Package Details: 3dslicer 5.0.2-1

Git Clone URL: https://aur.archlinux.org/3dslicer.git (read-only, click to copy)
Package Base: 3dslicer
Description: A free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research
Upstream URL: https://www.slicer.org
Licenses: BSD
Submitter: tmladek
Maintainer: hottea (lilac)
Last Packager: lilac
Votes: 17
Popularity: 0.000200
First Submitted: 2015-01-21 08:58 (UTC)
Last Updated: 2022-05-06 14:55 (UTC)

Latest Comments

hottea commented on 2022-06-24 13:50 (UTC) (edited on 2022-06-24 13:52 (UTC) by hottea)

@entshuld

  1. I have 3dslicer build successfully at 20220506, and publish at ArchLinuxCN, which is a third-party repo, see also the wiki.

  2. You could also build 3dslicer-git, which is also available at ArchLinuxCN. I could confirm that this builds successfully at 20220624 (today).

  3. You could the comments at https://aur.archlinux.org/packages/teem, I build teem with different svn revision and apply patch.

entshuld commented on 2022-06-24 09:18 (UTC)

@hottea I do have teem installed

#+begin_src bash :export both :results output
  pacman -Qs teem
#+end_src

#+RESULTS:
: local/teem 1.11.0-4
:     Group of libraries for processing scientific raster data.

I ran a diff on the PKGBUILD on your personal repo and the one here, and there was no difference, which makes me think that I will have the same error. I have noticed that you refer users to your personal repository instead of AUR. Is there a reason for that? (this is understandable if one is not the maintainer oof the package, because one is forced to offer an alternative)

hottea commented on 2022-06-21 02:06 (UTC)

@entshuld You could build teem. Or just install 3dslicer from here.

entshuld commented on 2022-06-20 17:24 (UTC)

I am unable to install:

-- SuperBuild -   JsonCpp[OK]
-- SuperBuild - Slicer[OK]
CMake Error at /usr/share/cmake/Modules/ExternalProject.cmake:3068 (get_property):
  get_property could not find TARGET teem.  Perhaps it has not yet been
  created.
Call Stack (most recent call first):
  /usr/share/cmake/Modules/ExternalProject.cmake:3193 (_ep_get_file_deps)
  /usr/share/cmake/Modules/ExternalProject.cmake:3643 (_ep_add_configure_command)
  SuperBuild.cmake:543 (ExternalProject_Add)
  CMakeLists.txt:755 (include)


CMake Error at /usr/share/cmake/Modules/ExternalProject.cmake:3070 (get_property):
  get_property could not find TARGET teem.  Perhaps it has not yet been
  created.
Call Stack (most recent call first):
  /usr/share/cmake/Modules/ExternalProject.cmake:3193 (_ep_get_file_deps)
  /usr/share/cmake/Modules/ExternalProject.cmake:3643 (_ep_add_configure_command)
  SuperBuild.cmake:543 (ExternalProject_Add)
  CMakeLists.txt:755 (include)


CMake Error at /usr/share/cmake/Modules/ExternalProject.cmake:1732 (get_property):
  get_property could not find TARGET teem.  Perhaps it has not yet been
  created.
Call Stack (most recent call first):
  /usr/share/cmake/Modules/ExternalProject.cmake:2019 (ExternalProject_Get_Property)
  /usr/share/cmake/Modules/ExternalProject.cmake:3072 (_ep_get_step_stampfile)
  /usr/share/cmake/Modules/ExternalProject.cmake:3193 (_ep_get_file_deps)
  /usr/share/cmake/Modules/ExternalProject.cmake:3643 (_ep_add_configure_command)
  SuperBuild.cmake:543 (ExternalProject_Add)
  CMakeLists.txt:755 (include)


CMake Error at /usr/share/cmake/Modules/ExternalProject.cmake:1734 (message):
  External project "teem" has no stamp_dir
Call Stack (most recent call first):
  /usr/share/cmake/Modules/ExternalProject.cmake:2019 (ExternalProject_Get_Property)
  /usr/share/cmake/Modules/ExternalProject.cmake:3072 (_ep_get_step_stampfile)
  /usr/share/cmake/Modules/ExternalProject.cmake:3193 (_ep_get_file_deps)
  /usr/share/cmake/Modules/ExternalProject.cmake:3643 (_ep_add_configure_command)
  SuperBuild.cmake:543 (ExternalProject_Add)
  CMakeLists.txt:755 (include)

hottea commented on 2022-05-28 10:25 (UTC)

@Smoerrebroed You need to patch source where std::unique_ptr is used, as @bartus mentioned. See also https://gcc.gnu.org/gcc-11/porting_to.html#header-dep-changes

Smoerrebroed commented on 2022-05-28 05:32 (UTC) (edited on 2022-05-28 05:35 (UTC) by Smoerrebroed)

After replacing teem with teem-svn:

 [ 23%] Building CXX object Common/DataModel/CMakeFiles/CommonDataModel-objects.dir/vtkStructuredGrid.cxx.o
 In file included from /var/data/Downloads/3dslicer/src/build/VTK/Common/DataModel/vtkSphericalPointIterator.cxx:15: /var/data/Downloads/3dslicer/src/build/VTK/Common/DataModel/vtkSphericalPointIterator.h:272:8: error: no template named 'unique_ptr' in namespace 'std'
  std::unique_ptr<SphericalPointIterator> Iterator;
  ~~~~~^
 /var/data/Downloads/3dslicer/src/build/VTK/Common/DataModel/vtkSphericalPointIterator.h:96:3: error: cannot initialize object parameter of type 'const vtkObject' with an expression of type 'const vtkSphericalPointIterator'
  vtkAbstractTypeMacro(vtkSphericalPointIterator, vtkObject);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

bartus commented on 2022-04-04 10:22 (UTC) (edited on 2022-04-04 10:23 (UTC) by bartus)

cmake call needs -DSlicer_USE_GIT_PROTOCOL=OFF in order to prime the git submodules after the anonymous git protocol was dropped by Github.

Otherwise, you get a build error:

checkout: https://github.com/Slicer/Slicer/issues/6297

Jerzy97 commented on 2021-11-02 10:24 (UTC)

I am also unable to build 3d Slicer. It cannot find the functions pthread_* during build.

Let me know if I can help by sharing Error files.

Kyuunex commented on 2021-09-30 16:26 (UTC)

does not build

mickhowe commented on 2021-09-18 23:31 (UTC)

-> Downloading 3dslicer.svg... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 curl: (22) The requested URL returned error: 404 ==> ERROR: Failure while downloading https://github.com/Slicer/Slicer/raw/v4.11/Resources/3DSlicerLogo-app-icon.svg Aborting... Please put it back

bartus commented on 2021-06-21 17:20 (UTC) (edited on 2021-06-21 17:38 (UTC) by bartus)

Here's a quick solution with cmakes ExternalProject_Add(PATCH_COMMAND)

Apply with: git am -s < <(curl -s http://ix.io/3qFH)

hottea commented on 2021-06-21 09:39 (UTC) (edited on 2021-06-21 09:39 (UTC) by hottea)

@bartus the 1st issue should be reported to the upstream. Replace the compiler to gcc10 did not fix it yet. 3dslicer builds a python distribution and some python packages, there might be the same gcc version issue.

bartus commented on 2021-06-20 17:23 (UTC) (edited on 2021-06-21 17:20 (UTC) by bartus)

Two things:

1st. Wont build against current gcc:11 version, need to pin gcc:10 or patch sources with missing <limits> header. Error is triggered in ITK/GDCM subproject.

https://gcc.gnu.org/gcc-11/porting_to.html#header-dep-changes

2nd. Please remove ${pkgver} form sources array, as it create redundant clone for 3dslicer repo each time version is updated.

hottea commented on 2021-02-26 09:00 (UTC)

@bartus You could simply install this pkg from Arch Linux Chinese Community Repository. I also maintain pkg teem there with cmake fix. So, if you'd like to build 3dslicer from source, you also need the teem pkg from ArchLiuxCN repo. You could check all pkg build log in ArchLinuxCN repo here.

bartus commented on 2021-02-26 08:04 (UTC) (edited on 2021-02-26 08:30 (UTC) by bartus)

Won't build after f921426afaf3 against modified teems package #792288 (cmake issue):

CMake Error at /usr/share/cmake-3.19/Modules/ExternalProject.cmake:3116 (get_property):
  get_property could not find TARGET teem.  Perhaps it has not yet been
  created.
Call Stack (most recent call first):
  /usr/share/cmake-3.19/Modules/ExternalProject.cmake:3433 (_ep_add_configure_command)
  SuperBuild.cmake:560 (ExternalProject_Add)
  CMakeLists.txt:687 (include)

Without modifying teems got this error.

-- SuperBuild -   teem[OK] (SYSTEM)
CMake Error at SuperBuild/External_teem.cmake:15 (find_package):
  Could not find a package configuration file provided by "Teem" with any of
  the following names:

    TeemConfig.cmake
    teem-config.cmake

hottea commented on 2021-02-18 07:31 (UTC)

@bartus sorry, but pkg teem is not maintained by me.

bartus commented on 2021-02-18 07:22 (UTC) (edited on 2021-02-18 07:30 (UTC) by bartus)

teem package cmake configuration is broken, already posted a patch to the maintainer

https://aur.archlinux.org/packages/teem/#comment-792288

Perhaps consider packaging the svn version of the teem for AUR as it had cmake configuration rewritten in 2019 ( teem:1.10.0 is from 2012 )

https://sourceforge.net/p/teem/code/6355/

hottea commented on 2020-10-25 08:17 (UTC) (edited on 2020-10-25 08:18 (UTC) by hottea)

Hi, I could now build 3dslicer from the source, see also the PKGBUILD. You could install it from Arch Linux Chinese Community Repository.

GuSec commented on 2020-09-14 22:31 (UTC) (edited on 2020-09-14 22:39 (UTC) by GuSec)

Two issues:

  • Symlinking /opt/3dslicer/Slicer is fragile to execution directory (only full path works from my home dir). Solution: Do what zotero does; wrap by symlink to path-resolving script, e.g.
#!/usr/bin/bash
exec "$(dirname "$(readlink -f "$0")")" "$@"
  • XDG desktop file fails due to icon suffix (.png), check with desktop-file-validate /usr/share/applications/3dslicer.desktop, thus not displaying the application. Solution: Drop file suffix in .desktop (icons found by stem alone).

I also suggest /usr/share as an install prefix rather than /opt, if possible.

hottea commented on 2019-11-19 01:14 (UTC)

@gdolle It's really hard to build 3dslicer from source. It would compile python 2.7 from source and bundle with 3dslicer.

gdolle commented on 2019-11-18 13:52 (UTC) (edited on 2019-11-18 13:53 (UTC) by gdolle)

I agree with @hottea, this should be named 3dslicer-bin (existing now). Maybe change this PKGBUILD to follow build from source instructions https://www.slicer.org/wiki/Documentation/Nightly/Developers/Build_Instructions#Linux

net147 commented on 2019-11-17 23:49 (UTC)

Fails to download https://www.slicer.org/slicerWiki/images/7/71/3DSlicerLogo-DesktopIcon-128x128.png with 404 Not Found.

ng0177 commented on 2019-09-30 10:50 (UTC)

My NVIDIA graphics card is not used i.e. turning of a volume blurs the model. Any advice?

hottea commented on 2019-05-28 14:09 (UTC)

emm, it seems that you create this package with official binary file. Why not 3dslicer-bin?

Roosted7 commented on 2018-10-30 08:46 (UTC)

Thanks 9-r! I just updated the package. Sorry it took a bit longer than it should have...

9-r commented on 2018-10-23 15:41 (UTC)

Could you update the PKGBUILD please. Version 4.10.0 has been release.

-> https://download.slicer.org/bitstream/887990

sha512sum: 28aa71ecf340f6e167bf1caa3e132bc9224199e967668238bdb4d92efbfc65ad763f81029e570f1c4615f13f9f7617fabfe54a41611c098f2cb9f63a903ab25c Slicer-4.10.0-linux-amd64.tar.gz

Roosted7 commented on 2018-07-14 07:24 (UTC)

Version 4.8.1 is out, could this PKGBUILD be updated?

source: https://download.slicer.org/bitstream/738960 sha512sum: 6f4a82f6304eccbe9cae75335cde6b523e75c3d8fc66cb6ecf5820f715ad519cd7507b847b3add9a50198d373d3e403f6843bb5caae0ee8748c3624e0718871f

Thanks :)

crmullins commented on 2017-11-21 02:09 (UTC)

Updated. Thanks m-pilia for the comment with updated info in the meantime -- I appended you to the contributors.

m-pilia commented on 2017-10-30 12:44 (UTC)

for version 4.8.0: source: http://download.slicer.org/bitstream/700004 sha512sum: a0b3f0129acf4db44d4b3ec70137ace4dbd0b737ccff97d6bd4419c099d90c33c356afbe3edf7208990a97ee20036ed6e30ffc9b73df4de266691fb0e62bf634

crmullins commented on 2017-02-11 20:13 (UTC)

Hi all, Sorry for the delay, I've been dragging my feet on these packages lately. Please let me know if you have any issues with this. Chris

commented on 2017-02-09 08:55 (UTC)

Hi @tmladek, I've updated the PKGBUILD submitted by @crmullins to build 3dslicer 4.6.2 Feel free to adapt it: https://gist.github.com/grzanka/4d2cb6e18dacb08dade128f49834bcf1 Cheers, Leszek

commented on 2017-02-09 08:50 (UTC)

It would be great to update to newer version. 4.6.2 is available: http://download.slicer.org/

gokcen commented on 2017-01-22 15:37 (UTC) (edited on 2017-01-22 15:38 (UTC) by gokcen)

Any plans to update?

crmullins commented on 2015-12-31 23:54 (UTC)

Hi @tmladek, I've made a PKGBUILD for Slicer 4.5.0 [1]. I've also added the mesa opengl utilities dependency (glu). I'd be happy to help maintain this in the future if you want. Cheers, Chris [1] https://gist.github.com/chrismullins/5a645e35d376661829d4