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pola-rs / r-polars

Polars R binding
https://pola-rs.github.io/r-polars/
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Binary installation failure - Ubuntu 20.04 - build dependency on specific version of glibc #86

Closed msummersgill closed 1 year ago

msummersgill commented 1 year ago

Following instructions to install binary package on a Linux OS, rpolars appears to install successfully. However, when I load the library, an error occurs and indicates a required object is not available.

Appears this may be related to the version of glibc used to build - 2.34- being different than the version installed on my machine - 2.31.

I am running a vanilla Ubuntu 20.04 image on top of Windows Subsystem for Linux. I confirmed that I can build the package fro m source and use within R 4.2.3, so to me that definitely points to this being a build related issue. Not sure if it's possible (or a good idea) to weaken the dependency to 2.3x, or 2.xx. Otherwise, a different binary will be necessary for each of a half dozen versions bundled with mainstream Linux OS's released in the last couple years.

install.packages(
   "https://github.com/pola-rs/r-polars/releases/latest/download/rpolars__x86_64-pc-linux-gnu.gz",
   repos = NULL
)

# Installing package into ‘/home/matthew14786/R/x86_64-pc-linux-gnu-library/4.2’
# (as ‘lib’ is unspecified)
# trying URL 'https://github.com/pola-rs/r-polars/releases/latest/download/rpolars__x86_64-pc-linux-gnu.gz'
# Content type 'application/octet-stream' length 31120278 bytes (29.7 MB)
# ==================================================
# downloaded 29.7 MB

# * installing *binary* package ‘rpolars’ ...
# * DONE (rpolars)
> library(rpolars)
# Error: package or namespace load failed for ‘rpolars’ in dyn.load(file, DLLpath = DLLpath, ...):
#  unable to load shared object '/home/matthew14786/R/x86_64-pc-linux-gnu-library/4.2/rpolars/libs/rpolars.so':
#  /usr/lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /home/matthew14786/R/x86_64-pc-linux-gnu-library/4.2/rpolars/libs/rpolars.so)

> sessionInfo()
# R version 4.2.3 (2023-03-15)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 20.04 LTS
# 
# Matrix products: default
# BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
# LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
# 
# 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] compiler_4.2.3 tools_4.2.3
sorhawell commented 1 year ago

Hi @msummersgill , thank you for reporting this.

I likely need to add in some footnotes for the linux binary. Yes binaries for linux are not as self-contained as for win and mac, and this pre-built here can be hit or miss.

The binary was build on a github machine "ubuntu-latest". I read in the glibc docs that all versions are backwards compatible. You might therefore get away with updating glibc to any version >=2.34

I you manage to use the binary by e.g. upgrading to 2.34, I would very lover to hear about it, to add this as footnotes.

I wanted to test binaries wsl, but unfortunately my spare windows computer had a bad tantrum to night.

msummersgill commented 1 year ago

After doing some reading, I'm more than a little bit wary of upgrading in place.

But it is not so easy for glibc. Glibc, by its virtue as THE system library, it is used by all programs including many of programs that are involved in an upgrade process - doing so is the equivalent of pulling out the rug under which one is standing. It can be done, but it's tricky.

-James, on Running new applications on old glibc

I'm a little bit out of my depth here, but the accepted answer to this stack over question makes me wonder if updating the makefile to include the following might make the resulting binary more broadly usable.

rustup target add x86_64-unknown-linux-musl
cargo build [... existing arguments...] --target x86_64-unknown-linux-musl
sorhawell commented 1 year ago

Many thanks @msummersgill for suggestions. I will give it a try :)

Some other SO I could also try out

sorhawell commented 1 year ago

@msummersgill I wanted to investigate the issue and got lucky:

Not sure why it worked, but maybe the glibc dependency is some how handled by app-get or something. Maybe it is this line Processing triggers for libc-bin (2.35-0ubuntu3.1) ...

In which way did you install WSL and R?

Windows Subsystem for Linux is now available in the Microsoft Store!
You can upgrade by running 'wsl.exe --update' or by visiting https://aka.ms/wslstorepage
Installing WSL from the Microsoft Store will give you the latest WSL updates, faster.
For more information please visit https://aka.ms/wslstoreinfo

To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

Welcome to Ubuntu 22.04.1 LTS (GNU/Linux 4.4.0-19041-Microsoft x86_64)

 * Documentation:  https://help.ubuntu.com
 * Management:     https://landscape.canonical.com
 * Support:        https://ubuntu.com/advantage

This message is shown once a day. To disable it please create the
/home/ubuntu/.hushlogin file.
ubuntu@DESKTOP-NIQG5GO:~$ wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo gpg --dearmor -o /usr/share/keyrings/r-project.gpg
[sudo] password for ubuntu:
ubuntu@DESKTOP-NIQG5GO:~$ echo "deb [signed-by=/usr/share/keyrings/r-project.gpg] https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" | sudo tee -a /etc/apt/sources.list.d/r-project.list
deb [signed-by=/usr/share/keyrings/r-project.gpg] https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/
ubuntu@DESKTOP-NIQG5GO:~$ sudo apt update
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Reading package lists... Done
Building dependency tree... Done
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73 packages can be upgraded. Run 'apt list --upgradable' to see them.
ubuntu@DESKTOP-NIQG5GO:~$ sudo apt install --no-install-recommends r-base
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following additional packages will be installed:
  fontconfig fontconfig-config fonts-dejavu-core libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
  libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libquadmath0 libsm6
  libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 r-base-core r-cran-boot r-cran-class
  r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart
  r-cran-spatial r-cran-survival r-recommended unzip x11-common xdg-utils zip
Suggested packages:
  tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html
Recommended packages:
  r-base-html r-doc-html r-base-dev libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  fontconfig fontconfig-config fonts-dejavu-core libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
  libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libquadmath0 libsm6
  libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 r-base r-base-core r-cran-boot r-cran-class
  r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart
  r-cran-spatial r-cran-survival r-recommended unzip x11-common xdg-utils zip
0 upgraded, 60 newly installed, 0 to remove and 73 not upgraded.
Need to get 57.4 MB of archives.
After this operation, 104 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
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ubuntu@DESKTOP-NIQG5GO:~$ sudo -i R

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages(
+   "https://github.com/pola-rs/r-polars/releases/latest/download/rpolars__x86_64-pc-linux-gnu.gz",
+   repos = NULL
+ )
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://github.com/pola-rs/r-polars/releases/latest/download/rpolars__x86_64-pc-linux-gnu.gz'
Content type 'application/octet-stream' length 31120278 bytes (29.7 MB)
==================================================
downloaded 29.7 MB

* installing *binary* package ‘rpolars’ ...
* DONE (rpolars)
> library(rpolars)
> pl$DataFrame(iris)
polars DataFrame: shape: (150, 5)
┌──────────────┬─────────────┬──────────────┬─────────────┬───────────┐
│ Sepal.Length ┆ Sepal.Width ┆ Petal.Length ┆ Petal.Width ┆ Species   │
│ ---          ┆ ---         ┆ ---          ┆ ---         ┆ ---       │
│ f64          ┆ f64         ┆ f64          ┆ f64         ┆ cat       │
╞══════════════╪═════════════╪══════════════╪═════════════╪═══════════╡
│ 5.1          ┆ 3.5         ┆ 1.4          ┆ 0.2         ┆ setosa    │
│ 4.9          ┆ 3.0         ┆ 1.4          ┆ 0.2         ┆ setosa    │
│ 4.7          ┆ 3.2         ┆ 1.3          ┆ 0.2         ┆ setosa    │
│ 4.6          ┆ 3.1         ┆ 1.5          ┆ 0.2         ┆ setosa    │
│ ...          ┆ ...         ┆ ...          ┆ ...         ┆ ...       │
│ 6.3          ┆ 2.5         ┆ 5.0          ┆ 1.9         ┆ virginica │
│ 6.5          ┆ 3.0         ┆ 5.2          ┆ 2.0         ┆ virginica │
│ 6.2          ┆ 3.4         ┆ 5.4          ┆ 2.3         ┆ virginica │
│ 5.9          ┆ 3.0         ┆ 5.1          ┆ 1.8         ┆ virginica │
└──────────────┴─────────────┴──────────────┴─────────────┴───────────┘

> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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] compiler_4.2.3
msummersgill commented 1 year ago

Windows Subsystem for Linux supports a handful of different distributions, which is why we are getting different results.

It looks like you are running Ubuntu 22.04 includes glibc 2.35, which is >= 2.34, the version used in the build process. The error I encountered was on Ubuntu 20.04, which includes glibc 2.31.

sorhawell commented 1 year ago

great, thx. I will try out compiling on 22.04 and loading on 20.04 or older. Things move a little slow these weeks as I have full time contract. I will also look into how binaries works effortlessly in py-polars

eitsupi commented 1 year ago

Is this problem still occurring?

I tried the install on ubuntu:facal based Docker container and it seems working fine. I close this for now but feel free to open it if it reoccurs.

sorhawell commented 1 year ago

It could perhaps happen again. glibc is backwards compatible, but not forward. If polars binary is compiled with a very recent glibc, it might not work for user having an old version of glibc.

One solution maybe to compile polars with an old glibc. Glibc is tightly connected to the OS. Maybe a docker container of ubuntu 18.04 or so could be used. I wonder what glibc R-universe and CRAN uses? This have so far only happend on the github binary release.

Realistically this issue goes on the "big backlog", until this issue has been flagged again.

eitsupi commented 1 year ago

I wonder what glibc R-universe and CRAN uses?

Posit Public Package Manager have some Linux binaries. I think P3M supports all Ubuntu LTSs.

lhcamilo commented 3 days ago

I can confirm the issue is affecting ubuntu 20.04 on the cluster in my university.

I may attempt to build the package once I finish setting up rust on the cluster.

Any tips for building the package? I have been looking at the github actions command to get an idea.

eitsupi commented 3 days ago

This issue is very old. You should now be able to install it without Rust as described in the README