Arch Linux User Repository

Since this package is outdated and I wanted a way to install openms, I made openms-bin that uses the deb package from the Github release. I put the maintainers and contributors of this package as contributors over there because I borrowed some stuff from here. I'm not really an AUR guru so please feel free to comment. Thank you guys for this package.

I'm not sure. If you are able to continue supporting it, I feel like generally a lot of Arch users prefer to build their packages from source. I couldn't quickly find it in the guidelines, though. If it's too cumbersome to maintain, perhaps someone would be up for adopting it.

levitsky you are right it is definitely way better to use the official deb package to build one for arch. If you agree I would request this package for deletion.

Since this package is outdated and I wanted a way to install openms, I made openms-bin that uses the deb package from the Github release. I put the maintainers and contributors of this package as contributors over there because I borrowed some stuff from here. I'm not really an AUR guru so please feel free to comment. Thank you guys for this package.

can you please change URL to the github release tarball? downloading from current url gives the following error:

curl: (60) SSL certificate problem: self-signed certificate
More details here: https://curl.se/docs/sslcerts.html

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.

also sqlite and libsvm are readily available from community repo so no need to build custom contribs as well

UPD: here are my changes to your PKGBUILD. isnan.patch fixes compiling issues for isnan() calls in some files.

diff --git a/.SRCINFO b/.SRCINFO
index f55f6bf..318e581 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -22,15 +22,18 @@ pkgbase = openms
    depends = qt5-svg
    depends = sqlite
    depends = xerces-c
-   source = https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/2.7.0/OpenMS-2.7.0-src.tar.gz
+   depends = libsvm
+   source = https://github.com/OpenMS/OpenMS/releases/download/Release2.7.0/OpenMS-2.7.0-src.tar.gz
    source = OpenMS-TOPPView.desktop
    source = OpenMS-TOPPAS.desktop
    source = OpenMS.sh
    source = cstddef.patch
+   source = isnan.patch
    sha256sums = 62bce6215bc88ca7d1f1b7abf15cea4061bdcfa10dbb1e652b1d8c2ff9b3f081
    sha256sums = 4f93d5c22a8267e4fbde6883ecc34a00abfc2ee5eafb46f6d81256ad8a33cdac
    sha256sums = 9b33c6c91d931802e88af89ade4beb6c8d05484d57d1ad804888511b7a8b00a0
    sha256sums = 2cf69cb56959f101614129d2a87dc078daca904e1701ed674d399afed1ff306d
    sha256sums = 75c05e06381237fe451abdd8802604d9d67c5dd00fb6f5a744afe4b84dfd0e41
+   sha256sums = b01551975058651a44f96560e2cac9cf3e3e717ce019a39302d1c4f558d57c34

 pkgname = openms
diff --git a/OpenMS-TOPPAS.desktop b/OpenMS-TOPPAS.desktop
old mode 100755
new mode 100644
diff --git a/OpenMS-TOPPView.desktop b/OpenMS-TOPPView.desktop
old mode 100755
new mode 100644
diff --git a/PKGBUILD b/PKGBUILD
old mode 100755
new mode 100644
index 6203816..df006d9
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -9,18 +9,20 @@ pkgdesc="C++ library and tools for LC/MS data management and analyses"
 arch=('i686' 'x86_64')
 url="http://www.openms.de"
 license=('BSD')
-depends=('boost' 'coin-or-mp' 'eigen' 'glpk' 'hdf5' 'qt5-base' 'qt5-svg' 'sqlite' 'xerces-c')
+depends=('boost' 'coin-or-mp' 'eigen' 'glpk' 'hdf5' 'qt5-base' 'qt5-svg' 'sqlite' 'xerces-c' libsvm)
 makedepends=('autoconf' 'automake' 'cmake' 'fakeroot' 'gcc' 'make' 'patch')
-source=("https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/${pkgver}/${_pkgname}-${pkgver}-src.tar.gz"
+source=("https://github.com/OpenMS/OpenMS/releases/download/Release${pkgver}/${_pkgname}-${pkgver}-src.tar.gz"
         "OpenMS-TOPPView.desktop"
         "OpenMS-TOPPAS.desktop"
         "OpenMS.sh"
-        "cstddef.patch")
+        "cstddef.patch"
+        "isnan.patch")
 sha256sums=('62bce6215bc88ca7d1f1b7abf15cea4061bdcfa10dbb1e652b1d8c2ff9b3f081'
             '4f93d5c22a8267e4fbde6883ecc34a00abfc2ee5eafb46f6d81256ad8a33cdac'
             '9b33c6c91d931802e88af89ade4beb6c8d05484d57d1ad804888511b7a8b00a0'
             '2cf69cb56959f101614129d2a87dc078daca904e1701ed674d399afed1ff306d'
-            '75c05e06381237fe451abdd8802604d9d67c5dd00fb6f5a744afe4b84dfd0e41')
+            '75c05e06381237fe451abdd8802604d9d67c5dd00fb6f5a744afe4b84dfd0e41'
+            'b01551975058651a44f96560e2cac9cf3e3e717ce019a39302d1c4f558d57c34')

 # Variables 
 _prefix="${_pkgname}-${pkgver}"
@@ -61,6 +63,7 @@ _build_openms() {
 prepare() {
   cd "${srcdir}"
   patch --strip=1 < cstddef.patch
+  patch -Np0 -i "${srcdir}/isnan.patch"
 }

 build() {
@@ -69,10 +72,7 @@ build() {
   local _contrib_build="contrib-build"

   # Build the required contribs, which cannot be covered by other Arch Linux packages
-  # Note: We also build SQLITE, since AUR offers sqlite2. If this is installed,
-  # the build process might erroneously link against sqlite2, which will then
-  # break the build
-  _build_contrib SQLITE LIBSVM KISSFFT WILDMAGIC
+  _build_contrib KISSFFT WILDMAGIC

   # Build OpenMS
   _build_openms OpenMS TOPP UTILS GUI

--- OpenMS-2.7.0/src/openms/source/QC/MQEvidenceExporter.cpp    2021-09-14 00:50:44.000000000 +0300
+++ OpenMS-2.7.0/src/openms/source/QC/MQEvidenceExporter.cpp    2023-04-21 18:17:29.966396843 +0300
@@ -307,29 +307,29 @@
   file_ << ptr_best_hit->getMetaValue("missed_cleavages", "NA") << "\t"; // missed cleavages

   const double& uncalibrated_mz_error_ppm = ptr_best_hit->getMetaValue("uncalibrated_mz_error_ppm", NAN);
   const double& calibrated_mz_error_ppm = ptr_best_hit->getMetaValue("calibrated_mz_error_ppm", NAN);

-  if (isnan(uncalibrated_mz_error_ppm) && isnan(calibrated_mz_error_ppm))
+  if (std::isnan(uncalibrated_mz_error_ppm) && std::isnan(calibrated_mz_error_ppm))
   {
     file_ << "NA" << "\t"; // Mass error [ppm]
     file_ << "NA" << "\t"; // Uncalibrated Mass error [ppm]
     file_ << "NA" << "\t"; // Mass error [Da]
     file_ << "NA" << "\t"; // Uncalibrated Mass error [Da]
     file_ << "NA" << "\t"; // Uncalibrated - Calibrated m/z [ppm]
     file_ << "NA" << "\t"; // Uncalibrated - Calibrated m/z [mDa]
   }
-  else if (isnan(calibrated_mz_error_ppm))
+  else if (std::isnan(calibrated_mz_error_ppm))
     {
       file_ << "NA" << "\t"; // Mass error [ppm]
       file_ << uncalibrated_mz_error_ppm << "\t"; // Uncalibrated Mass error [ppm]
       file_ << "NA" << "\t"; // Mass error [Da]
       file_ << OpenMS::Math::ppmToMass(uncalibrated_mz_error_ppm, f.getMZ()) << "\t"; // Uncalibrated Mass error [Da]
       file_ << "NA" << "\t"; // Uncalibrated - Calibrated m/z [ppm]
       file_ << "NA" << "\t"; // Uncalibrated - Calibrated m/z [mDa]
     }
-    else if (isnan(uncalibrated_mz_error_ppm))
+    else if (std::isnan(uncalibrated_mz_error_ppm))
       {
         file_ << calibrated_mz_error_ppm << "\t"; // Mass error [ppm]
         file_ << "NA" << "\t"; // Uncalibrated Mass error [ppm]
         file_ << OpenMS::Math::ppmToMass(calibrated_mz_error_ppm, f.getMZ()) << "\t"; // Mass error [Da]
         file_ << "NA" << "\t"; // Uncalibrated Mass error [Da]

Please apply this MR as a patch: https://github.com/OpenMS/OpenMS/pull/5127

Should work now

Yes, I think we have to wait for the fix in Eigen.

Build of 2.6.0 fails for me. The following eigen bug seems related: https://bugs.archlinux.org/task/68118

[ 3%] Building CXX object src/openms/CMakeFiles/OpenMS.dir/source/MATH/STATISTICS/GammaDistributionFitter.cpp.o In file included from /usr/include/eigen3/Eigen/Core:88, from /usr/include/eigen3/unsupported/Eigen/NonLinearOptimization:15, from /home/lev/.cache/yay/openms/src/OpenMS-2.6.0/src/openms/source/MATH/STATISTICS/GammaDistributionFitter.cpp:42: /usr/include/eigen3/Eigen/src/Core/products/Parallelizer.h: In function ‘void Eigen::internal::parallelize_gemm(const Functor&, Index, Index, Index, bool)’: /usr/include/eigen3/Eigen/src/Core/products/Parallelizer.h:162:19: error: ‘eigen_assert_exception’ is not a member of ‘Eigen’ 162 | if (errorCount) EIGEN_THROW_X(Eigen::eigen_assert_exception()); | ^~~~~~~~~~~~~ make[3]: *** [src/openms/CMakeFiles/OpenMS.dir/build.make:528: src/openms/CMakeFiles/OpenMS.dir/source/MATH/STATISTICS/GammaDistributionFitter.cpp.o] Error 1 make[2]: *** [CMakeFiles/Makefile2:3060: src/openms/CMakeFiles/OpenMS.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:3067: src/openms/CMakeFiles/OpenMS.dir/rule] Error 2 make: *** [Makefile:584: OpenMS] Error 2 ==> ERROR: A failure occurred in build(). Aborting...

OpenMS Version 2.5.0 is working. No errors.

Build is failing on mine as well. CMake Errors.