Arch Linux User Repository

Done, thanks to Arcalium

Hi, during installation with yay the installation terminates with:

gwyzip-minizip1.h:23:10: fatal error: unzip.h: No such file or directory
   23 | #include <unzip.h> 

System is Arch Linux 2026.03.01 - any headers changed ?

Edit: Minizip is in a subfolder in newer version, which prevents it to be found. I fixed this as well as the previous Gwyddion::dump.3pm issue with the following PKGBUILD file:

 
pkgname=gwyddion
pkgver=2.70
pkgrel=1
pkgdesc="A data visualization and processing tool for scanning probe miscroscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry, useful also for general image and 2D data analysis"
url="https://gwyddion.net/"
license=("GPL")
arch=('i686' 'x86_64')
depends=(gtkglext fftw pygtk minizip)
makedepends=('pkgconf' 'minizip')
optdepends=('libxml2: import of SPML and APE DAX data files'
            'zlib: import of SPML data files and import of gzip-compressed data from other file formats (Createc, NRRD, RHK SM4 PRM metadata)'
            'perl: development of plug-in'
            'ruby: development of plug-in'
            'fpc: development of plug-in'
            'gtksourceview2: Pygwy console syntax highlighting'
            'bzip2: import of bzip2-compressed data from NRRD'
            'libpng: export of height fields to 16bit greyscale PNG images and import from 16bit PNG images'
            'libwebp: WebP format support for the image export'
            'libzip: import of APE DAX, NanoObserver, NanoScanTech, OpenGPS and Sensofar PLUX data files'
            'cfitsio: import of Flexible Image Transport System (FITS) files'
            'openexr: import and export of OpenEXR HDR images'
            'hdf5: import of Ergo data files')
source=(https://downloads.sourceforge.net/sourceforge/gwyddion/$pkgname-$pkgver.tar.xz)
sha256sums=('942f4e041945a850bc32d05193a115ac8a5118a6f841afa6d4dea510f9913f59')

prepare() {
  cd "$pkgname-$pkgver"

  # Make sure core_perl is available
  export PATH="/usr/bin/core_perl:$PATH"

  # Generate the missing manpage so install doesn't fail
  (
    cd perl
    pod2man Gwyddion/dump.pm Gwyddion::dump.3pm
  )

  # Also remove the broken install target just in case
  sed -i '/install-data-local:/,+3d' perl/Makefile
}

build() {
  cd "$pkgname-$pkgver"

  # Ensure compiler can find unzip.h from minizip
  export CPPFLAGS="-I/usr/include/minizip"
  export CFLAGS="-I/usr/include/minizip $CFLAGS"

  ./configure --prefix=/usr --sysconfdir=/etc \
              --localstatedir=/var --libexecdir=/usr/lib \
              --with-minizip \
              PYTHON=python2
  make PYTHON=python2
}

package() {
  cd "$pkgname-$pkgver"

  # Again ensure pod2man is in PATH when installing
  export PATH="/usr/bin/core_perl:$PATH"

  make DESTDIR="$pkgdir" GCONF_DISABLE_MAKEFILE_SCHEMA_INSTALL=1 \
       PYTHON=python2 install
}

Oops, I missed the hard pygtk dependency there. I was actually going to suggest that having a gwyddion and gwyddion-python2 package would make sense, but doing it this way works as well. Thank you for keeping this as a possibility; it is really quite helpful for our research.

While pygtk is a dependency, python 2 should be installed.

For those who don't need pygwy, I created gwyddion-no-python2

Yes, we do need pygwy, and the continuing possibility of using it in Arch Linux is one of the reasons I use it now; we moved away from NixOS in part because of their hostility toward it even being possible. It continues to be the best way to do batch conversions of images. I'm not sure if the developers' strong views on Gtk versions, and consequently their unwillingness to move to Python 3, has changed recently, but even if it has, pygwy would likely continue to be Python 2 only for some time.

The package should cleanly install without pygwy if the AUR python2 isn't installed, however, shouldn't it?

Does anyone use pygwy? There is an assumption to exclude this option, as it depends on python 2.

https://archlinux.org/news/removing-python2-from-the-repositories/

As I run Gwyddion, multiple warnings occur:

(gwyddion:370620): Gwyddion-Program-WARNING: Function proc::fix_zero does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function proc::calibrate does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function proc::level does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function proc::align_rows does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function proc::grain_mark does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function proc::grain_filter does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function proc::shade does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function proc::laplace does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function graph::graph_cd does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function graph::graph_level does not exist

(gwyddion:370620): Gwyddion-Program-WARNING: Function graph::graph_export_ascii does not exist

(gwyddion:370620): GwyModule-CRITICAL: gwy_process_func_get_run_types: assertion 'func_info' failed

(gwyddion:370620): GwyApp-WARNING: Processing function <mask_remove> for data view context menu is not available.

(gwyddion:370620): GwyModule-CRITICAL: gwy_process_func_get_run_types: assertion 'func_info' failed

(gwyddion:370620): GwyApp-WARNING: Processing function <fix_zero> for data view context menu is not available.

(gwyddion:370620): GwyModule-CRITICAL: gwy_process_func_get_run_types: assertion 'func_info' failed

(gwyddion:370620): GwyApp-WARNING: Processing function <presentation_remove> for data view context menu is not available.

(gwyddion:370620): GwyModule-CRITICAL: gwy_process_func_get_run_types: assertion 'func_info' failed

(gwyddion:370620): GwyApp-WARNING: Processing function <level> for data view context menu is not available.
Memory protection violation

The last warning appears when I try to extract profiles from the data. Than the program just stops.

@cge That was the issue in my case. Thank you.

The problem with Gwyddion::dump.3pm is likely that while Gwyddion checks for pod2man, if it isn't available, it seems that it tries to use it anyway. pod2man is in /usr/bin/core_perl, so if that isn't in your path, it will cause this error.

I should clarify here that this can be a problem even if the perl package is installed, if /usr/bin/core_perl isn't in the path.