\Users\liang\AppData\Local\Temp\RtmpeKePxh\downloaded_packages
pak::lib_status()
#> Error in load_private_package("glue"): Cannot load glue from the private library
Created on 2021-12-04 by the reprex package (v2.0.1)
Session info
sessioninfo::session_info()
#> - Session info --------------------------------------------------------------
#> hash: palms up together: medium skin tone, roll of paper, person surfing: light skin tone
#>
#> setting value
#> version R version 4.1.2 (2021-11-01)
#> os Windows 10 x64 (build 22000)
#> system x86_64, mingw32
#> ui RTerm
#> language en
#> collate Chinese (Simplified)_China.936
#> ctype Chinese (Simplified)_China.936
#> tz Asia/Taipei
#> date 2021-12-04
#> pandoc 2.14.0.3 @ C:/Program Files/RStudio/bin/pandoc/ (via rmarkdown)
#>
#> - Packages -------------------------------------------------------------------
#> package * version date (UTC) lib source
#> backports 1.4.0 2021-11-23 [1] CRAN (R 4.1.2)
#> cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.1)
#> crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.1)
#> digest 0.6.28 2021-09-23 [1] CRAN (R 4.1.1)
#> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
#> fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
#> fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0)
#> glue 1.5.0 2021-11-07 [1] CRAN (R 4.1.2)
#> highr 0.9 2021-04-16 [1] 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 [1] CRAN (R 4.1.0)
#> pak 0.2.0 2021-12-01 [1] CRAN (R 4.1.2)
#> pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.1)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
#> R.cache 0.15.0 2021-04-30 [1] CRAN (R 4.1.0)
#> R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.1.0)
#> R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.1.0)
#> R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.1.1)
#> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0)
#> rlang 0.99.0.9001 2021-11-29 [1] Github (r-lib/rlang@67da1e1)
#> rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.1)
#> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
#> sessioninfo 1.2.1 2021-11-02 [1] CRAN (R 4.1.2)
#> stringi 1.7.5 2021-10-04 [1] CRAN (R 4.1.1)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
#> styler 1.6.2 2021-09-23 [1] CRAN (R 4.1.1)
#> tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.2)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
#> vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0)
#> withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0)
#> xfun 0.28 2021-11-04 [1] CRAN (R 4.1.2)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0)
#>
#> [1] C:/Users/liang/Documents/R/win-library/4.1
#> [2] C:/Program Files/R/R-4.1.2/library
#>
#> ------------------------------------------------------------------------------
The reason might be that there is no manual dependent data building step, and the compiled data is corrupted for Windows?
Yes, the binary from CRAN is corrupt, unfortunately. You can try to install it from source and then it will create the bundle on your computer:
install.packages("pak", type = "source")
I'll submit a new version to CRAN soon.
NOTE: Apologies, this wasn't a pak issue but more so a problem with using R with conda. I was able to successfully install pak on Linux using a "normal", non-conda installation of R.
Original post:
Are we sure it's specific to only Windows? I've had the same issue with pak on Linux when installing directly from CRAN:
> install.packages("pak", repos = "https://cloud.r-project.org")
trying URL 'https://cloud.r-project.org/src/contrib/pak_0.2.1.tar.gz'
Content type 'application/x-gzip' length 68695 bytes (67 KB)
==================================================
downloaded 67 KB
* 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): Failed
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (pak)
The downloaded source packages are in
‘/tmp/RtmpovfTI8/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
And my sessionInfo():
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS
Matrix products: default
BLAS/LAPACK: /anaconda/envs/rinla/lib/libopenblasp-r0.3.18.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] pak_0.2.1 ps_1.6.0 fansi_1.0.2 utf8_1.2.2
[5] crayon_1.4.2 R6_2.5.1 lifecycle_1.0.1 magrittr_2.0.1
[9] pillar_1.6.4 rlang_0.4.12 cli_3.1.1 callr_3.7.0
[13] vctrs_0.3.8 ellipsis_0.3.2 tools_4.1.2 glue_1.6.1
[17] compiler_4.1.2 processx_3.5.2 pkgconfig_2.0.3 tibble_3.1.6
pak does install when using CRAN, but it gives the same error regarding glue. And, as can be seen, the deps data stage is failing.
If, however, I use the development version, it works properly:
install.packages("pak", repos = "https://r-lib.github.io/p/pak/devel/")
It is strange that install.packages("pak", type = "source") works in my one linux server but not the following one. I tried many times but it does not work. However, install.packages("pak", repos = "https://r-lib.github.io/p/pak/devel/") solved this issue.
> install.packages("pak", type = "source")
Installing package into ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/pak_0.3.0.tar.gz'
Content type 'application/octet-stream' length 88564 bytes (86 KB)
==================================================
downloaded 86 KB
* 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 (23): ..........10..........20...23
** 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
** 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 (pak)
The downloaded source packages are in
‘/tmp/RtmpLnvjAf/downloaded_packages’
> pak::pkg_install("fastverse")
Error in load_private_package("glue") :
Cannot load glue from the private library
Restarting R session...
> pak::pkg_install("fastverse")
Error in load_private_package("glue") :
Cannot load glue from the private library
> install.packages("pak", type = "source")
Error in install.packages : Updating loaded packages
Restarting R session...
> install.packages("pak", type = "source")
Installing package into ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/pak_0.3.0.tar.gz'
Content type 'application/octet-stream' length 88564 bytes (86 KB)
==================================================
downloaded 86 KB
* 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 (23): ..........10..........20...23
** 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
** 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 (pak)
The downloaded source packages are in
‘/tmp/RtmpfoDGJA/downloaded_packages’
> pak::pkg_install("fastverse")
Error in load_private_package("glue") :
Cannot load glue from the private library
> sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.1 (2020-06-06)
os CentOS Linux 7 (Core)
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Asia/Shanghai
date 2022-04-25
rstudio 1.3.959 Middlemist Red (server)
pandoc NA
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cli 3.2.0 2022-02-14 [1] CRAN (R 4.0.1)
pak 0.3.0 2022-04-11 [1] CRAN (R 4.0.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.0.1)
[1] /home/wangsx/R/x86_64-pc-linux-gnu-library/4.0
[2] /opt/R/4.0.1/lib/R/library
@ShixiangWang that is weird indeed. Can you try another mirror, just to rule out a broken mirror?
I tried another mirror, the same problem. @gaborcsardi
> remove.packages("pak")
Removing package from ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
> install.packages("pak", repos = "http://cran.us.r-project.org", type = "source")
Installing package into ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.us.r-project.org/src/contrib/pak_0.3.0.tar.gz'
Content type 'application/x-gzip' length 88564 bytes (86 KB)
==================================================
downloaded 86 KB
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
* 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 (23): ..........10..........20...23
** inst
** byte-compile and prepare package for lazy loading
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
** 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
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
** testing if installed package can be loaded from temporary location
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
** testing if installed package keeps a record of temporary installation path
* DONE (pak)
The downloaded source packages are in
‘/tmp/RtmpIRoGU7/downloaded_packages’
> pak::pkg_install("dplyr")
Error in load_private_package("glue") :
Cannot load glue from the private library
The second approach still works.
> install.packages("pak", repos = "https://r-lib.github.io/p/pak/devel/")
Installing package into ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://r-lib.github.io/p/pak/devel/src/contrib/../../linux/x86_64/pak_0.3.0.9000_R-4-0_x86_64-linux.tar.gz'
Content type 'application/gzip' length 7640747 bytes (7.3 MB)
==================================================
downloaded 7.3 MB
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
* installing *binary* package ‘pak’ ...
* DONE (pak)
The downloaded source packages are in
‘/tmp/RtmpzV1YsJ/downloaded_packages’
> pak::pkg_install("dplyr")
✓ Loading metadata database ... done
ℹ No downloads are needed
✓ 1 pkg + 17 deps: kept 17 [5.4s]
@ShixiangWang I can't reproduce this, unfortunately.
It seems that you are loading some packages from .Rprofile, can you to omit remove this from your profile, temporarily? Just to see if this is causing any trouble.
@gaborcsardi Thanks. I comment all lines in ~/.Rprofile and ~/.R/Makevars. It works.
> remove.packages("pak")
Removing package from ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
> install.packages("pak", repos = "http://cran.us.r-project.org", type = "source")
Installing package into ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.us.r-project.org/src/contrib/pak_0.3.0.tar.gz'
Content type 'application/x-gzip' length 88564 bytes (86 KB)
==================================================
downloaded 86 KB
* 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 (23): ..........10..........20...23
** 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
** 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 (pak)
The downloaded source packages are in
‘/tmp/RtmpPzadxa/downloaded_packages’
> pak::pkg_install("dplyr")
⠋ Updating metadata database [0/6] | Downloading [0 B / 0 B]
Found Updating metadata database ... done
ℹ No downloads are needed
✔ 1 pkg + 17 deps: kept 16 [23.7s]
~/.Rprofile
old_path = Sys.getenv("PATH")
Sys.setenv(PATH = paste(old_path, "~/miniconda3/bin/", sep = ":"))
options(BioC_mirror="https://mirrors.bfsu.edu.cn/bioconductor")
options("repos" = c(CRAN="https://mirrors.bfsu.edu.cn/CRAN/"))
library(usethis)
library(skimr)
library(fastverse)
library(ggplot2)
Makevars
CXX11=/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -fPIC
CXX14=/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++14 -fPIC
Thanks, this is really useful! Can you please try one a couple of more things, to pin this down?
Can you install glue from source? (With your profile and env file.)
Can you try one commenting out only Makevars and install pak from source?
Can you try commenting out only the miniconda path line, and install pak from source?
Thanks very much!
I cannot reinstall glue in case 1 as the .Rprofile loaded it.
> install.packages("glue")
Installing package into ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/glue_1.6.2.tar.gz'
Content type 'application/octet-stream' length 106510 bytes (104 KB)
==================================================
downloaded 104 KB
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/opt/R/4.0.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c glue.c -o glue.o
gcc -std=gnu99 -I"/opt/R/4.0.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I"/opt/R/4.0.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c trim.c -o trim.o
gcc -std=gnu99 -shared -L/opt/R/4.0.1/lib/R/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/opt/R/4.0.1/lib/R/lib -lR
installing to /home/wangsx/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-glue/00new/glue/libs
** R
** inst
** byte-compile and prepare package for lazy loading
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
Error in unloadNamespace("glue") :
namespace ‘glue’ is imported by ‘usethis’, ‘ggplot2’, ‘tidyselect’, ‘dplyr’, ‘pillar’ so cannot be unloaded
Execution halted
ERROR: lazy loading failed for package ‘glue’
* removing ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0/glue’
* restoring previous ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0/glue’
Warning in install.packages :
installation of package ‘glue’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpzgG8Fu/downloaded_packages’
Case 2, comment the Makevars. Same as previous, dont work anymore.
> install.packages("pak", type = "source")
Installing package into ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/pak_0.3.0.tar.gz'
Content type 'application/octet-stream' length 88564 bytes (86 KB)
==================================================
downloaded 86 KB
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
* 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 (23): ..........10..........20...23
** inst
** byte-compile and prepare package for lazy loading
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
** 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
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
** testing if installed package can be loaded from temporary location
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
-- Attaching packages --------------------------------------- fastverse 0.2.3 --
v data.table 1.14.2 v collapse 1.7.6
v magrittr 2.0.3 v matrixStats 0.61.0
v kit 0.0.11 v fst 0.9.8
** testing if installed package keeps a record of temporary installation path
* DONE (pak)
The downloaded source packages are in
‘/tmp/RtmpYU6Qbc/downloaded_packages’
> pak::pkg_install("dplyr")
Error in load_private_package("glue") :
Cannot load glue from the private library
Case 3, comment out PATH update (remove conda to path). Same as above.
Case 4, comment the library loading, works!
#old_path = Sys.getenv("PATH")
#Sys.setenv(PATH = paste(old_path, "~/miniconda3/bin/", sep = ":"))
options(BioC_mirror="https://mirrors.bfsu.edu.cn/bioconductor")
options("repos" = c(CRAN="https://mirrors.bfsu.edu.cn/CRAN/"))
# library(usethis)
# library(skimr)
# library(fastverse)
# library(ggplot2)
> install.packages("pak", type = "source")
Installing package into ‘/home/wangsx/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/pak_0.3.0.tar.gz'
Content type 'application/octet-stream' length 88564 bytes (86 KB)
==================================================
downloaded 86 KB
* 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 (23): ..........10..........20...23
** 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
** 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 (pak)
The downloaded source packages are in
‘/tmp/RtmpNCVpbr/downloaded_packages’
> pak::pkg_install("dplyr")
⠋ Updating metadata database [0/6] | Downloading [0 B / 0 B]
Found Updating metadata database ... done
ℹ No downloads are needed
✔ 1 pkg + 17 deps: kept 16 [24.2s]
Great, thank you, this is invaluable! There is a chance that I can fix this, but if not, then we could at least give a better error message.
Btw. it is not great to unconditionally load packages in .Rprofile. This is why you cannot even install glue, because the installer process also loads the profile, and then R tries to unload glue, but can't because other packages depend on it.
The installer process probably should not load any packages, but this something that you or I can fix.
One way to work around this is to check for the environment variable that is always set for the install:
if (Sys.getenv("R_INSTALL_PKG") == "") {
library(usethis)
library(skimr)
library(fastverse)
library(ggplot2)
}