External Email - Use Caution
Hi,
I'm trying to create a freesurfer (v7.3.3) package definition for guix. I have some problems during freesurfers configure step though. I'm using the following definitions to build freesurfer (this may not help much if you don't know guix, but you may still see what might be wrong in the attached build log).
``` (use-modules (gnu packages algebra) (gnu packages check) (gnu packages commencement) (gnu packages compression) (gnu packages fontutils) (gnu packages geo) (gnu packages gl) (gnu packages image) (gnu packages image-processing) (gnu packages llvm) (gnu packages maths) (gnu packages pdf) (gnu packages perl) (gnu packages python) (gnu packages qt) (gnu packages serialization) (gnu packages shells) (gnu packages sqlite) (gnu packages tcl) (gnu packages vim) (gnu packages xiph) (gnu packages xml) (gnu packages xorg) (guix build-system cmake) (guix download) (guix gexp) (guix git-download) ((guix licenses) #:prefix license:) (guix packages))
(define-public itk (package (name "itk") (version "5.3.0") (source (origin (method git-fetch) (uri (git-reference (url "https://secure-web.cisco.com/1KgpkMc1pvHUPomaJMVqKQnZBVMErQsj49d1dySfD5xTF-4...") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1bx98lzafj83fxylm0qnxkn05rdlrvfc672f0n843hgis2wk0gfh")))) (build-system cmake-build-system) (arguments `(#:configure-flags (list "-DBUILD_EXAMPLES=OFF" "-DITK_FORBID_DOWNLOADS=ON" "-DITK_USE_KWSTYLE=OFF" ; requires git during build "-DITK_USE_SYSTEM_LIBRARIES=ON" "-DITK_USE_CLANG_FORMAT=OFF" (string-append "-DGTEST_ROOT=" (assoc-ref %build-inputs "googletest"))) #:phases ,#~(modify-phases %standard-phases (add-before 'configure 'unpack-test-data (lambda _ (invoke "tar" "xzf" #$(this-package-native-input "test-data") "--strip-components=1")))))) (native-inputs `(("cppcheck" ,cppcheck) ("eigen" ,eigen) ("googletest" ,(package-source googletest)) ("perl" ,perl) ("python" ,python) ("test-data" ,(origin (method url-fetch) (uri (string-append "https://secure-web.cisco.com/14JbcCit8VdllWuNGvNogUu6Rm4HBxrjFJ5eN_gcCfjbdtn..." version "/InsightData-" version ".tar.gz")) (sha256 (base32 "1iyr037x7yqkdhd3w427pp6ba947l79acplq4cx9jicrbfgbxy2k")))))) (inputs (list expat hdf5 libjpeg-turbo libpng libtiff zlib)) (outputs (list "out" "debug")) (synopsis "Spatially-oriented architecture for processing, segmentation, and registration of scientific images") (description "The Insight Toolkit (ITK) is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. Typically the sampled representation is an image acquired from such medical instrumentation as CT or MRI scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with a MRI scan in order to combine the information contained in both.") (home-page "https://secure-web.cisco.com/1e3XSo-gh-p-0Y5bOrS4AAQKhvfMxcv9IpC5tdPa-bv-CJc...") (license license:asl2.0)))
(define-public freesurfer (package (name "freesurfer") (version "7.3.3") (source (origin (method git-fetch) (uri (git-reference (url "https://secure-web.cisco.com/1wexvnLD388FTeoOYQDV62Yu0pE_NZYF0g3QWqMApqiUTsn...") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "1vn9vs6q451qp8ak62fc21zv91gm2f0f5wiijh4xj4zys3fyvi93")) (modules '((guix build utils))) (snippet '(begin (substitute* "CMakeLists.txt" (("ARMADILLO") "Armadillo") (("OPENGL") "OpenGL")) (substitute* "cmake/FindOpenCV.cmake" (("opencv2 PATH_SUFFIXES include") "opencv2 opencv4/opencv2 PATH_SUFFIXES include")))))) (build-system cmake-build-system) (arguments `(#:configure-flags (list "-DMARTINOS_BUILD=OFF" "-DBUILD_GUIS=OFF"))) (native-inputs `(("gfortran-toolchain" ,gfortran-toolchain) ("gl2ps" ,gl2ps) ("googletest" ,(package-source googletest)) ("perl" ,perl) ("python" ,python) ("tcl" ,tcl) ("tcsh" ,tcsh) ("xxd" ,xxd))) (inputs (list armadillo openblas double-conversion eigen expat freetype hdf5 glew itk jsoncpp lapack libharu libjpeg-turbo libpng libtheora libtiff libx11 libxt libxml2 libxmu lz4 mesa netcdf opencv petsc proj qtbase-5 qtx11extras sqlite vtk zlib)) (outputs (list "out" "debug")) (synopsis "Software suite for processing human brain MRI") (description "FreeSurfer is a software package for the analysis and visualization of neuroimaging data from cross-sectional and longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging.
FreeSurfer provides full processing streams for structural and functional MRI and includes tools for linear and nonlinear registration, cortical and subcortical segmentation, cortical surface reconstruction, statistical analysis of group morphometry, diffusion MRI, PET analysis, and much more. It is also the structural MRI analysis software of choice for the Human Connectome Project.") (home-page "https://secure-web.cisco.com/1PZCRDcDOn3O1uoFNsBeYHfpLQY2DOO20fJU6mAm8xv-5H1...") ;; it's an open source license but afaict it isn't free as in freedom. (license #f)))
```
The output of `guix describe`: ``` Generation 168 Feb 01 2023 13:00:36 (current) guix 14323ed repository URL: https://secure-web.cisco.com/15q8zTqQfZSwuvTajUs5f9N2aYltiq9edRi1PUyW8JzLdAG... branch: master commit: 14323edcc37d9efaae2491cf5f57ea0621412d7e nonguix c694cf9 repository URL: https://secure-web.cisco.com/1XwNEBscgHWCPMrio9mZuc4l17saADnyXjvBec6Pavy9o8T... branch: master commit: c694cf9211db3cc8673f0e73708d53b75d26518b ```
Now to my questions/remarks: - As i can see in the wiki i am actually supposed to set `FS_PACKAGES_DIR` but as far as i understand this setting it doesn't make sense in guix. What is the exact purpose of this variable? Every dependency of freesurfer that is specified in the `native-inputs` (which is for dependencies only used at build time) and `inputs` fields is available during the build (and _only_ what is specified there). The configure output in the log also clearly shows that all dependencies are actually found (besides ANN that isn't packaged and i haven't packaged it myself until now; i should probably do that...)
- cmake searches for `FindARMADILLO.cmake` but the file is called `FindArmadillo.cmake` which results in CMake erroring out because it can't find `FindARMADILLO.cmake`. The find_package for Armadillo is commented out on dev though.
- The actual error i hit currently are quite a bunch of these for different files, cmake reported earlier that it could find all X11 deps though. Googling for it seems to suggest that this could be due to transitive dependencies interfering with each other (vtk also imports libx11; but this is just a guess) ``` CMake Error at cmake/functions.cmake:234 (add_executable): Target "lineprof_test" links to target "X11::X11" but the target was not found. Perhaps a find_package() call is missing for an IMPORTED target, or an ALIAS target is missing? Call Stack (most recent call first): lineprof/CMakeLists.txt:31 (add_test_executable) ```
- even though i have lapack and openblas and the gfortran toolchain inside the build environment, i get: ``` CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: BLAS_LIBRARIES linked by target "lineprof_test" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/lineprof linked by target "surf2vol" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/fem_elastic GFORTRAN_LIBRARIES linked by target "lineprof_test" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/lineprof linked by target "surf2vol" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/fem_elastic LAPACK_LIBRARIES linked by target "lineprof_test" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/lineprof linked by target "surf2vol" in directory /tmp/guix-build-freesurfer-7.3.3.drv-0/source/fem_elastic ``` How am i supposed to let the build system know these variables? As the files are there i would have expected cmake to pick those up itself
thanks in advance for any help :-) Malte