Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

New unlisted system dependency udunits2 #125

Closed
dhvalden opened this issue Jul 9, 2024 · 2 comments · Fixed by #126
Closed

New unlisted system dependency udunits2 #125

dhvalden opened this issue Jul 9, 2024 · 2 comments · Fixed by #126
Assignees

Comments

@dhvalden
Copy link

dhvalden commented Jul 9, 2024

While installing INLA:

  Configuration failed because libudunits2.so was not found. Try installing:
    * deb: libudunits2-dev (Debian, Ubuntu, ...)
    * rpm: udunits2-devel (Fedora, EPEL, ...)
    * brew: udunits (OSX)

While is a ependency of INLA, it carries to abn since INLA is a dependency of abn.

@abhishektiwari
Copy link

+1, Getting this error on Mac/Ubuntu

Error: Error installing package 'units':
=================================

* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 0.8-5
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether clang++ -std=gnu++17 accepts -g... yes
checking for clang++ -std=gnu++17 option to enable C++11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for _Bool... no
checking for stdbool.h that conforms to C99... yes
checking for error_at_line... no
checking for gcc... clang
checking whether the compiler supports GNU C... yes
checking whether clang accepts -g... yes
checking for clang option to enable C11 features... none needed
checking for XML_ParserCreate in -lexpat... yes
checking for udunits2.h... no
checking for udunits2/udunits2.h... no
checking for ut_read_xml in -ludunits2... no
configure: error: in `/private/var/folders/jc/7dkljn7n3hb2w2jsw27d0ghh0000gn/T/RtmpKCSXbm/R.INSTALL148a21dfc0/units':
configure: error: 
--------------------------------------------------------------------------------
  Configuration failed because libudunits2.so was not found. Try installing:
    * deb: libudunits2-dev (Debian, Ubuntu, ...)
    * rpm: udunits2-devel (Fedora, EPEL, ...)
    * brew: udunits (OSX)
  If udunits2 is already installed in a non-standard location, use:
    --configure-args='--with-udunits2-lib=/usr/local/lib'
  if the library was not found, and/or:
    --configure-args='--with-udunits2-include=/usr/include/udunits2'
  if the header was not found, replacing paths with appropriate values.
  You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.
--------------------------------------------------------------------------------

See `config.log' for more details
ERROR: configuration failed for package ‘units’
* removing ‘/Users/abhishektiwari/Labs/joss/Abn/renv/staging/1/units’
install of package 'units' failed [error code 1]

j-i-l added a commit that referenced this issue Jul 14, 2024
* on label install check mac & windows

* fixing running condition

* installing dependencies for macos

* try installing gsl package

* dedicated window pipeline

* fixing os parameter

* dedicated macos workflow

* Revert "try installing gsl package"

This reverts commit b6678f5.

* minor label formatting

* fixing container declaration

* installing jags

* adding jags path

* trying again with install

* installing rjags providing Jags home

* try with silent mode fore setup exe'

* adding more R versions

* install INLA

* renaming workflow

* debugging - show gls configs

* fixing to always report

* create configure file with autoconf

* installing automake

* debugging - gsl path

* providing flags for clang/gcc as well

* debugging - check jags location

* try to detect the paths for jags

* passing the args to Makevars

* better test

* debugging

* unconditional try

* debugging

* separate install of rjags

* simplify

* working with only configure.ac file

* providing jags paths does not help

* started with Fedora installation workflow

* started with restructuring installation section

* adding installing ... sections

* workflow to Fedora

* in a container it is

* installing missing tools

* specify mirror

* missing gfortran and deps

* wip on README

* fixing INLA installation mirror

* more details on jags

* adding mirrors

* Info about GSL

* fixing installation command

* done with extre installation steps

* harmonizing structure

* fixing gsl download

* providig mirror

* separately install rjags

* install R-devtools

* adding BiocManager deps

* fixing testthat call

* installing INLA separately

* fixing name

* intalling R on macos

* test without cmake

* getting the tests and run testthat

* properly handling renv

* attempt to link (r)jags

* intalling alos Suggests

* fixing path to jags.pc

* installing Suggests

* also install rjags explicitly

* install pkg-config for rjags

* working config on fedora server

* try with the pkg-config path

* without specifying type

* debugging

* fixed R script run

* check runtime linkage

* better highlighting

* debugging

* provide path to jags library

* try without pkg_config_path

* details about fedora and jags

* including entropy package

* to revert - test with actual version

* run autoconf before installing from source

* started with prereq part

* started with macos prereqs

* separate location for build and test

* Ubuntu installation workflow

* Ubuntu based workflow

* debugging folder permisssions

* allow adm group to write to /usr/local/lib

* install dependencies

* completing installing from ... parts

* formatting

* specify which dependencies

* identical testing workflow

* fixing pkg root

* adding dependencies for testing

* adding udunits for INLA #125

* typeo

* adiding curl dev for inla dep.

* installing INLA dependencies

* try to avoid version check issue in devtools

* installing openssl heasders

* installing openssl dev

* fixing package name

* first make dir writeable

* macos install gdal for s2>fmesher>INLA

* installing gdal for INLA

* fixing folder perms for R site-library

* jpeg headers for INLA dependency

* includig gdal headers for INLA

* adding gdal headers for INLA

* adding testthat again

* try install avoiding useing local .o and .so

* testing the install via CRAN

* bouncing moments dependency

* fixing typeo

* proj headers for sf>fmesher>INLA

* adding proj headers for INLA

* adding configure built with configure.ac - see #127

* specify mirror for CRAN install

* adding some more info to configure

* fixing typeo

* uniform naming

* loading library

* cleaning up windows workflow

* cleaning up macos workflow

* cleaning up fedora workflow

* cleaning up ubuntu workflow

* installing geos headers for INLA

* installing geos>terra>INLA

* corrected comment

* building from source

* how to install from source

* adding pandoc to build from source

* do not build vignettes

* fixing devtools info for mac +

* do not build vignettes

* specify repos

* ditch the matrix

* using autoreconf

* removing virtual env setup for now (is untested)

* only claim what we really tested

* minor completion by adding mirror

* adding install status badges

* minor formatting

* running on specific branch

* more structure in INLA part

* test headers

* formatting dropdowns as headers

* properly set targeted branch

* minor formatting

* adding rjags install for ubunut

* fixing typos

* fixing #129 - typo

* better indentation

* fixing some permissions for fedora

* simply ignore the installation issue for html docs
@j-i-l
Copy link
Collaborator

j-i-l commented Jul 17, 2024

Indeed, both on Fedora and on Ubuntu udunits2 is reported missing when trying to install INLA and it turns out udunits2 is not even be the only package INLA misses.

I've added the list of INLA dependencies on Fedora and Ubuntu in #124 (comment) and we also carried out the installation procedure for INLA on a MacOS and on a Windows server and documented the required steps in the Prior to installing section.

IMHO, installing INLA is a bit tedious. Unfortunately we cannot easily drop INLA as a dependency at the moment.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

3 participants