[SOLVED]Can't install packages for R scripting

callmer · 2021-02-03 20:07:00

Hi if you have experience with R please help. I've installed R and installed package with it install.packages("tidyverse"). My R_LIBS_USER is the directory where tidyverse installed. But when I try to load package in R library('tidyverse') I get error there isn't such package. I asked in R reddit community, someone said that this is particular matter of arch, so Any ideas? Thanks in advance.
solution: just install make and gcc

Last edited by callmer (2021-02-05 13:22:35)

ugjka · 2021-02-03 20:33:38

Was sudo involved?

nilesOien · 2021-02-04 00:52:35

I just installed tidyverse to check with

install.packages("tidyverse")

After that the command

library('tidyverse')

Shows this :

── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.3.3     ✔ purrr   0.3.4
✔ tibble  3.0.4     ✔ dplyr   1.0.2
✔ tidyr   1.1.2     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.0
── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Which, aside from the conflicts, seems OK, it can find tidyverse. I'm wondering if the compilation of the tidyverse failed. Is Arch up to date? Are the compilers necessary to install the tidyverse installed? Are libblas and liblapack installed?

In R, what does this command show :

sessionInfo(package = NULL)

On my system after loading tidyverse, I get this :

> sessionInfo(package = NULL)
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.9.0
LAPACK: /usr/lib/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] forcats_0.5.0   stringr_1.4.0   dplyr_1.0.2     purrr_0.3.4    
[5] readr_1.4.0     tidyr_1.1.2     tibble_3.0.4    ggplot2_3.3.3  
[9] tidyverse_1.3.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5        pillar_1.4.7      compiler_4.0.3    cellranger_1.1.0 
 [5] dbplyr_2.0.0      tools_4.0.3       jsonlite_1.7.2    lubridate_1.7.9.2
 [9] lifecycle_0.2.0   gtable_0.3.0      pkgconfig_2.0.3   rlang_0.4.10     
[13] reprex_0.3.0      cli_2.2.0         rstudioapi_0.13   DBI_1.1.0        
[17] haven_2.3.1       withr_2.3.0       xml2_1.3.2        httr_1.4.2       
[21] generics_0.1.0    vctrs_0.3.6       fs_1.5.0          hms_0.5.3        
[25] grid_4.0.3        tidyselect_1.1.0  glue_1.4.2        R6_2.5.0         
[29] fansi_0.4.1       readxl_1.3.1      modelr_0.1.8      magrittr_2.0.1   
[33] ps_1.5.0          backports_1.2.1   scales_1.1.1      ellipsis_0.3.1   
[37] assertthat_0.2.1  rvest_0.3.6       colorspace_2.0-0  stringi_1.5.3    
[41] munsell_0.5.0     broom_0.7.3       crayon_1.3.4

callmer · 2021-02-04 07:30:04

ugjka wrote:

Was sudo involved?

yes

callmer · 2021-02-04 07:45:08

nilesOien wrote:

I just installed tidyverse to check with

install.packages("tidyverse")

After that the command

library('tidyverse')

Shows this :

── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.3.3     ✔ purrr   0.3.4
✔ tibble  3.0.4     ✔ dplyr   1.0.2
✔ tidyr   1.1.2     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.0
── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Which, aside from the conflicts, seems OK, it can find tidyverse. I'm wondering if the compilation of the tidyverse failed. Is Arch up to date? Are the compilers necessary to install the tidyverse installed? Are libblas and liblapack installed?

In R, what does this command show :

sessionInfo(package = NULL)

On my system after loading tidyverse, I get this :

> sessionInfo(package = NULL)
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.9.0
LAPACK: /usr/lib/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] forcats_0.5.0   stringr_1.4.0   dplyr_1.0.2     purrr_0.3.4    
[5] readr_1.4.0     tidyr_1.1.2     tibble_3.0.4    ggplot2_3.3.3  
[9] tidyverse_1.3.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5        pillar_1.4.7      compiler_4.0.3    cellranger_1.1.0 
 [5] dbplyr_2.0.0      tools_4.0.3       jsonlite_1.7.2    lubridate_1.7.9.2
 [9] lifecycle_0.2.0   gtable_0.3.0      pkgconfig_2.0.3   rlang_0.4.10     
[13] reprex_0.3.0      cli_2.2.0         rstudioapi_0.13   DBI_1.1.0        
[17] haven_2.3.1       withr_2.3.0       xml2_1.3.2        httr_1.4.2       
[21] generics_0.1.0    vctrs_0.3.6       fs_1.5.0          hms_0.5.3        
[25] grid_4.0.3        tidyselect_1.1.0  glue_1.4.2        R6_2.5.0         
[29] fansi_0.4.1       readxl_1.3.1      modelr_0.1.8      magrittr_2.0.1   
[33] ps_1.5.0          backports_1.2.1   scales_1.1.1      ellipsis_0.3.1   
[37] assertthat_0.2.1  rvest_0.3.6       colorspace_2.0-0  stringi_1.5.3    
[41] munsell_0.5.0     broom_0.7.3       crayon_1.3.4

arch version 5.10.11-arch1-1
sessionInfo

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.9.0
LAPACK: /usr/lib/liblapack.so.3.9.0

locale:
[1] C

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

loaded via a namespace (and not attached):
[1] compiler_4.0.3

Yes, I think it's here. I don't have enough locales (but does it matter?) other attached packages and loaded via a namespace packages. But how can I solve it?

seth · 2021-02-04 08:04:44

callmer wrote:

ugjka wrote:
Was sudo involved?
yes

ugjka's question implied the answer.
Don't randomly throw around sudo.

callmer · 2021-02-04 08:21:11

seth wrote:

callmer wrote:
ugjka wrote:
Was sudo involved?
yes
ugjka's question implied the answer.
Don't randomly throw around sudo.

I had to use sudo, otherwise I wouldn't able to install packages. I think the problem is rather in my last message.

seth · 2021-02-04 08:27:13

Ok, let's specify this:
How *exactly* was sudo involved?

callmer · 2021-02-04 08:41:08

seth wrote:

Ok, let's specify this:
How *exactly* was sudo involved?

I opened R via sudo

sudo R

, and there I do all my actions

seth · 2021-02-04 08:43:40

head => desk

printenv | grep R_
sudo printenv | grep R_
cat ~/.Renviron
sudo cat /root/.Renviron

callmer · 2021-02-04 09:08:38

seth wrote:

head => desk

printenv | grep R_
sudo printenv | grep R_
cat ~/.Renviron
sudo cat /root/.Renviron

Please don't do this, I still need it's help )) Sorry my noobing but i didn't get your point. i have only one Renviron in /etc/ https://github.com/aro1999/my_arch/blob/master/Renviron and here is outputs of printenv's where I can't see anything related with R

 printenv | grep R
COLORTERM=truecolor
XAUTHORITY=/home/ararat/.Xauthority
DESKTOP_STARTUP_ID=i3/kitty/517-6-arch_TIME2256893
TERMINFO=/usr/lib/kitty/terminfo
TERM=xterm-kitty
USER=ararat
XDG_VTNR=1
XDG_RUNTIME_DIR=/run/user/1000
JOURNAL_STREAM=8:23711
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus

sudo printenv | grep R 
COLORTERM=truecolor
XAUTHORITY=/home/ararat/.Xauthority
TERM=xterm-kitty
USER=root
SUDO_USER=ararat
[ararat@arch ~]$

Last edited by callmer (2021-02-04 09:14:00)

a821 · 2021-02-04 12:51:35

I don't see R_LIBS_USER in your environment. Run the following to see R's library paths

Rscript -e '.libPaths()'

seth · 2021-02-04 14:37:24

https://github.com/aro1999/my_arch/blob/master/Renviron

R_LIBS_USER=${R_LIBS_USER-'/tmp/Rtmpo1Zrao/downloaded_packages/'}

You're installing libs into what's hopefully a tmpfs and they're gone after a reboot.
Please read up https://wiki.archlinux.org/index.php/R#Configuration

callmer · 2021-02-04 17:18:46

seth wrote:

https://github.com/aro1999/my_arch/blob/master/Renviron
R_LIBS_USER=${R_LIBS_USER-'/tmp/Rtmpo1Zrao/downloaded_packages/'}
You're installing libs into what's hopefully a tmpfs and they're gone after a reboot.
Please read up https://wiki.archlinux.org/index.php/R#Configuration

Sorry, I read config and couldn't find suitable info for my case. what about env, I changed R_LIBS_USER to /usr/lib/R/library (where default R packages are located) then I copied installed packages from /tmp to here (then I realized that they are tar.gz files) I decompressed them into the folders (with similiar content default packages had) and I thought "finally I got it!!!" but I got

'tidyverse isn't a valid installed package"

instead )))

seth · 2021-02-04 18:00:33

stop running R as root (sudo), that's insane.
Use ~/.Renviron to set meaningful user paths to a location where you have write permissions (ie. somewhere in you $HOME) and install packages there using R tzhat you did NOT start using sudo.

callmer · 2021-02-04 19:07:10

seth wrote:

stop running R as root (sudo), that's insane.
Use ~/.Renviron to set meaningful user paths to a location where you have write permissions (ie. somewhere in you $HOME) and install packages there using R tzhat you did NOT start using sudo.

ok, I reinstalled and tried all again and I got the issue. there are packages that can't be installed beacause of some dependencies

dependencies '1','2','3' aren't available for package 'somepackage'

so only those tar.gz files are being installed in /tmp but i can use mini libs from tidyverse in R, however not the whole tideverse. Now I am seek of how to install these dependencies, still can't find anything.

ugjka · 2021-02-04 19:08:40

Why are you installing in /tmp?

seth · 2021-02-04 20:37:54

Also don't paraphrase, post the actual error messages (actually the complete IO, ie. what command you issue and what -errors- the system responds)

a821 · 2021-02-04 21:21:54

callmer wrote:

I changed R_LIBS_USER to /usr/lib/R/library

That's wrong. This should be the default place for the R_LIBS_USER library (file: /etc/R/Renviron)

R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/4.0'}

If you do not want to create "~/.Renviron", then you can simply create "~/R/x86_64-pc-linux-gnu-library/4.0" and the libraries will be installed there.

And please do not ignore our comments.

callmer · 2021-02-05 09:47:20

seth wrote:

Also don't paraphrase, post the actual error messages (actually the complete IO, ie. what command you issue and what -errors- the system responds)

install.packages('tidyverse',repos='https://cloud.r-project.org/',dependencies=TRUE) > 
my_arch/error.txtInstalling package into '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0'(as 'lib' is unspecified)also installing the dependencies 'colorspace', 'sys', 'farver', 'munsell', 'askpass', 'lazyeval', 'base64enc', 'pkgbuild', 'diffobj', 'rematch2', 'backports', 'ellipsis', 'blob', 'lifecycle', 'tidyselect', 'vctrs', 'digest', 'isoband', 'scales', 'Rcpp', 'curl', 'mime', 'openssl', 'fansi', 'utf8', 'cellranger', 'progress', 'callr', 'fs', 'selectr', 'stringi', 'rex', 'yaml', 'markdown', 'xfun', 'htmltools', 'tinytex', 'brio', 'pkgload', 'processx', 'ps', 'waldo', 'broom', 'cli', 'dbplyr', 'dplyr', 'forcats', 'ggplot2', 'haven', 'hms', 'httr', 'jsonlite', 'lubridate', 'magrittr', 'modelr', 'pillar', 'purrr', 'readr', 'readxl', 'reprex', 'rlang', 'rvest', 'stringr', 'tibble', 'tidyr', 'xml2', 'covr', 'feather', 'glue', 'knitr', 'rmarkdown', 'testthat'trying URL '[url]https://cloud.r-project.org/src/contrib/colorspace_2.0-0.tar.gz[/url]'Content type 'application/x-gzip' length 2203295 bytes (2.1 MB)==================================================downloaded 2.1 MBtrying URL '[url]https://cloud.r-project.org/src/contrib/sys_3.4.tar.gz[/url]'Content type 'application/x-gzip' length 20138 bytes (19 KB)==================================================downloaded 19 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/farver_2.0.3.tar.gz[/url]'Content type 'application/x-gzip' length 1279579 bytes (1.2 MB)==================================================downloaded 1.2 MBtrying URL '[url]https://cloud.r-project.org/src/contrib/munsell_0.5.0.tar.gz[/url]'Content type 'application/x-gzip' length 182653 bytes (178 KB)==================================================downloaded 178 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/askpass_1.1.tar.gz[/url]'Content type 'application/x-gzip' length 5730 bytes==================================================downloaded 5730 bytestrying URL '[url]https://cloud.r-project.org/src/contrib/lazyeval_0.2.2.tar.gz[/url]'Content type 'application/x-gzip' length 83482 bytes (81 KB)==================================================downloaded 81 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz[/url]'Content type 'application/x-gzip' length 7833 bytes==================================================downloaded 7833 bytestrying URL '[url]https://cloud.r-project.org/src/contrib/pkgbuild_1.2.0.tar.gz[/url]'Content type 'application/x-gzip' length 30383 bytes (29 KB)==================================================downloaded 29 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/diffobj_0.3.3.tar.gz[/url]'Content type 'application/x-gzip' length 472233 bytes (461 KB)==================================================downloaded 461 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/rematch2_2.1.2.tar.gz[/url]'Content type 'application/x-gzip' length 13366 bytes (13 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'[url]https://cloud.r-project.org/src/contrib/tidyselect_1.1.0.tar.gz[/url]'Content type 'application/x-gzip' length 90842 bytes (88 KB)==================================================downloaded 88 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/vctrs_0.3.6.tar.gz[/url]'Content type 'application/x-gzip' length 778016 bytes (759 KB)==================================================downloaded 759 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/digest_0.6.27.tar.gz[/url]'Content type 'application/x-gzip' length 164373 bytes (160 KB)==================================================downloaded 160 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/isoband_0.2.3.tar.gz[/url]'Content type 'application/x-gzip' length 1902568 bytes (1.8 MB)==================================================downloaded 1.8 MBtrying URL '[url]https://cloud.r-project.org/src/contrib/scales_1.1.1.tar.gz[/url]'Content type 'application/x-gzip' length 515201 bytes (503 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'[url]https://cloud.r-project.org/src/contrib/fs_1.5.0.tar.gz[/url]'Content type 'application/x-gzip' length 796244 bytes (777 KB)==================================================downloaded 777 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/selectr_0.4-2.tar.gz[/url]'Content type 'application/x-gzip' length 41371 bytes (40 KB)==================================================downloaded 40 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/stringi_1.5.3.tar.gz[/url]'Content type 'application/x-gzip' length 7293930 bytes (7.0 MB)==================================================downloaded 7.0 MBtrying URL '[url]https://cloud.r-project.org/src/contrib/rex_1.2.0.tar.gz[/url]'Content type 'application/x-gzip' length 91925 bytes (89 KB)==================================================downloaded 89 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/yaml_2.2.1.tar.gz[/url]'Content type 'application/x-gzip' length 92670 bytes (90 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'application/x-gzip' length 11652 bytes (11 KB)==================================================downloaded 11 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/pkgload_1.1.0.tar.gz[/url]'Content type 'application/x-gzip' length 58046 bytes (56 KB)==================================================downloaded 56 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/processx_3.4.5.tar.gz[/url]'Content type 'application/x-gzip' length 135121 bytes (131 KB)==================================================downloaded 131 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/ps_1.5.0.tar.gz[/url]'Content type 'application/x-gzip' length 115131 bytes (112 KB)==================================================downloaded 112 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/waldo_0.2.3.tar.gz[/url]'Content type 'application/x-gzip' length 25726 bytes (25 KB)==================================================downloaded 25 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/broom_0.7.4.tar.gz[/url]'Content type 'application/x-gzip' length 629713 bytes (614 KB)==================================================downloaded 614 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/cli_2.3.0.tar.gz[/url]'Content type 'application/x-gzip' length 134000 bytes (130 KB)==================================================downloaded 130 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/dbplyr_2.1.0.tar.gz[/url]'Content type 'application/x-gzip' length 579687 bytes (566 KB)==================================================downloaded 566 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/dplyr_1.0.4.tar.gz[/url]'Content type 'application/x-gzip' length 953686 bytes (931 KB)==================================================downloaded 931 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/forcats_0.5.1.tar.gz[/url]'Content type 'application/x-gzip' length 258301 bytes (252 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'[url]https://cloud.r-project.org/src/contrib/jsonlite_1.7.2.tar.gz[/url]'Content type 'application/x-gzip' length 421716 bytes (411 KB)==================================================downloaded 411 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/lubridate_1.7.9.2.tar.gz[/url]'Content type 'application/x-gzip' length 472640 bytes (461 KB)==================================================downloaded 461 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/magrittr_2.0.1.tar.gz[/url]'Content type 'application/x-gzip' length 265580 bytes (259 KB)==================================================downloaded 259 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/modelr_0.1.8.tar.gz[/url]'Content type 'application/x-gzip' length 121333 bytes (118 KB)==================================================downloaded 118 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/pillar_1.4.7.tar.gz[/url]'Content type 'application/x-gzip' length 113345 bytes (110 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'[url]https://cloud.r-project.org/src/contrib/rlang_0.4.10.tar.gz[/url]'Content type 'application/x-gzip' length 915685 bytes (894 KB)==================================================downloaded 894 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/rvest_0.3.6.tar.gz[/url]'Content type 'application/x-gzip' length 2806156 bytes (2.7 MB)==================================================downloaded 2.7 MBtrying URL '[url]https://cloud.r-project.org/src/contrib/stringr_1.4.0.tar.gz[/url]'Content type 'application/x-gzip' length 135777 bytes (132 KB)==================================================downloaded 132 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/tibble_3.0.6.tar.gz[/url]'Content type 'application/x-gzip' length 681013 bytes (665 KB)==================================================downloaded 665 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/tidyr_1.1.2.tar.gz[/url]'Content type 'application/x-gzip' length 881544 bytes (860 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'application/x-gzip' length 891732 bytes (870 KB)==================================================downloaded 870 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/rmarkdown_2.6.tar.gz[/url]'Content type 'application/x-gzip' length 3213194 bytes (3.1 MB)==================================================downloaded 3.1 MBtrying URL '[url]https://cloud.r-project.org/src/contrib/testthat_3.0.1.tar.gz[/url]'Content type 'application/x-gzip' length 678199 bytes (662 KB)==================================================downloaded 662 KBtrying URL '[url]https://cloud.r-project.org/src/contrib/tidyverse_1.3.0.tar.gz[/url]'Content type 'application/x-gzip' length 712837 bytes (696 KB)==================================================downloaded 696 KB* installing *source* package 'colorspace' ...** package 'colorspace' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'colorspace'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/colorspace'* installing *source* package 'sys' ...** package 'sys' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'sys'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/sys'* installing *source* package 'farver' ...** package 'farver' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'farver'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/farver'* installing *source* package 'lazyeval' ...** package 'lazyeval' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'lazyeval'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/lazyeval'* installing *source* package 'base64enc' ...** package 'base64enc' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'base64enc'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/base64enc'* installing *source* package 'diffobj' ...** package 'diffobj' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'diffobj'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/diffobj'* installing *source* package 'backports' ...** package 'backports' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'backports'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/backports'* installing *source* package 'digest' ...** package 'digest' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'digest'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/digest'* installing *source* package 'Rcpp' ...** package 'Rcpp' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'Rcpp'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/Rcpp'* installing *source* package 'curl' ...** package 'curl' successfully unpacked and MD5 sums checked** using staged installation/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not foundUsing PKG_CFLAGS=Using PKG_LIBS=-lcurl------------------------- ANTICONF ERROR ---------------------------Configuration failed because libcurl was not found. Try installing:* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)* rpm: libcurl-devel (Fedora, CentOS, RHEL)* csw: libcurl_dev (Solaris)If libcurl is already installed, check that 'pkg-config' is in yourPATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-configis unavailable you can set INCLUDE_DIR and LIB_DIR manually via:R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'--------------------------------------------------------------------ERROR: configuration failed for package 'curl'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/curl'* installing *source* package 'mime' ...** package 'mime' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'mime'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/mime'* installing *source* package 'fansi' ...** package 'fansi' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'fansi'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/fansi'* installing *source* package 'utf8' ...** package 'utf8' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'utf8'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/utf8'* installing *source* package 'fs' ...** package 'fs' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'fs'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/fs'* installing *source* package 'stringi' ...** package 'stringi' successfully unpacked and MD5 sums checked** using staged installationchecking for R_HOME... /usr/lib64/Rchecking for R... /usr/lib64/R/bin/Rchecking for endianness... littlechecking for R >= 3.1.0 for C++11 use... yeschecking for R < 3.4.0 for CXX1X flag use... nochecking for cat... /usr/bin/cat/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not foundchecking for local ICUDT_DIR... icu61/datachecking for gcc... nochecking for cc... nochecking for cl.exe... noconfigure: error: in `/tmp/RtmpeWPecj/R.INSTALL4095de3dfc5/stringi':configure: error: no acceptable C compiler found in $PATHSee `config.log' for more detailsERROR: configuration failed for package 'stringi'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/stringi'* installing *source* package 'yaml' ...** package 'yaml' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'yaml'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/yaml'* installing *source* package 'xfun' ...** package 'xfun' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'xfun'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/xfun'* installing *source* package 'brio' ...** package 'brio' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'brio'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/brio'* installing *source* package 'ps' ...** package 'ps' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'ps'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/ps'* installing *source* package 'jsonlite' ...** package 'jsonlite' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'jsonlite'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/jsonlite'* installing *source* package 'magrittr' ...** package 'magrittr' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'magrittr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/magrittr'* installing *source* package 'rlang' ...** package 'rlang' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'rlang'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/rlang'* installing *source* package 'xml2' ...** package 'xml2' successfully unpacked and MD5 sums checked** using staged installationFound pkg-config cflags and libs!/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not found/usr/lib64/R/bin/config: line 180: make: command not found/usr/lib64/R/bin/config: line 181: make: command not found/usr/lib64/R/bin/config: line 182: make: command not found/usr/lib64/R/bin/config: line 183: make: command not found/usr/lib64/R/bin/config: line 184: make: command not found/usr/lib64/R/bin/config: line 332: make: command not foundUsing PKG_CFLAGS=-I/usr/include/libxml2Using PKG_LIBS=-lxml2 -lz -llzma -licui18n -licuuc -licudata -lm -ldl------------------------- ANTICONF ERROR ---------------------------Configuration failed because libxml-2.0 was not found. Try installing:* deb: libxml2-dev (Debian, Ubuntu, etc)* rpm: libxml2-devel (Fedora, CentOS, RHEL)* csw: libxml2_dev (Solaris)If libxml-2.0 is already installed, check that 'pkg-config' is in yourPATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-configis unavailable you can set INCLUDE_DIR and LIB_DIR manually via:R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'--------------------------------------------------------------------ERROR: configuration failed for package 'xml2'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/xml2'* installing *source* package 'glue' ...** package 'glue' successfully unpacked and MD5 sums checked** using staged installation** libssh: line 1: make: command not foundWarning in system(cmd) : error in running commandERROR: compilation failed for package 'glue'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/glue'ERROR: dependency 'colorspace' is not available for package 'munsell'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/munsell'ERROR: dependency 'sys' is not available for package 'askpass'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/askpass'ERROR: dependency 'rlang' is not available for package 'ellipsis'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/ellipsis'ERROR: dependencies 'glue', 'rlang' are not available for package 'lifecycle'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/lifecycle'ERROR: dependency 'lazyeval' is not available for package 'rex'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/rex'ERROR: dependencies 'xfun', 'mime' are not available for package 'markdown'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/markdown'ERROR: dependencies 'digest', 'base64enc', 'rlang' are not available for package 'htmltools'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/htmltools'ERROR: dependency 'xfun' is not available for package 'tinytex'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/tinytex'ERROR: dependency 'ps' is not available for package 'processx'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/processx'ERROR: dependency 'glue' is not available for package 'cli'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/cli'ERROR: dependency 'Rcpp' is not available for package 'lubridate'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/lubridate'ERROR: dependencies 'magrittr', 'rlang' are not available for package 'purrr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/purrr'ERROR: dependencies 'glue', 'magrittr', 'stringi' are not available for package 'stringr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/stringr'ERROR: dependencies 'ellipsis', 'digest', 'glue', 'rlang' are not available for package 'vctrs'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/vctrs'ERROR: dependencies 'farver', 'lifecycle', 'munsell' are not available for package 'scales'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/scales'ERROR: dependency 'askpass' is not available for package 'openssl'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/openssl'ERROR: dependency 'processx' is not available for package 'callr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/callr'ERROR: dependency 'stringr' is not available for package 'selectr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/selectr'ERROR: dependencies 'markdown', 'stringr', 'yaml', 'xfun' are not available for package 'knitr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/knitr'ERROR: dependencies 'callr', 'cli' are not available for package 'pkgbuild'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/pkgbuild'ERROR: dependencies 'rlang', 'vctrs' are not available for package 'blob'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/blob'ERROR: dependencies 'ellipsis', 'glue', 'purrr', 'rlang', 'vctrs' are not available for package 'tidyselect'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/tidyselect'ERROR: dependencies 'ellipsis', 'lifecycle', 'rlang', 'vctrs' are not available for package 'hms'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/hms'ERROR: dependencies 'curl', 'jsonlite', 'mime', 'openssl' are not available for package 'httr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/httr'ERROR: dependencies 'cli', 'ellipsis', 'fansi', 'lifecycle', 'rlang', 'utf8', 'vctrs' are not available for package 'pillar'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/pillar'ERROR: dependencies 'knitr', 'yaml', 'htmltools', 'jsonlite', 'tinytex', 'xfun', 'stringr' are not available for package 'rmarkdown'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/rmarkdown'ERROR: dependency 'hms' is not available for package 'progress'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/progress'ERROR: dependencies 'cli', 'pkgbuild', 'rlang' are not available for package 'pkgload'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/pkgload'ERROR: dependencies 'callr', 'cli', 'fs', 'glue', 'knitr', 'rlang', 'rmarkdown' are not available for package 'reprex'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/reprex'ERROR: dependencies 'xml2', 'httr', 'magrittr', 'selectr' are not available for package 'rvest'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/rvest'ERROR: dependencies 'cli', 'ellipsis', 'fansi', 'lifecycle', 'magrittr', 'pillar', 'rlang', 'vctrs' are not available for package 'tibble'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/tibble'ERROR: dependencies 'digest', 'jsonlite', 'rex', 'httr', 'yaml' are not available for package 'covr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/covr'ERROR: dependency 'tibble' is not available for package 'rematch2'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/rematch2'ERROR: dependency 'tibble' is not available for package 'cellranger'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/cellranger'ERROR: dependencies 'ellipsis', 'glue', 'lifecycle', 'magrittr', 'rlang', 'tibble', 'tidyselect', 'vctrs' are not available for package 'dplyr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/dplyr'ERROR: dependencies 'ellipsis', 'magrittr', 'rlang', 'tibble' are not available for package 'forcats'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/forcats'ERROR: dependencies 'cli', 'hms', 'rlang', 'tibble', 'lifecycle' are not available for package 'readr'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/readr'ERROR: dependencies 'Rcpp', 'tibble', 'hms' are not available for package 'feather'* removing '/home/ararat/R/x86_64-pc-linux-gnu-library/4.0/feather'ERROR: dependencies 'cli', 'diffobj', 'fansi', 'glue', 'rematch2', 'rlang', 'tibble' are not available for package 'waldo'

Last edited by callmer (2021-02-05 09:48:23)

callmer · 2021-02-05 09:50:50

a821 wrote:

callmer wrote:
I changed R_LIBS_USER to /usr/lib/R/library
That's wrong. This should be the default place for the R_LIBS_USER library (file: /etc/R/Renviron)
R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/4.0'}
If you do not want to create "~/.Renviron", then you can simply create "~/R/x86_64-pc-linux-gnu-library/4.0" and the libraries will be installed there.
And please do not ignore our comments.

My apologizes, I forgot that you don't see my responds to the other users. after I reinstalled R now it's R_LIBS_USER is folder in my ~(by default), now I have another problem of dependencies which about I wrote in my previous reply.

callmer · 2021-02-05 09:51:42

ugjka wrote:

Why are you installing in /tmp?

packages that fault to install send those tar.gz s to /tmp. I can't configure it as I know.

seth · 2021-02-05 11:16:26

You somehow botched the format and posted all messages of my_arch/error.txt into an unreadable 37000 character wide single line…

a821 · 2021-02-05 11:31:22

I somehow manage to see from the mess:

make command not found
configure: error: no acceptable C compiler found in $PATH

I mean... the error is clear.

ugjka · 2021-02-05 11:59:11

Install base-devel with pacman

Arch Linux

#1 2021-02-03 20:07:00

[SOLVED]Can't install packages for R scripting

#2 2021-02-03 20:33:38

Re: [SOLVED]Can't install packages for R scripting

#3 2021-02-04 00:52:35

Re: [SOLVED]Can't install packages for R scripting

#4 2021-02-04 07:30:04

Re: [SOLVED]Can't install packages for R scripting

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Re: [SOLVED]Can't install packages for R scripting

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Re: [SOLVED]Can't install packages for R scripting

#7 2021-02-04 08:21:11

Re: [SOLVED]Can't install packages for R scripting

#8 2021-02-04 08:27:13

Re: [SOLVED]Can't install packages for R scripting

#9 2021-02-04 08:41:08

Re: [SOLVED]Can't install packages for R scripting

#10 2021-02-04 08:43:40

Re: [SOLVED]Can't install packages for R scripting

#11 2021-02-04 09:08:38

Re: [SOLVED]Can't install packages for R scripting

#12 2021-02-04 12:51:35

Re: [SOLVED]Can't install packages for R scripting

#13 2021-02-04 14:37:24

Re: [SOLVED]Can't install packages for R scripting

#14 2021-02-04 17:18:46

Re: [SOLVED]Can't install packages for R scripting

#15 2021-02-04 18:00:33

Re: [SOLVED]Can't install packages for R scripting

#16 2021-02-04 19:07:10

Re: [SOLVED]Can't install packages for R scripting

#17 2021-02-04 19:08:40

Re: [SOLVED]Can't install packages for R scripting

#18 2021-02-04 20:37:54

Re: [SOLVED]Can't install packages for R scripting

#19 2021-02-04 21:21:54

Re: [SOLVED]Can't install packages for R scripting

#20 2021-02-05 09:47:20

Re: [SOLVED]Can't install packages for R scripting

#21 2021-02-05 09:50:50

Re: [SOLVED]Can't install packages for R scripting

#22 2021-02-05 09:51:42

Re: [SOLVED]Can't install packages for R scripting

#23 2021-02-05 11:16:26

Re: [SOLVED]Can't install packages for R scripting

#24 2021-02-05 11:31:22

Re: [SOLVED]Can't install packages for R scripting

#25 2021-02-05 11:59:11

Re: [SOLVED]Can't install packages for R scripting

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