Are there any binaries available for Ubuntu 18 (bionic) for 3.6.3?

Posit Professional products Package Management
1

I'm trying to use the 3.6.x binaries for Ubuntu 18 (bionic) from the public package manager

I am using this package URL https://packagemanager.rstudio.com/all/linux/bionic/latest

which sources from

https://packagemanager.rstudio.com/all/linux/bionic/latest/src/contrib/PACKAGES.gz

However I notice that (most) packages are not compiled and has NeedsCompilation: YES set in PACKAGES.

According to documentation, at least RPostgreSQL, dpylr should have binaries but I am unable to find either for any distro.

Am I doing something wrong?

Thanks!
Evan

2

I cannot reproduce this. I a fresh docker container I get:

> R.version.string
[1] "R version 3.6.3 (2020-02-29)"
> system("lsb_release -a")
Distributor ID:	Ubuntu
Description:	Ubuntu 18.04.4 LTS
Release:	18.04
Codename:	bionic
No LSB modules are available.
> options("repos")
$repos
                                                              CRAN 
"https://packagemanager.rstudio.com/cran/__linux__/bionic/latest/" 
attr(,"RStudio")
[1] TRUE

> install.packages("dplyr")
Installing package into ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependencies ‘cli’, ‘pillar’, ‘purrr’, ‘digest’, ‘ellipsis’, ‘generics’, ‘glue’, ‘lifecycle’, ‘magrittr’, ‘R6’, ‘rlang’, ‘tibble’, ‘tidyselect’, ‘vctrs’

trying URL 'https://packagemanager.rstudio.com/cran/__linux__/bionic/latest/src/contrib/cli_2.0.2.tar.gz'
Content type 'binary/octet-stream' length 390769 bytes (381 KB)
==================================================
downloaded 381 KB

trying URL 'https://packagemanager.rstudio.com/cran/__linux__/bionic/latest/src/contrib/pillar_1.4.4.tar.gz'
Content type 'binary/octet-stream' length 179593 bytes (175 KB)
==================================================
downloaded 175 KB

trying URL 'https://packagemanager.rstudio.com/cran/__linux__/bionic/latest/src/contrib/purrr_0.3.4.tar.gz'
[...]

So binary packages are used for R 3.6.3 on bionic.

3

Untar this package

https://packagemanager.rstudio.com/cran/linux/bionic/latest/src/contrib/dplyr_1.0.0.tar.gz

There are no binaries inside this package from what I can tell.

I see from your log dependencies of dplyr were installed but not necessarily dplyr itself. Was Dplyr installed as a binary package?

On docker r-base 3.6.3:

options(repos=c(CRAN="xxxx://packagemanager.rstudio.com/cran/__linux__/bionic/latest/"))
> install.packages("dplyr")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘cli’, ‘pillar’, ‘purrr’, ‘ellipsis’, ‘lifecycle’, ‘rlang’, ‘tibble’, ‘tidyselect’, ‘vctrs’

trying URL 'xxxx://packagemanager.rstudio.com/cran/__linux__/bionic/latest/src/contrib/cli_2.0.2.tar.gz'
Content type 'binary/octet-stream' length 116047 bytes (113 KB)
==================================================
downloaded 113 K

But then all packages are compiled for the most part except for ones with no C dependencies.

dplyr compiles from source here

* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-j1tBvV/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c filter.cpp -o filter.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-j1tBvV/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c funs.cpp -o funs.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-j1tBvV/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c group_by.cpp -o group_by.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-j1tBvV/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c group_data.cpp -o group_data.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-j1tBvV/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c imports.cpp -o imports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-j1tBvV/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG
4

You will get the standard source package when downloading with a browser. If you use R's download.file, you will get a binary package for the R version you are using, see also https://docs.rstudio.com/rspm/admin/serving-binaries/#binaries-r-configuration-linux. For me, the above installation ends as

[...]
* installing *binary* package ‘vctrs’ ...
* DONE (vctrs)
* installing *binary* package ‘pillar’ ...
* DONE (pillar)
* installing *binary* package ‘tidyselect’ ...
* DONE (tidyselect)
* installing *binary* package ‘tibble’ ...
* DONE (tibble)
* installing *binary* package ‘dplyr’ ...
* DONE (dplyr)

The downloaded source packages are in
	‘/tmp/Rtmp1fpIIA/downloaded_packages’
>

So there might be a problem with the user string of your R installation. You can test this with

source("https://docs.rstudio.com/rspm/admin/check-user-agent.R")

See also https://docs.rstudio.com/rspm/admin/serving-binaries/#binary-user-agents.

4 Likes
5

OOOHHH MY GOD.

It fixed it.

That check user agent just fixed everything and now it install binary packages and it is awesome. You don't know how much I cried for this.

Thanks soooo much.