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-4FwrJqic4QH24BS9A6FBEYTsie5s6QjHF0t3oUiyHbksw5PN1DApfmLPKVbSP_xhn7z9By42NVRA216Pm__lnJXQKlCZ7sMPCVl31xoayVBrdUkbqszGSz63mPjuIwpNDDrjGDsPzv1RMC0f-0_V5B14dce0LmASzaVZAW5U7EgZz6r_HrtKURXUiGIaD79wJIM8Xu0dkyqZHduy_zW9Ro9Kt5gX0bekAR35_MfXAiXqGp5QQaKWMb4LZqjQ_keQaYVK343qyRjCO2TfCNAnmAs84qSPvXhUC9Z4gvVPA/https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium%2FITK";)
(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_gcCfjbdtn1TR7ZH-n2wrcmPq7CZxgCRHwwEdWumZnIwOL1kmEL1_iKt6zFd0WJe9UtzAmwdYnCcmuOkUfEm9JIZyA6_w-fwA9GeHGN7oD7hDOv1voukf2O4a7OJg-j5GIGJjPp1FM2Hdd9jXZOwwvnhOE51e9iVxZHcmjltg4IuTTx9Zj8mdJRZjxJJhfZdfF04qv1o0wowDjPRDGBwzbf6RBo176tQvxWz-a2ZULLo569ay62shBk8ED4ds_isWIOi_ZgLTf8iSvlFJx5FPxBt7Ly_i6JCwGB-cjo1hFRnN1V60w/https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium%2FITK%2Freleases%2Fdownload%2Fv";
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-CJc9uWXFvT5klLm99Bhapat7Fb4Am3pOZPJWF0yVNRziCFY7O8dPieoOuQe0OlZF4ARvFE4cGghABR9MHUcSElZhvMGEi0PuM-pCsPrgyeybhb61x8wKLUU0tZM59O-niNZzjXeOP8_BY0lGtleq1_2TTQXYQ9XapTQNQnMkcq0dbETzLrYVMhQ64kRdA3iYh2TY-r6NsqrTfxTp3Rm27naRXAvFq9tzoed1r-yex8_c9xkUSV8s1ocNeclvMNnlRuFzf4KxfyxEz1rPlpd-Xg6Su7YMKscNbtNCf2Y9pfg/https%3A%2F%2Fitk.org";)
(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_NZYF0g3QWqMApqiUTsn231GfHllUclG4IFtS4wMTL58eDPMTfcd16Vft_k0Y1SAd2Qi-hjo21_OZxolydk0rlE_vgDqjxMbTiY1OmKc2gKsH6hckCJhCN-faYWYWmsWpUY0Wok6CHWEwm1MAuHH1gPsKOGawZp5NcZ427najqR-VdQcd3nDS1VBRoE9GRrmk_p_6Kn9WeSWRPJA6E8k6-1Wx-iYkkd6TxJmzMggMqfwXfuTeRlLeB4S99fIz0ZYUyJDVUOvMACmIHWdbhYiN6OMCJtLHDoIWvZutSbBCg_RTSagO3bcnE9c8h-w/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2F";)
(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-5H1JMAtg-9f3EpaywU_8arU5HmixF2gY3p_mP2HqeBU4YlFUBZ-GnR1yoQTKl7bdPqTL9B1Q8t5ZL7aevfRvtKrS8OQe5XLxeJENL2HCwiVNCIx9SKifQZu-VWFGSkAy9FYNV-_zu-CJ61gLOqBSJ0XEeWLcBsEg8Wy-egqBKi2q6Na-Kv4sl-a_pUFQHcnXdNZ9Kg8dOgZ4s2EFR1n_0xkIHV6ckguBFLwInc7RPGg9pX5ngN_aHxqaGyAsyavJEjKm4B0njm8fl5FpQe7YZHC_vhpmuVrQNaQjlA8Qahg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu";)
;; 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/15q8zTqQfZSwuvTajUs5f9N2aYltiq9edRi1PUyW8JzLdAG213MOvlRnxZDWqq-8C6Kb5Btiw1T0P4bMSjAuJ6oveHMQTyRjkx8KmCGAWnK23ApSa3gKeisw3cbU4Nz7PsZp2ymyTvl7VoJnb-mCHgpuIJ3AJyFdh73-YiV8_F7EL3OvRM27LxXiMTwtpkr52kKdtcr6x8omkOTEEzlmzSYkyfCqGUTpSMAh_7ew_IussqZNMokuw6uCqhT8W46Ia2WVUz5G9Vy7EGn_N_tC3_rKT_iOwqR6ER9UHxLtk2GFTQJE6Sa6UufIDvXm1524xgq_UIDqzC076oZdBmN3tKQ/https%3A%2F%2Fgit.savannah.gnu.org%2Fgit%2Fguix.git
branch: master
commit: 14323edcc37d9efaae2491cf5f57ea0621412d7e
nonguix c694cf9
repository URL:
https://secure-web.cisco.com/1XwNEBscgHWCPMrio9mZuc4l17saADnyXjvBec6Pavy9o8TnuWqn0j7ITxgBFWNSddGhaYYVzxZiO3CykwdngBi4QrOUmX7U6qzQXnZaLGgWN0MATczXMmePtAts03i_nURxTpIdQbhBWPnb802ytD7LOEH5UBGbPGmgHRm_5Dm9bgEfyAbGOPepEohQy5xfVd3to2d7AZRcbvgL6ZJsTYoHLaZ-8XvTyuRA1KVRQUK5dy9l0KMvF-PwHsv186xnJEPv13ofH7ixyR7rsLSJCxt6lleeA1l_9Nqt9tm1TRYWVYVwj2ZEhwKnJRgGCDmRJTmVCCqdWxcdwHOk3ZIIKrQ/https%3A%2F%2Fgitlab.com%2Fnonguix%2Fnonguix
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
ymdp15kmccal02aaaqq0ck9qp6s9dc-freesurfer-7.3.3.drv.gz
Description: application/gzip
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