R package with system dependencies: pkg-config: symbol lookup error

HPC Support HPC issues
1

I just started using the cluster, trying use R with the standard package tidyverse.

Upon using install.packages(“tidyverse”), there is an error due to the fact that the R-dependency textshaping has a system dependency.

Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:

  • deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
  • rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
  • csw: libharfbuzz_dev libfribidi_dev (Solaris)
  • brew: harfbuzz fribidi (OSX)

So I tried to load these dependencies with:

module load GCCcore/12.2.0 HarfBuzz/5.3.1
module load GCCcore/13.2.0 FriBidi/1.0.13

But I still get a (slightly different) error:

pkg-config: symbol lookup error: pkg-config: undefined symbol: pkgconf_pkg_dir_list_build
pkg-config: symbol lookup error: pkg-config: undefined symbol: pkgconf_pkg_dir_list_build
Using PKG_CFLAGS=
Using PKG_LIBS=-lfreetype -lharfbuzz -lfribidi -lpng

If harfbuzz freetype2 fribidi is already installed, check that ‘pkg-config’ is in your
PATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars=‘INCLUDE_DIR=… LIB_DIR=…’

Could you please advise me on what is the pkg-config: symbol lookup error: pkg-config: undefined symbol: pkgconf_pkg_dir_list_build error, and what should be done to have
install.packages("textshaping")
to run?

Thanks!

Minimal reprex:

module load GCC/11.3.0  OpenMPI/4.1.4 R/4.2.1
module load GCCcore/12.2.0 HarfBuzz/5.3.1
module load GCCcore/13.2.0 FriBidi/1.0.13
R
install.packages("textshaping")
2

Dear @Matthieu.Stigler

you can’t load the software that are requesting different version of GCC or OpenMPI at the same time: you need to stick the the same common base for all the software you load.

For your case, this should work:

(baobab)-[sagon@login2 ~]$ ml purge
(baobab)-[sagon@login2 ~]$ ml GCC/11.3.0  OpenMPI/4.1.4 R/4.2.1 HarfBuzz/4.2.1 FriBidi/1.0.12

Best

3

Thanks a lot @Yann.Sagon for looking into it!

Unfortunately, I still see the same error message, despite using your new line, see below output and a minimal reproducible example.

I wonder whether I am missing the -dev versions of HarfBuzz or FriBidi, noting that the error message mentions:

Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:

  • deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
  • rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
  • csw: libharfbuzz_dev libfribidi_dev (Solaris)

Is it possible that baobab’s FriBidi/1.0.12 corresponds to the non-devel version of harfbuzz-devel? How can I check that, in particular whether the file hb-ft.h is included?

Thanks!!

minimum reproducible code

module load GCC/11.3.0 OpenMPI/4.1.4 R/4.2.1 HarfBuzz/4.2.1 FriBidi/1.0.12
R
install.packages("textshaping")

error message

pkg-config: symbol lookup error: pkg-config: undefined symbol: pkgconf_pkg_dir_list_build
pkg-config: symbol lookup error: pkg-config: undefined symbol: pkgconf_pkg_dir_list_build
Using PKG_CFLAGS=
Using PKG_LIBS=-lfreetype -lharfbuzz -lfribidi -lpng
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:

  • deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
  • rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
  • csw: libharfbuzz_dev libfribidi_dev (Solaris)
  • brew: harfbuzz fribidi (OSX)
    If harfbuzz freetype2 fribidi is already installed, check that ‘pkg-config’ is in your
    PATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.pc file . If pkg-config
    is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
    R CMD INSTALL --configure-vars=‘INCLUDE_DIR=… LIB_DIR=…’
    -------------------------- [ERROR MESSAGE] ---------------------------
    :1:10: fatal error: hb-ft.h: No such file or directory
    compilation terminated.
4

Hello,

You can check like that:

(baobab)-[testsagon1@login2 ~]$ ls $EBROOTHARFBUZZ/include/harfbuzz/hb-ft.h
/opt/ebsofts/HarfBuzz/4.2.1-GCCcore-11.3.0/include/harfbuzz/hb-ft.h

It seems the error is due to

pkg-config: symbol lookup error: pkg-config: undefined symbol: pkgconf_pkg_dir_list_build

You are using pkg-config from the OS which is version 1.4.2. I tried with pkg-config from EasyBuild and I could install the package successfully (this time I tested it!)

module load GCC/11.3.0 OpenMPI/4.1.4 R/4.2.1 HarfBuzz/4.2.1 FriBidi/1.0.12 pkg-config/0.29.2

Best

Yann

5

Excellent, that did the trick, thanks a lopt @Yann.Sagon !!

As an aside, I’m slightly confused by the package numbers… are we here really downgrading pkg-config from 1.4.2. to 0.29, or are these different version numbers?

Thanks!

6

I have no idea, I didn’t checked.