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fix MSIP part in KNIME #7573

Closed timosachsenberg closed 3 weeks ago

timosachsenberg commented 3 weeks ago

User description

Description

change to R.exe on windows

Checklist

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Click to expand If your PR is failing you can check out - The details of the action statuses at the end of the PR or the "Checks" tab. - http://cdash.openms.de/index.php?project=OpenMS and look for your PR. Use the "Show filters" capability on the top right to search for your PR number. If you click in the column that lists the failed tests you will get detailed error messages.

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PR Type

enhancement, configuration changes

Description

Changes walkthrough 📝

Relevant files
Enhancement
MetaProSIP.cpp
Update R executable path handling for platform specificity
src/topp/MetaProSIP.cpp
  • Updated the default R executable path based on the operating system.
  • Added platform-specific logic for setting the R executable.
  • Introduced constants for option requirements and advanced status.
    		• +16/-1   
    Configuration changes
    knime_package_support.cmake
    Add MetaProSIP to CMake parameter removal list                     
    cmake/knime_package_support.cmake
  • Added MetaProSIP to the list of tools for parameter removal.
  • Updated CMake configuration to handle R executable parameter.
    		• +2/-0     

    💡 PR-Agent usage: Comment /help on the PR to get a list of all available PR-Agent tools and their descriptions

    codiumai-pr-agent-pro[bot] commented 3 weeks ago

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    PR Reviewer Guide 🔍

    ⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪
    🧪 No relevant tests
    🔒 No security concerns identified
    ⚡ Key issues to review

    Platform-specific Code
    The PR introduces platform-specific code for Windows and non-Windows systems. This might need careful testing on different platforms to ensure compatibility.
    codiumai-pr-agent-pro[bot] commented 3 weeks ago

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    PR Code Suggestions ✨

    CategorySuggestion                                                                                                                                    Score
    Maintainability
    Use a preprocessor macro to define platform-specific default values ___ **Consider using a preprocessor macro to define the default R executable path based on
    the platform, which would simplify the code and make it easier to maintain.** [src/topp/MetaProSIP.cpp [2048-2052]](https://github.com/OpenMS/OpenMS/pull/7573/files#diff-7fd3f3a8eac3e23c45ecd072fd7e1d9d345b5799d3ff72f1a61bf7fcb5562341R2048-R2052) ```diff #ifdef OPENMS_WINDOWSPLATFORM - "R.exe", +#define DEFAULT_R_EXECUTABLE "R.exe" #else - "R", +#define DEFAULT_R_EXECUTABLE "R" #endif +DEFAULT_R_EXECUTABLE, ``` - [ ] **Apply this suggestion**
    Suggestion importance[1-10]: 8 Why: Defining platform-specific default values using a preprocessor macro simplifies the code and enhances maintainability by centralizing the platform-specific logic. This is a good practice for managing platform-dependent code.
    		8
    Enhancement
    Use enums for boolean constants to improve code clarity and type safety ___ **Consider using a constant or enum for the boolean values is_required and
    is_advanced_option to improve code readability and maintainability.** [src/topp/MetaProSIP.cpp [2043-2044]](https://github.com/OpenMS/OpenMS/pull/7573/files#diff-7fd3f3a8eac3e23c45ecd072fd7e1d9d345b5799d3ff72f1a61bf7fcb5562341R2043-R2044) ```diff -static const bool is_required(false); -static const bool is_advanced_option(true); +enum class OptionType { REQUIRED = true, OPTIONAL = false }; +enum class OptionVisibility { ADVANCED = true, BASIC = false }; +static const OptionType is_required = OptionType::OPTIONAL; +static const OptionVisibility is_advanced_option = OptionVisibility::BASIC; ``` - [ ] **Apply this suggestion**
    Suggestion importance[1-10]: 7 Why: Using enums instead of boolean constants can improve code readability and maintainability by providing more descriptive names and reducing the risk of errors. However, the current implementation with boolean constants is not incorrect, so this is a minor improvement.
    		7
    Best practice
    Use a constant for long string literals to improve maintainability ___ **Consider using a constant string for the description of the R executable parameter
    to improve maintainability and reduce the risk of typos.** [src/topp/MetaProSIP.cpp [2053]](https://github.com/OpenMS/OpenMS/pull/7573/files#diff-7fd3f3a8eac3e23c45ecd072fd7e1d9d345b5799d3ff72f1a61bf7fcb5562341R2053-R2053) ```diff -"The R executable. Provide a full or relative path, or make sure it can be found in your PATH environment.", +static const char* R_EXECUTABLE_DESCRIPTION = "The R executable. Provide a full or relative path, or make sure it can be found in your PATH environment."; +R_EXECUTABLE_DESCRIPTION, ``` - [ ] **Apply this suggestion**
    Suggestion importance[1-10]: 6 Why: Using a constant for long string literals can improve maintainability by reducing the risk of typos and making the code easier to update. However, this change is not crucial and offers only a small improvement.
    		6
    timosachsenberg commented 3 weeks ago

    @jpfeuffer adding it to the knime script will make it impossible to use a different R version right? Should I remove that part?

    github-actions[bot] commented 3 weeks ago

    PR Reviewer Guide 🔍

    ⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪
    🧪 No relevant tests
    🔒 No security concerns identified
    ⚡ Key issues to review

    Platform Dependency
    The code uses preprocessor directives to differentiate between Windows and other platforms for the R executable path. Ensure this change is tested on all supported platforms to avoid runtime errors.
    github-actions[bot] commented 3 weeks ago

    PR Code Suggestions ✨

    CategorySuggestion                                                                                                                                    Score
    Maintainability
    Use a function to determine the R executable name based on the runtime environment ___ **Replace the platform-dependent conditional compilation for the R executable path
    with a function that determines the executable name based on the runtime
    environment. This approach enhances code readability and maintainability.** [src/topp/MetaProSIP.cpp [2048-2051]](https://github.com/OpenMS/OpenMS/pull/7573/files#diff-7fd3f3a8eac3e23c45ecd072fd7e1d9d345b5799d3ff72f1a61bf7fcb5562341R2048-R2051) ```diff -#ifdef OPENMS_WINDOWSPLATFORM - "R.exe", -#else - "R", -#endif +getRExecutableName() ```
    Suggestion importance[1-10]: 8 Why: Replacing platform-dependent conditional compilation with a function improves code readability and maintainability, making it easier to manage and extend.
    		8
    Improve variable naming for clarity ___ **Consider using a more descriptive variable name instead of is_required and
    is_advanced_option for clarity and maintainability. For example,
    is_r_executable_required and is_r_executable_advanced.** [src/topp/MetaProSIP.cpp [2043-2044]](https://github.com/OpenMS/OpenMS/pull/7573/files#diff-7fd3f3a8eac3e23c45ecd072fd7e1d9d345b5799d3ff72f1a61bf7fcb5562341R2043-R2044) ```diff -static const bool is_required(false); -static const bool is_advanced_option(true); +static const bool is_r_executable_required(false); +static const bool is_r_executable_advanced(true); ```
    Suggestion importance[1-10]: 7 Why: The suggestion to use more descriptive variable names enhances code readability and maintainability, but it is not crucial for functionality.
    		7
    Clarity
    Clarify the use of boolean flags in function arguments ___ **Ensure that the is_required and is_advanced_option variables are used consistently
    and correctly. The current use of !is_advanced_option might be confusing. Consider
    directly using false for clarity if the intention is to always have this as a
    non-advanced option.** [src/topp/MetaProSIP.cpp [2054-2055]](https://github.com/OpenMS/OpenMS/pull/7573/files#diff-7fd3f3a8eac3e23c45ecd072fd7e1d9d345b5799d3ff72f1a61bf7fcb5562341R2054-R2055) ```diff is_required, -!is_advanced_option, +false, ```
    Suggestion importance[1-10]: 6 Why: Using `false` directly instead of `!is_advanced_option` can improve clarity, but the current implementation is not incorrect, so the improvement is minor.
    		6
    Best practice
    Standardize parameter naming to lowercase ___ **Ensure consistency in parameter naming by using lowercase for R_executable to match
    the naming style of other parameters in the script, such as executable and
    comet_executable.** [cmake/knime_package_support.cmake [257]](https://github.com/OpenMS/OpenMS/pull/7573/files#diff-983fbc97a96e1dda7bc982573ffeeceb8a2b16d8747f28ef95530385f4c39312R257-R257) ```diff --DTOOLNAME=MetaProSIP -DPARAM=R_executable +-DTOOLNAME=MetaProSIP -DPARAM=r_executable ```
    Suggestion importance[1-10]: 5 Why: Consistent naming conventions improve code readability and maintainability, but this change is more about style than functionality.
    		5
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    CI Failure Feedback 🧐

    **Action:** build-and-test (macos-14, xcode, 15.0.1)
    **Failed stage:** [Build](https://github.com/OpenMS/OpenMS/actions/runs/10680997257/job/29603699658) [❌]
    **Failed test name:** ""
    **Failure summary:** The action failed due to the following reasons:
  • There was an error during the project configuration step, as indicated by the message "Error(s) when
    configuring the project".
  • The build process encountered a critical error because the 'build.ninja' file could not be found, as
    indicated by the error message "ninja: error: loading 'build.ninja': No such file or directory".
  • The process completed with exit code 255, which typically indicates a failure in the script
    execution.
    • Relevant error logs: ```yaml 1: ##[group]Operating System 2: macOS ... 212: ##[endgroup] 213: ##[group]Run DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 214: DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 215: echo $DO_PACKAGE 216: if [[ "macos-14" == ubuntu-* ]]; then 217:  echo "tp_folder=Linux" >> $GITHUB_OUTPUT 218:  echo "xvfb=xvfb-run -a" >> $GITHUB_OUTPUT 219:  echo "static_boost=OFF" >> $GITHUB_OUTPUT 220:  # always run doxygen on Ubuntu (because its fast), to detect Doxygen errors ... 279:  sudo add-apt-repository universe 280:  sudo apt update  281:  sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache 282:  sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev 283:  sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \ 284:  libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev 285:  286:  echo "cmake_prefix=" >> $GITHUB_OUTPUT 287:  ## always run doxygen on Ubuntu to detect Doxygen errors ... 662: shell: /bin/bash --noprofile --norc -e -o pipefail {0} 663: env: 664: TERM: xterm-256color 665: Qt5_DIR: /opt/homebrew/opt/qt@5/lib/cmake/Qt5 666: ##[endgroup] 667: Submodule 'THIRDPARTY' (https://github.com/OpenMS/THIRDPARTY) registered for path 'THIRDPARTY' 668: Cloning into '/Users/runner/work/OpenMS/OpenMS/OpenMS/THIRDPARTY'... 669: Submodule path 'THIRDPARTY': checked out 'd6594eb775ebca0255f0129d946d7e582b37ac37' 670: ##[group]Run # do not fail immediately 671: # do not fail immediately 672: set +e 673: mkdir $GITHUB_WORKSPACE/OpenMS/bld/ 674:  ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake 675: retVal=$? 676: if [ $retVal -ne 0 ]; then 677:  echo -e "\033[0;31m Errors in build:" ... 691: CI_PROVIDER: GitHub-Actions 692: CMAKE_GENERATOR: Ninja 693: SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 694: BUILD_NAME: 7573-MacOS-ARM64-xcode-15.0.1-class-topp-1710 695: ENABLE_STYLE_TESTING: OFF 696: ENABLE_TOPP_TESTING: ON 697: ENABLE_CLASS_TESTING: ON 698: ENABLE_DOCS: OFF 699: ENABLE_GCC_WERROR: OFF ... 711: CCACHE_COMPRESS: true 712: CCACHE_COMPRESSLEVEL: 12 713: CCACHE_MAXSIZE: 400M 714: CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime 715: CCACHE_COMPILERCHECK: content 716: WITH_THERMORAWFILEPARSER_TEST: OFF 717: Eigen3_DIR: 718: ##[endgroup] 719: tools/ci/cibuild.cmake: Loading the following vars from ENV if available: ADDRESS_SANITIZER;CMAKE_PREFIX_PATH;CMAKE_BUILD_TYPE;CMAKE_GENERATOR_PLATFORM;Boost_DEBUG;BOOST_USE_STATIC;OPENMS_CONTRIB_LIBS;ENABLE_CLASS_TESTING;ENABLE_GCC_WERROR;ENABLE_STYLE_TESTING;ENABLE_TOPP_TESTING;ENABLE_TUTORIALS;ENABLE_UPDATE_CHECK;MT_ENABLE_OPENMP;SEARCH_ENGINES_DIRECTORY;PACKAGE_TYPE;PYOPENMS;PY_MEMLEAK_DISABLE;PY_NO_OPTIMIZATION;PY_NO_OUTPUT;PY_NUM_MODULES;PY_NUM_THREADS;WITH_GUI;WITH_THERMORAWFILEPARSER_TEST 720: -- CTEST_SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 721: tools/ci/cibuild.cmake: Found ADDRESS_SANITIZER with value Off 722: tools/ci/cibuild.cmake: Found CMAKE_PREFIX_PATH with value /opt/homebrew/opt/qt@5/lib/cmake;/opt/homebrew/opt/qt@5 723: tools/ci/cibuild.cmake: Found BOOST_USE_STATIC with value OFF 724: tools/ci/cibuild.cmake: Found OPENMS_CONTRIB_LIBS with value /Users/runner/work/OpenMS/OpenMS/OpenMS/contrib 725: tools/ci/cibuild.cmake: Found ENABLE_CLASS_TESTING with value ON 726: tools/ci/cibuild.cmake: Found ENABLE_GCC_WERROR with value OFF ... 741: -- Found Git: /opt/homebrew/bin/git (found version "2.46.0") 742: Updating the repository: /Users/runner/work/OpenMS/OpenMS/OpenMS 743: Use GIT repository type 744: New revision of repository is: fe4483ac2b3250179fd929ad4b748c0b8f9120c8 745: Gathering version information (one . per revision): 746: Configure project 747: Each . represents 1024 bytes of output 748: ... Size of output: 2K 749: Error(s) when configuring the project 750: Submit files 751: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 752: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1019/Update.xml 753: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1019/Configure.xml 754: Submission successful 755: Build project 756: Each symbol represents 1024 bytes of output. 757: '!' represents an error and '*' a warning. 758: ! Size of output: 0K 759: Error(s) when building project 760: 1 Compiler errors 761: 1 Compiler warnings 762: Submit files 763: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 764: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1019/Build.xml 765: Submission successful 766: CMake Error at /Users/runner/work/OpenMS/OpenMS/OpenMS/tools/ci/cibuild.cmake:175 (message): 767: There were errors: Please check the build results at: 768: https://cdash.openms.de/index.php?project=OpenMS&begin=2023-01-01&end=2030-01-01&filtercount=1&field1=buildname&compare1=63&value1=7573-MacOS-ARM64-xcode-15%2E0%2E1-class-topp-1710 769:  Errors in build: 770: ninja: error: loading 'build.ninja': No such file or directory 771: ##[error]Process completed with exit code 255. ```
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    codiumai-pr-agent-pro[bot] commented 3 weeks ago

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    CI Failure Feedback 🧐

    **Action:** build-and-test (macos-13, xcode, 14.2)
    **Failed stage:** [Build](https://github.com/OpenMS/OpenMS/actions/runs/10680997257/job/29603699292) [❌]
    **Failure summary:** The action failed due to the following reasons:
  • There was an error during the build process, as indicated by the message "Error(s) when building
    project".
  • Specifically, the error "ninja: error: loading 'build.ninja': No such file or directory" suggests
    that the build system could not find the 'build.ninja' file, which is necessary for the Ninja build
    system to execute the build process.
  • This missing file likely caused the build to fail, resulting in the process completing with exit
    code 255.
    • Relevant error logs: ```yaml 1: ##[group]Operating System 2: macOS ... 225: ##[endgroup] 226: ##[group]Run DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 227: DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 228: echo $DO_PACKAGE 229: if [[ "macos-13" == ubuntu-* ]]; then 230:  echo "tp_folder=Linux" >> $GITHUB_OUTPUT 231:  echo "xvfb=xvfb-run -a" >> $GITHUB_OUTPUT 232:  echo "static_boost=OFF" >> $GITHUB_OUTPUT 233:  # always run doxygen on Ubuntu (because its fast), to detect Doxygen errors ... 292:  sudo add-apt-repository universe 293:  sudo apt update  294:  sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache 295:  sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev 296:  sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \ 297:  libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev 298:  299:  echo "cmake_prefix=" >> $GITHUB_OUTPUT 300:  ## always run doxygen on Ubuntu to detect Doxygen errors ... 619: shell: /bin/bash --noprofile --norc -e -o pipefail {0} 620: env: 621: TERM: xterm-256color 622: Qt5_DIR: /usr/local/opt/qt@5/lib/cmake/Qt5 623: ##[endgroup] 624: Submodule 'THIRDPARTY' (https://github.com/OpenMS/THIRDPARTY) registered for path 'THIRDPARTY' 625: Cloning into '/Users/runner/work/OpenMS/OpenMS/OpenMS/THIRDPARTY'... 626: Submodule path 'THIRDPARTY': checked out 'd6594eb775ebca0255f0129d946d7e582b37ac37' 627: ##[group]Run # do not fail immediately 628: # do not fail immediately 629: set +e 630: mkdir $GITHUB_WORKSPACE/OpenMS/bld/ 631:  ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake 632: retVal=$? 633: if [ $retVal -ne 0 ]; then 634:  echo -e "\033[0;31m Errors in build:" ... 648: CI_PROVIDER: GitHub-Actions 649: CMAKE_GENERATOR: Ninja 650: SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 651: BUILD_NAME: 7573-MacOS-X64-xcode-14.2-class-topp-1710 652: ENABLE_STYLE_TESTING: OFF 653: ENABLE_TOPP_TESTING: ON 654: ENABLE_CLASS_TESTING: ON 655: ENABLE_DOCS: OFF 656: ENABLE_GCC_WERROR: OFF ... 668: CCACHE_COMPRESS: true 669: CCACHE_COMPRESSLEVEL: 12 670: CCACHE_MAXSIZE: 400M 671: CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime 672: CCACHE_COMPILERCHECK: content 673: WITH_THERMORAWFILEPARSER_TEST: OFF 674: Eigen3_DIR: 675: ##[endgroup] 676: tools/ci/cibuild.cmake: Loading the following vars from ENV if available: ADDRESS_SANITIZER;CMAKE_PREFIX_PATH;CMAKE_BUILD_TYPE;CMAKE_GENERATOR_PLATFORM;Boost_DEBUG;BOOST_USE_STATIC;OPENMS_CONTRIB_LIBS;ENABLE_CLASS_TESTING;ENABLE_GCC_WERROR;ENABLE_STYLE_TESTING;ENABLE_TOPP_TESTING;ENABLE_TUTORIALS;ENABLE_UPDATE_CHECK;MT_ENABLE_OPENMP;SEARCH_ENGINES_DIRECTORY;PACKAGE_TYPE;PYOPENMS;PY_MEMLEAK_DISABLE;PY_NO_OPTIMIZATION;PY_NO_OUTPUT;PY_NUM_MODULES;PY_NUM_THREADS;WITH_GUI;WITH_THERMORAWFILEPARSER_TEST 677: -- CTEST_SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 678: -- CTEST_BINARY_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld 679: tools/ci/cibuild.cmake: Found ADDRESS_SANITIZER with value Off 680: tools/ci/cibuild.cmake: Found CMAKE_PREFIX_PATH with value /usr/local/opt/qt@5/lib/cmake;/usr/local/opt/qt@5 681: tools/ci/cibuild.cmake: Found BOOST_USE_STATIC with value OFF 682: tools/ci/cibuild.cmake: Found OPENMS_CONTRIB_LIBS with value /Users/runner/work/OpenMS/OpenMS/OpenMS/contrib 683: tools/ci/cibuild.cmake: Found ENABLE_CLASS_TESTING with value ON 684: tools/ci/cibuild.cmake: Found ENABLE_GCC_WERROR with value OFF ... 698: -- Found Git: /usr/local/bin/git (found version "2.46.0") 699: Updating the repository: /Users/runner/work/OpenMS/OpenMS/OpenMS 700: Use GIT repository type 701: New revision of repository is: fe4483ac2b3250179fd929ad4b748c0b8f9120c8 702: Gathering version information (one . per revision): 703: Configure project 704: Each . represents 1024 bytes of output 705: ... Size of output: 2K 706: Error(s) when configuring the project 707: Submit files 708: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 709: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1020/Update.xml 710: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1020/Configure.xml 711: Submission successful 712: Build project 713: Each symbol represents 1024 bytes of output. 714: '!' represents an error and '*' a warning. 715: ! Size of output: 0K 716: Error(s) when building project 717: 1 Compiler errors 718: 1 Compiler warnings 719: Submit files 720: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 721: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1020/Build.xml 722: Submission successful 723: CMake Error at /Users/runner/work/OpenMS/OpenMS/OpenMS/tools/ci/cibuild.cmake:175 (message): 724: There were errors: Please check the build results at: 725: https://cdash.openms.de/index.php?project=OpenMS&begin=2023-01-01&end=2030-01-01&filtercount=1&field1=buildname&compare1=63&value1=7573-MacOS-X64-xcode-14%2E2-class-topp-1710 726:  Errors in build: 727: ninja: error: loading 'build.ninja': No such file or directory 728: ##[error]Process completed with exit code 255. ```
    ✨ CI feedback usage guide:
    The CI feedback tool (`/checks)` automatically triggers when a PR has a failed check. The tool analyzes the failed checks and provides several feedbacks: - Failed stage - Failed test name - Failure summary - Relevant error logs In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR: ``` /checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}" ``` where `{repo_name}` is the name of the repository, `{run_number}` is the run number of the failed check, and `{job_number}` is the job number of the failed check. #### Configuration options - `enable_auto_checks_feedback` - if set to true, the tool will automatically provide feedback when a check is failed. Default is true. - `excluded_checks_list` - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list. - `enable_help_text` - if set to true, the tool will provide a help message with the feedback. Default is true. - `persistent_comment` - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true. - `final_update_message` - if `persistent_comment` is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true. See more information about the `checks` tool in the [docs](https://pr-agent-docs.codium.ai/tools/ci_feedback/).
    jpfeuffer commented 3 weeks ago

    Hmm yes I think the script removes the parameter completely. You could also create another script that removes the input file tag such that it is handled as a normal string parameter. In case adding the .exe did not solve it.

    codiumai-pr-agent-pro[bot] commented 3 weeks ago

    PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

    CI Failure Feedback 🧐

    **Action:** build-and-test (macos-14, xcode, 15.0.1)
    **Failed stage:** [Build](https://github.com/OpenMS/OpenMS/actions/runs/10681130403/job/29604113960) [❌]
    **Failed test name:** ""
    **Failure summary:** The action failed due to the following reasons:
  • There was an error during the configuration of the project, as indicated by the message "Error(s)
    when configuring the project".
  • The build process encountered errors, specifically a compiler error, as noted by "1 Compiler
    errors".
  • The critical error causing the failure was "ninja: error: loading 'build.ninja': No such file or
    directory", indicating that the build system could not find the necessary 'build.ninja' file to
    proceed with the build.
    • Relevant error logs: ```yaml 1: ##[group]Operating System 2: macOS ... 161: ##[endgroup] 162: ##[group]Run DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 163: DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 164: echo $DO_PACKAGE 165: if [[ "macos-14" == ubuntu-* ]]; then 166:  echo "tp_folder=Linux" >> $GITHUB_OUTPUT 167:  echo "xvfb=xvfb-run -a" >> $GITHUB_OUTPUT 168:  echo "static_boost=OFF" >> $GITHUB_OUTPUT 169:  # always run doxygen on Ubuntu (because its fast), to detect Doxygen errors ... 228:  sudo add-apt-repository universe 229:  sudo apt update  230:  sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache 231:  sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev 232:  sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \ 233:  libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev 234:  235:  echo "cmake_prefix=" >> $GITHUB_OUTPUT 236:  ## always run doxygen on Ubuntu to detect Doxygen errors ... 611: shell: /bin/bash --noprofile --norc -e -o pipefail {0} 612: env: 613: TERM: xterm-256color 614: Qt5_DIR: /opt/homebrew/opt/qt@5/lib/cmake/Qt5 615: ##[endgroup] 616: Submodule 'THIRDPARTY' (https://github.com/OpenMS/THIRDPARTY) registered for path 'THIRDPARTY' 617: Cloning into '/Users/runner/work/OpenMS/OpenMS/OpenMS/THIRDPARTY'... 618: Submodule path 'THIRDPARTY': checked out 'd6594eb775ebca0255f0129d946d7e582b37ac37' 619: ##[group]Run # do not fail immediately 620: # do not fail immediately 621: set +e 622: mkdir $GITHUB_WORKSPACE/OpenMS/bld/ 623:  ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake 624: retVal=$? 625: if [ $retVal -ne 0 ]; then 626:  echo -e "\033[0;31m Errors in build:" ... 640: CI_PROVIDER: GitHub-Actions 641: CMAKE_GENERATOR: Ninja 642: SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 643: BUILD_NAME: 7573-MacOS-ARM64-xcode-15.0.1-class-topp-1711 644: ENABLE_STYLE_TESTING: OFF 645: ENABLE_TOPP_TESTING: ON 646: ENABLE_CLASS_TESTING: ON 647: ENABLE_DOCS: OFF 648: ENABLE_GCC_WERROR: OFF ... 661: CCACHE_COMPRESSLEVEL: 12 662: CCACHE_MAXSIZE: 400M 663: CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime 664: CCACHE_COMPILERCHECK: content 665: WITH_THERMORAWFILEPARSER_TEST: OFF 666: Eigen3_DIR: 667: ##[endgroup] 668: -- CTEST_SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 669: tools/ci/cibuild.cmake: Loading the following vars from ENV if available: ADDRESS_SANITIZER;CMAKE_PREFIX_PATH;CMAKE_BUILD_TYPE;CMAKE_GENERATOR_PLATFORM;Boost_DEBUG;BOOST_USE_STATIC;OPENMS_CONTRIB_LIBS;ENABLE_CLASS_TESTING;ENABLE_GCC_WERROR;ENABLE_STYLE_TESTING;ENABLE_TOPP_TESTING;ENABLE_TUTORIALS;ENABLE_UPDATE_CHECK;MT_ENABLE_OPENMP;SEARCH_ENGINES_DIRECTORY;PACKAGE_TYPE;PYOPENMS;PY_MEMLEAK_DISABLE;PY_NO_OPTIMIZATION;PY_NO_OUTPUT;PY_NUM_MODULES;PY_NUM_THREADS;WITH_GUI;WITH_THERMORAWFILEPARSER_TEST 670: tools/ci/cibuild.cmake: Found ADDRESS_SANITIZER with value Off 671: tools/ci/cibuild.cmake: Found CMAKE_PREFIX_PATH with value /opt/homebrew/opt/qt@5/lib/cmake;/opt/homebrew/opt/qt@5 672: tools/ci/cibuild.cmake: Found BOOST_USE_STATIC with value OFF 673: tools/ci/cibuild.cmake: Found OPENMS_CONTRIB_LIBS with value /Users/runner/work/OpenMS/OpenMS/OpenMS/contrib 674: tools/ci/cibuild.cmake: Found ENABLE_CLASS_TESTING with value ON 675: tools/ci/cibuild.cmake: Found ENABLE_GCC_WERROR with value OFF ... 690: -- Found Git: /opt/homebrew/bin/git (found version "2.46.0") 691: Updating the repository: /Users/runner/work/OpenMS/OpenMS/OpenMS 692: Use GIT repository type 693: New revision of repository is: e1b09d4c4d95f75e20a11ecc96ffdc5bc0eeddac 694: Gathering version information (one . per revision): 695: Configure project 696: Each . represents 1024 bytes of output 697: ... Size of output: 2K 698: Error(s) when configuring the project 699: Submit files 700: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 701: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1027/Update.xml 702: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1027/Configure.xml 703: Submission successful 704: Build project 705: Each symbol represents 1024 bytes of output. 706: '!' represents an error and '*' a warning. 707: ! Size of output: 0K 708: Error(s) when building project 709: 1 Compiler errors 710: 1 Compiler warnings 711: Submit files 712: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 713: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1027/Build.xml 714: Submission successful 715: CMake Error at /Users/runner/work/OpenMS/OpenMS/OpenMS/tools/ci/cibuild.cmake:175 (message): 716: There were errors: Please check the build results at: 717: https://cdash.openms.de/index.php?project=OpenMS&begin=2023-01-01&end=2030-01-01&filtercount=1&field1=buildname&compare1=63&value1=7573-MacOS-ARM64-xcode-15%2E0%2E1-class-topp-1711 718:  Errors in build: 719: ninja: error: loading 'build.ninja': No such file or directory 720: ##[error]Process completed with exit code 255. ```
    ✨ CI feedback usage guide:
    The CI feedback tool (`/checks)` automatically triggers when a PR has a failed check. The tool analyzes the failed checks and provides several feedbacks: - Failed stage - Failed test name - Failure summary - Relevant error logs In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR: ``` /checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}" ``` where `{repo_name}` is the name of the repository, `{run_number}` is the run number of the failed check, and `{job_number}` is the job number of the failed check. #### Configuration options - `enable_auto_checks_feedback` - if set to true, the tool will automatically provide feedback when a check is failed. Default is true. - `excluded_checks_list` - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list. - `enable_help_text` - if set to true, the tool will provide a help message with the feedback. Default is true. - `persistent_comment` - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true. - `final_update_message` - if `persistent_comment` is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true. See more information about the `checks` tool in the [docs](https://pr-agent-docs.codium.ai/tools/ci_feedback/).
    codiumai-pr-agent-pro[bot] commented 3 weeks ago

    PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

    CI Failure Feedback 🧐

    **Action:** build-and-test (macos-13, xcode, 14.2)
    **Failed stage:** [Build](https://github.com/OpenMS/OpenMS/actions/runs/10681130403/job/29604113600) [❌]
    **Failed test name:** ""
    **Failure summary:** The action failed due to the following reasons:
  • There was an error during the project configuration step, as indicated by the message "Error(s) when
    configuring the project".
  • The build process encountered a critical error because the 'build.ninja' file could not be found, as
    indicated by the error message "ninja: error: loading 'build.ninja': No such file or directory".
  • The process completed with exit code 255, which typically indicates a failure in the build process.
    • Relevant error logs: ```yaml 1: ##[group]Operating System 2: macOS ... 229: ##[endgroup] 230: ##[group]Run DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 231: DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 232: echo $DO_PACKAGE 233: if [[ "macos-13" == ubuntu-* ]]; then 234:  echo "tp_folder=Linux" >> $GITHUB_OUTPUT 235:  echo "xvfb=xvfb-run -a" >> $GITHUB_OUTPUT 236:  echo "static_boost=OFF" >> $GITHUB_OUTPUT 237:  # always run doxygen on Ubuntu (because its fast), to detect Doxygen errors ... 296:  sudo add-apt-repository universe 297:  sudo apt update  298:  sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache 299:  sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev 300:  sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \ 301:  libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev 302:  303:  echo "cmake_prefix=" >> $GITHUB_OUTPUT 304:  ## always run doxygen on Ubuntu to detect Doxygen errors ... 623: shell: /bin/bash --noprofile --norc -e -o pipefail {0} 624: env: 625: TERM: xterm-256color 626: Qt5_DIR: /usr/local/opt/qt@5/lib/cmake/Qt5 627: ##[endgroup] 628: Submodule 'THIRDPARTY' (https://github.com/OpenMS/THIRDPARTY) registered for path 'THIRDPARTY' 629: Cloning into '/Users/runner/work/OpenMS/OpenMS/OpenMS/THIRDPARTY'... 630: Submodule path 'THIRDPARTY': checked out 'd6594eb775ebca0255f0129d946d7e582b37ac37' 631: ##[group]Run # do not fail immediately 632: # do not fail immediately 633: set +e 634: mkdir $GITHUB_WORKSPACE/OpenMS/bld/ 635:  ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake 636: retVal=$? 637: if [ $retVal -ne 0 ]; then 638:  echo -e "\033[0;31m Errors in build:" ... 652: CI_PROVIDER: GitHub-Actions 653: CMAKE_GENERATOR: Ninja 654: SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 655: BUILD_NAME: 7573-MacOS-X64-xcode-14.2-class-topp-1711 656: ENABLE_STYLE_TESTING: OFF 657: ENABLE_TOPP_TESTING: ON 658: ENABLE_CLASS_TESTING: ON 659: ENABLE_DOCS: OFF 660: ENABLE_GCC_WERROR: OFF ... 673: CCACHE_COMPRESSLEVEL: 12 674: CCACHE_MAXSIZE: 400M 675: CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime 676: CCACHE_COMPILERCHECK: content 677: WITH_THERMORAWFILEPARSER_TEST: OFF 678: Eigen3_DIR: 679: ##[endgroup] 680: -- CTEST_SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 681: tools/ci/cibuild.cmake: Loading the following vars from ENV if available: ADDRESS_SANITIZER;CMAKE_PREFIX_PATH;CMAKE_BUILD_TYPE;CMAKE_GENERATOR_PLATFORM;Boost_DEBUG;BOOST_USE_STATIC;OPENMS_CONTRIB_LIBS;ENABLE_CLASS_TESTING;ENABLE_GCC_WERROR;ENABLE_STYLE_TESTING;ENABLE_TOPP_TESTING;ENABLE_TUTORIALS;ENABLE_UPDATE_CHECK;MT_ENABLE_OPENMP;SEARCH_ENGINES_DIRECTORY;PACKAGE_TYPE;PYOPENMS;PY_MEMLEAK_DISABLE;PY_NO_OPTIMIZATION;PY_NO_OUTPUT;PY_NUM_MODULES;PY_NUM_THREADS;WITH_GUI;WITH_THERMORAWFILEPARSER_TEST 682: tools/ci/cibuild.cmake: Found ADDRESS_SANITIZER with value Off 683: tools/ci/cibuild.cmake: Found CMAKE_PREFIX_PATH with value /usr/local/opt/qt@5/lib/cmake;/usr/local/opt/qt@5 684: -- CTEST_BINARY_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld 685: tools/ci/cibuild.cmake: Found BOOST_USE_STATIC with value OFF 686: tools/ci/cibuild.cmake: Found OPENMS_CONTRIB_LIBS with value /Users/runner/work/OpenMS/OpenMS/OpenMS/contrib 687: tools/ci/cibuild.cmake: Found ENABLE_CLASS_TESTING with value ON 688: tools/ci/cibuild.cmake: Found ENABLE_GCC_WERROR with value OFF ... 702: -- Found Git: /usr/local/bin/git (found version "2.46.0") 703: Updating the repository: /Users/runner/work/OpenMS/OpenMS/OpenMS 704: Use GIT repository type 705: New revision of repository is: e1b09d4c4d95f75e20a11ecc96ffdc5bc0eeddac 706: Gathering version information (one . per revision): 707: Configure project 708: Each . represents 1024 bytes of output 709: ... Size of output: 2K 710: Error(s) when configuring the project 711: Submit files 712: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 713: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1029/Update.xml 714: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1029/Configure.xml 715: Submission successful 716: Build project 717: Each symbol represents 1024 bytes of output. 718: '!' represents an error and '*' a warning. 719: ! Size of output: 0K 720: Error(s) when building project 721: 1 Compiler errors 722: 1 Compiler warnings 723: Submit files 724: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 725: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1029/Build.xml 726: CMake Error at /Users/runner/work/OpenMS/OpenMS/OpenMS/tools/ci/cibuild.cmake:175 (message): 727: Submission successful 728: There were errors: Please check the build results at: 729:  Errors in build: 730: https://cdash.openms.de/index.php?project=OpenMS&begin=2023-01-01&end=2030-01-01&filtercount=1&field1=buildname&compare1=63&value1=7573-MacOS-X64-xcode-14%2E2-class-topp-1711 731: ninja: error: loading 'build.ninja': No such file or directory 732: ##[error]Process completed with exit code 255. ```
    ✨ CI feedback usage guide:
    The CI feedback tool (`/checks)` automatically triggers when a PR has a failed check. The tool analyzes the failed checks and provides several feedbacks: - Failed stage - Failed test name - Failure summary - Relevant error logs In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR: ``` /checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}" ``` where `{repo_name}` is the name of the repository, `{run_number}` is the run number of the failed check, and `{job_number}` is the job number of the failed check. #### Configuration options - `enable_auto_checks_feedback` - if set to true, the tool will automatically provide feedback when a check is failed. Default is true. - `excluded_checks_list` - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list. - `enable_help_text` - if set to true, the tool will provide a help message with the feedback. Default is true. - `persistent_comment` - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true. - `final_update_message` - if `persistent_comment` is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true. See more information about the `checks` tool in the [docs](https://pr-agent-docs.codium.ai/tools/ci_feedback/).
    codiumai-pr-agent-pro[bot] commented 3 weeks ago

    PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

    CI Failure Feedback 🧐

    **Action:** build-and-test (windows-2022, cl.exe, default)
    **Failed stage:** [Test](https://github.com/OpenMS/OpenMS/actions/runs/10681130403/job/29604113264) [❌]
    **Failed test name:** BilinearInterpolation_test
    **Failure summary:** The action failed because the test BilinearInterpolation_test did not pass. The specific failure
    occurred due to a mismatch in expected data:
  • The test compared two data sets using TEST_NOT_EQUAL and found them to be equal, which was not
    expected.
  • The data sets compared were:
    - '10000 18.9 20.333\n10010 -0.13 10012'
    - The same data set
    was expected to be different, leading to the test failure.
    • Relevant error logs: ```yaml 1: ##[group]Operating System 2: Microsoft Windows Server 2022 ... 201: ##[endgroup] 202: ##[group]Run DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "cl.exe" != "clang++" ]] && echo true || echo false) 203: DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "cl.exe" != "clang++" ]] && echo true || echo false) 204: echo $DO_PACKAGE 205: if [[ "windows-2022" == ubuntu-* ]]; then 206:  echo "tp_folder=Linux" >> $GITHUB_OUTPUT 207:  echo "xvfb=xvfb-run -a" >> $GITHUB_OUTPUT 208:  echo "static_boost=OFF" >> $GITHUB_OUTPUT 209:  # always run doxygen on Ubuntu (because its fast), to detect Doxygen errors ... 284:  # 'ARM' is supported. 285:  $arch 286:  } 287: } 288:  289: New-Variable arch -Value (Normalize-Arch 'x64') -Option Constant 290:  291: function Locate-VSWhere { 292:  $path = Get-Command 'vswhere' -ErrorAction SilentlyContinue ... 353:  $script_name = 'VsDevCmd.bat' 354:  $script_path = Join-Path $tools_path $script_name 355:  356:  if (!(Test-Path $script_path -Type Leaf)) { 357:  throw "Couldn't find script '$script_name'" 358:  } 359:  360:  # OK, the following issue is royally stupid. At one point, I 361:  # started getting errors like this: 362:  # 363:  # Conversion from JSON failed with error: Unexpected character encountered while parsing value: W. ... 368:  # which is insanely low. I don't know what it does if the input 369:  # exceeds the nesting depth of 2, but I do know that starting from 370:  # Powershell 7.1, ConvertTo-Json prints a "helpful" warning in this 371:  # case. The warning looks like this: 372:  # 373:  # WARNING: Resulting JSON is truncated as serialization has exceeded the set depth of 2. 374:  # 375:  # Apparently, PowerShell on windows-2016 images got upgraded, hence 376:  # the failure to parse the letter W. I _accidentally_ fixed it by ... 1453:  sudo add-apt-repository universe 1454:  sudo apt update  1455:  sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache 1456:  sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev 1457:  sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \ 1458:  libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev 1459:  1460:  echo "cmake_prefix=" >> $GITHUB_OUTPUT 1461:  ## always run doxygen on Ubuntu to detect Doxygen errors ... 1807: Downloading package from source 'https://community.chocolatey.org/api/v2/' 1808: Ghostscript v10.3.1 [Approved] 1809: Ghostscript package files install completed. Performing other installation steps. 1810: The install of Ghostscript was successful. 1811: Deployed to 'C:\ProgramData\chocolatey\lib\Ghostscript' 1812: Downloading package from source 'https://community.chocolatey.org/api/v2/' 1813: graphviz v12.1.0 [Approved] 1814: graphviz package files install completed. Performing other installation steps. 1815: Attempt to use original download file name failed for 'C:\ProgramData\chocolatey\lib\Graphviz\tools\graphviz-12.1.0 (64-bit) EXE installer.exe'. ... 2541: Python3_ROOT_DIR: C:\hostedtoolcache\windows\Python\3.11.9\x64 2542: Qt5_Dir: D:\a\OpenMS\Qt\5.15.2\msvc2019_64 2543: QT_PLUGIN_PATH: D:\a\OpenMS\Qt\5.15.2\msvc2019_64\plugins 2544: QML2_IMPORT_PATH: D:\a\OpenMS\Qt\5.15.2\msvc2019_64\qml 2545: ##[endgroup] 2546: Submodule 'THIRDPARTY' (https://github.com/OpenMS/THIRDPARTY) registered for path 'THIRDPARTY' 2547: Cloning into 'D:/a/OpenMS/OpenMS/OpenMS/THIRDPARTY'... 2548: Submodule path 'THIRDPARTY': checked out 'd6594eb775ebca0255f0129d946d7e582b37ac37' 2549: ##[group]Run # do not fail immediately 2550: # do not fail immediately 2551: set +e 2552: mkdir $GITHUB_WORKSPACE/OpenMS/bld/ 2553:  ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake 2554: retVal=$? 2555: if [ $retVal -ne 0 ]; then 2556:  echo -e "\033[0;31m Errors in build:" ... 2776: CI_PROVIDER: GitHub-Actions 2777: CMAKE_GENERATOR: Ninja 2778: SOURCE_DIRECTORY: D:\a\OpenMS\OpenMS/OpenMS 2779: BUILD_NAME: 7573-Windows-X64-cl.exe-default-class-topp-1711 2780: ENABLE_STYLE_TESTING: OFF 2781: ENABLE_TOPP_TESTING: ON 2782: ENABLE_CLASS_TESTING: ON 2783: ENABLE_DOCS: OFF 2784: ENABLE_GCC_WERROR: OFF ... 2797: CCACHE_COMPRESSLEVEL: 12 2798: CCACHE_MAXSIZE: 400M 2799: CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime 2800: CCACHE_COMPILERCHECK: content 2801: WITH_THERMORAWFILEPARSER_TEST: OFF 2802: Eigen3_DIR: C:\ProgramData\chocolatey\lib\eigen\share\cmake 2803: ##[endgroup] 2804: -- CTEST_SOURCE_DIRECTORY: D:\a\OpenMS\OpenMS/OpenMS 2805: tools/ci/cibuild.cmake: Loading the following vars from ENV if available: ADDRESS_SANITIZER;CMAKE_PREFIX_PATH;CMAKE_BUILD_TYPE;CMAKE_GENERATOR_PLATFORM;Boost_DEBUG;BOOST_USE_STATIC;OPENMS_CONTRIB_LIBS;ENABLE_CLASS_TESTING;ENABLE_GCC_WERROR;ENABLE_STYLE_TESTING;ENABLE_TOPP_TESTING;ENABLE_TUTORIALS;ENABLE_UPDATE_CHECK;MT_ENABLE_OPENMP;SEARCH_ENGINES_DIRECTORY;PACKAGE_TYPE;PYOPENMS;PY_MEMLEAK_DISABLE;PY_NO_OPTIMIZATION;PY_NO_OUTPUT;PY_NUM_MODULES;PY_NUM_THREADS;WITH_GUI;WITH_THERMORAWFILEPARSER_TEST 2806: -- CTEST_BINARY_DIRECTORY: D:\a\OpenMS\OpenMS/OpenMS/bld 2807: tools/ci/cibuild.cmake: Found ADDRESS_SANITIZER with value Off 2808: tools/ci/cibuild.cmake: Found CMAKE_PREFIX_PATH with value /lib/cmake; 2809: tools/ci/cibuild.cmake: Found BOOST_USE_STATIC with value ON 2810: tools/ci/cibuild.cmake: Found OPENMS_CONTRIB_LIBS with value D:\a\OpenMS\OpenMS/OpenMS/contrib 2811: tools/ci/cibuild.cmake: Found ENABLE_CLASS_TESTING with value ON 2812: tools/ci/cibuild.cmake: Found ENABLE_GCC_WERROR with value OFF ... 2833: ......... Size of output: 8K 2834: Submit files 2835: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 2836: Uploaded: D:/a/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1029/Update.xml 2837: Uploaded: D:/a/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1029/Configure.xml 2838: Submission successful 2839: Build project 2840: Each symbol represents 1024 bytes of output. 2841: '!' represents an error and '*' a warning. ... 2856: .................................................. Size: 1083K 2857: .................................................. Size: 1083K 2858: .................................................. Size: 1083K 2859: .................................................. Size: 1083K 2860: .................................................. Size: 1083K 2861: .................................................. Size: 1083K 2862: .................................................. Size: 1083K 2863: .................................. Size of output: 1084K 2864: 0 Compiler errors ... 3246: Start 656: TOPPWRITEINI_IDFilter 3247: 74/2351 Test #654: TOPPWRITEINI_IDFileConverter ............................... Passed 0.04 sec 3248: Start 658: TOPPWRITEINI_IDMapper 3249: 75/2351 Test #658: TOPPWRITEINI_IDMapper ...................................... Passed 0.03 sec 3250: Start 660: TOPPWRITEINI_IDMassAccuracy 3251: 76/2351 Test #660: TOPPWRITEINI_IDMassAccuracy ................................ Passed 0.03 sec 3252: Start 662: TOPPWRITEINI_IDMerger 3253: 77/2351 Test #662: TOPPWRITEINI_IDMerger ...................................... Passed 0.03 sec 3254: Start 664: TOPPWRITEINI_IDPosteriorErrorProbability 3255: 78/2351 Test #664: TOPPWRITEINI_IDPosteriorErrorProbability ................... Passed 0.04 sec ... 4264: Start 1950: TOPP_FalseDiscoveryRate_4 4265: 583/2351 Test #1946: TOPP_FalseDiscoveryRate_2 .................................. Passed 0.24 sec 4266: Start 1952: TOPP_FalseDiscoveryRate_5 4267: 584/2351 Test #1950: TOPP_FalseDiscoveryRate_4 .................................. Passed 0.13 sec 4268: Start 1954: TOPP_FalseDiscoveryRate_6 4269: 585/2351 Test #1948: TOPP_FalseDiscoveryRate_3 .................................. Passed 0.26 sec 4270: Start 1956: TOPP_FalseDiscoveryRate_7 4271: 586/2351 Test #1952: TOPP_FalseDiscoveryRate_5 .................................. Passed 0.18 sec 4272: Start 1958: TOPP_IDPosteriorErrorProbability_1 4273: 587/2351 Test #1956: TOPP_FalseDiscoveryRate_7 .................................. Passed 0.17 sec 4274: Start 1960: TOPP_IDPosteriorErrorProbability_2 4275: 588/2351 Test #1954: TOPP_FalseDiscoveryRate_6 .................................. Passed 0.22 sec 4276: Start 1962: TOPP_IDPosteriorErrorProbability_3 4277: 589/2351 Test #1958: TOPP_IDPosteriorErrorProbability_1 ......................... Passed 0.14 sec 4278: Start 1964: TOPP_IDPosteriorErrorProbability_4 4279: 590/2351 Test #1962: TOPP_IDPosteriorErrorProbability_3 ......................... Passed 0.04 sec 4280: Start 1966: TOPP_IDPosteriorErrorProbability_5 4281: 591/2351 Test #1964: TOPP_IDPosteriorErrorProbability_4 ......................... Passed 0.04 sec 4282: Start 1968: TOPP_IDPosteriorErrorProbability_6 4283: 592/2351 Test #1960: TOPP_IDPosteriorErrorProbability_2 ......................... Passed 0.17 sec 4284: Start 1971: TOPP_IDPosteriorErrorProbability_8 4285: 593/2351 Test #1971: TOPP_IDPosteriorErrorProbability_8 ......................... Passed 0.05 sec 4286: Start 1973: TOPP_ProteinQuantifier_1 4287: 594/2351 Test #1966: TOPP_IDPosteriorErrorProbability_5 ......................... Passed 0.17 sec 4288: Start 1976: TOPP_ProteinQuantifier_2 4289: 595/2351 Test #1973: TOPP_ProteinQuantifier_1 ................................... Passed 0.05 sec 4290: Start 1979: TOPP_ProteinQuantifier_3 4291: 596/2351 Test #1968: TOPP_IDPosteriorErrorProbability_6 ......................... Passed 0.16 sec ... 5023: 962/2351 Test #237: SiriusFragmentAnnotation_test .............................. Passed 0.03 sec 5024: Start 238: BasicStatistics_test 5025: 963/2351 Test #232: MSDataChainingConsumer_test ................................ Passed 0.21 sec 5026: Start 239: BilinearInterpolation_test 5027: 964/2351 Test #238: BasicStatistics_test ....................................... Passed 0.04 sec 5028: Start 240: BSpline2d_test 5029: 965/2351 Test #240: BSpline2d_test ............................................. Passed 0.04 sec 5030: Start 241: CubicSpline2d_test 5031: 966/2351 Test #239: BilinearInterpolation_test .................................***Failed 0.07 sec ... 5041: : passed 5042: checking ContainerType const& getData() const ... : passed 5043: checking template< typename SourceContainer > void setData( SourceContainer const & data ) ... 5044: - line 173: TEST_NOT_EQUAL(bifd.getData(),bifd3.getData()): got ' 10000 18.9 20.333 5045: 10010 -0.13 10012 5046: ', forbidden is ' 10000 18.9 20.333 5047: 10010 -0.13 10012 5048: ' 5049: : failed ... 5091: : passed 5092: checking (void addValue( KeyType arg_pos_0, KeyType arg_pos_1, ValueType arg_value )) ... 5093: : passed 5094: checking (ValueType value( KeyType arg_pos_0, KeyType arg_pos_1 ) const) ... 5095: : passed 5096: checking (created temporary files)... 5097: : passed 5098: Output of successful tests were suppressed. Set the environment variable 'OPENMS_TEST_VERBOSE=True' to enable them. 5099: FAILED 5100: Failed lines: 173 ... 5115: Start 249: LinearRegression_test 5116: 974/2351 Test #248: LinearInterpolation_test ................................... Passed 0.04 sec 5117: Start 250: MathFunctions_test 5118: 975/2351 Test #249: LinearRegression_test ...................................... Passed 0.04 sec 5119: Start 251: NNLS_test 5120: 976/2351 Test #250: MathFunctions_test ......................................... Passed 0.04 sec 5121: Start 252: NonNegativeLeastSquaresSolver_test 5122: 977/2351 Test #251: NNLS_test .................................................. Passed 0.04 sec 5123: Start 253: PosteriorErrorProbabilityModel_test ... 5126: 979/2351 Test #254: QuadraticRegression_test ................................... Passed 0.03 sec 5127: Start 255: RANSAC_test 5128: 980/2351 Test #255: RANSAC_test ................................................ Passed 0.03 sec 5129: Start 256: RANSACModel_test 5130: 981/2351 Test #256: RANSACModel_test ........................................... Passed 0.04 sec 5131: Start 257: RANSACModelLinear_test 5132: 982/2351 Test #257: RANSACModelLinear_test ..................................... Passed 0.05 sec 5133: Start 258: RANSACModelQuadratic_test 5134: 983/2351 Test #253: PosteriorErrorProbabilityModel_test ........................ Passed 0.20 sec ... 5711: Start 547: CachedMzML_test 5712: 1272/2351 Test #547: CachedMzML_test ............................................ Passed 0.23 sec 5713: Start 548: CachedMzMLHandler_test 5714: 1273/2351 Test #548: CachedMzMLHandler_test ..................................... Passed 0.22 sec 5715: Start 549: Contaminants_test 5716: 1274/2351 Test #549: Contaminants_test .......................................... Passed 0.03 sec 5717: Start 550: DBSuitability_test 5718: 1275/2351 Test #550: DBSuitability_test ......................................... Passed 0.04 sec 5719: Start 551: FragmentMassError_test 5720: 1276/2351 Test #551: FragmentMassError_test ..................................... Passed 0.04 sec ... 5843: Start 657: TOPPWRITEINI_IDFilter_SectionName 5844: 1338/2351 Test #655: TOPPWRITEINI_IDFileConverter_SectionName ................... Passed 0.02 sec 5845: Start 659: TOPPWRITEINI_IDMapper_SectionName 5846: 1339/2351 Test #657: TOPPWRITEINI_IDFilter_SectionName .......................... Passed 0.02 sec 5847: Start 661: TOPPWRITEINI_IDMassAccuracy_SectionName 5848: 1340/2351 Test #659: TOPPWRITEINI_IDMapper_SectionName .......................... Passed 0.02 sec 5849: Start 663: TOPPWRITEINI_IDMerger_SectionName 5850: 1341/2351 Test #661: TOPPWRITEINI_IDMassAccuracy_SectionName .................... Passed 0.02 sec 5851: Start 665: TOPPWRITEINI_IDPosteriorErrorProbability_SectionName 5852: 1342/2351 Test #663: TOPPWRITEINI_IDMerger_SectionName .......................... Passed 0.02 sec 5853: Start 667: TOPPWRITEINI_IDRipper_SectionName 5854: 1343/2351 Test #665: TOPPWRITEINI_IDPosteriorErrorProbability_SectionName ....... Passed 0.02 sec ... 6133: Start 903: TOPPWRITECTD_IDFilter 6134: 1483/2351 Test #902: TOPPWRITECTD_IDFileConverter ............................... Passed 0.04 sec 6135: Start 904: TOPPWRITECTD_IDMapper 6136: 1484/2351 Test #904: TOPPWRITECTD_IDMapper ...................................... Passed 0.05 sec 6137: Start 905: TOPPWRITECTD_IDMassAccuracy 6138: 1485/2351 Test #905: TOPPWRITECTD_IDMassAccuracy ................................ Passed 0.03 sec 6139: Start 906: TOPPWRITECTD_IDMerger 6140: 1486/2351 Test #906: TOPPWRITECTD_IDMerger ...................................... Passed 0.04 sec 6141: Start 907: TOPPWRITECTD_IDPosteriorErrorProbability 6142: 1487/2351 Test #907: TOPPWRITECTD_IDPosteriorErrorProbability ................... Passed 0.04 sec ... 7357: Start 1951: TOPP_FalseDiscoveryRate_4_out1 7358: 2095/2351 Test #1951: TOPP_FalseDiscoveryRate_4_out1 ............................. Passed 0.05 sec 7359: Start 1953: TOPP_FalseDiscoveryRate_5_out1 7360: 2096/2351 Test #1953: TOPP_FalseDiscoveryRate_5_out1 ............................. Passed 0.05 sec 7361: Start 1955: TOPP_FalseDiscoveryRate_6_out1 7362: 2097/2351 Test #1955: TOPP_FalseDiscoveryRate_6_out1 ............................. Passed 0.07 sec 7363: Start 1957: TOPP_FalseDiscoveryRate_7_out1 7364: 2098/2351 Test #1949: TOPP_FalseDiscoveryRate_3_out1 ............................. Passed 0.20 sec 7365: Start 1959: TOPP_IDPosteriorErrorProbability_1_out1 7366: 2099/2351 Test #1957: TOPP_FalseDiscoveryRate_7_out1 ............................. Passed 0.04 sec 7367: Start 1961: TOPP_IDPosteriorErrorProbability_2_out1 7368: 2100/2351 Test #1959: TOPP_IDPosteriorErrorProbability_1_out1 .................... Passed 0.04 sec 7369: Start 1963: TOPP_IDPosteriorErrorProbability_3_out1 7370: 2101/2351 Test #1963: TOPP_IDPosteriorErrorProbability_3_out1 .................... Passed 0.04 sec 7371: Start 1965: TOPP_IDPosteriorErrorProbability_4_out1 7372: 2102/2351 Test #1961: TOPP_IDPosteriorErrorProbability_2_out1 .................... Passed 0.08 sec 7373: Start 1967: TOPP_IDPosteriorErrorProbability_5_out1 7374: 2103/2351 Test #1965: TOPP_IDPosteriorErrorProbability_4_out1 .................... Passed 0.04 sec 7375: Start 1969: TOPP_IDPosteriorErrorProbability_6_out1 7376: 2104/2351 Test #1967: TOPP_IDPosteriorErrorProbability_5_out1 .................... Passed 0.04 sec 7377: Start 1970: TOPP_IDPosteriorErrorProbability_7 7378: 2105/2351 Test #1969: TOPP_IDPosteriorErrorProbability_6_out1 .................... Passed 0.04 sec 7379: Start 1972: TOPP_IDPosteriorErrorProbability_8_out1 7380: 2106/2351 Test #1972: TOPP_IDPosteriorErrorProbability_8_out1 .................... Passed 0.04 sec 7381: Start 1974: TOPP_ProteinQuantifier_1_out1 7382: 2107/2351 Test #1974: TOPP_ProteinQuantifier_1_out1 .............................. Passed 0.03 sec 7383: Start 1975: TOPP_ProteinQuantifier_1_out2 7384: 2108/2351 Test #1975: TOPP_ProteinQuantifier_1_out2 .............................. Passed 0.03 sec 7385: Start 1977: TOPP_ProteinQuantifier_2_out1 7386: 2109/2351 Test #1977: TOPP_ProteinQuantifier_2_out1 .............................. Passed 0.03 sec 7387: Start 1978: TOPP_ProteinQuantifier_2_out2 7388: 2110/2351 Test #1970: TOPP_IDPosteriorErrorProbability_7 ......................... Passed 0.16 sec ... 7861: Start 2350: Tutorial_TOPP 7862: 2347/2351 Test #2349: Tutorial_TheoreticalSpectrumGenerator ...................... Passed 0.03 sec 7863: Start 2351: Tutorial_Unlabeled 7864: 2348/2351 Test #2350: Tutorial_TOPP .............................................. Passed 0.03 sec 7865: 2349/2351 Test #2351: Tutorial_Unlabeled ......................................... Passed 0.03 sec 7866: 2350/2351 Test #2318: TOPP_ExecutePipeline_1 ..................................... Passed 3.67 sec 7867: Start 22: StopWatch_test 7868: 2351/2351 Test #22: StopWatch_test ............................................. Passed 0.36 sec 7869: 99% tests passed, 1 tests failed out of 2351 7870: Total Test time (real) = 145.01 sec 7871: The following tests FAILED: 7872: 239 - BilinearInterpolation_test (Failed) 7873: Submit files 7874: Send to group: Continuous 7875: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 7876: Uploaded: D:/a/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1029/Test.xml 7877: Uploaded: D:/a/OpenMS/OpenMS/OpenMS/bld/Testing/20240903-1029/Done.xml 7878: Submission successful 7879: CMake Error at D:/a/OpenMS/OpenMS/OpenMS/tools/ci/citest.cmake:44 (message): 7880: There were errors: Please check the test results at: 7881: https://cdash.openms.de/index.php?project=OpenMS&begin=2023-01-01&end=2030-01-01&filtercount=1&field1=buildname&compare1=63&value1=7573-Windows-X64-cl%2Eexe-default-class-topp-1711 7882: ##[error]Process completed with exit code 127. ```
    ✨ CI feedback usage guide:
    The CI feedback tool (`/checks)` automatically triggers when a PR has a failed check. The tool analyzes the failed checks and provides several feedbacks: - Failed stage - Failed test name - Failure summary - Relevant error logs In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR: ``` /checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}" ``` where `{repo_name}` is the name of the repository, `{run_number}` is the run number of the failed check, and `{job_number}` is the job number of the failed check. #### Configuration options - `enable_auto_checks_feedback` - if set to true, the tool will automatically provide feedback when a check is failed. Default is true. - `excluded_checks_list` - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list. - `enable_help_text` - if set to true, the tool will provide a help message with the feedback. Default is true. - `persistent_comment` - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true. - `final_update_message` - if `persistent_comment` is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true. See more information about the `checks` tool in the [docs](https://pr-agent-docs.codium.ai/tools/ci_feedback/).
    codiumai-pr-agent-pro[bot] commented 3 weeks ago

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    CI Failure Feedback 🧐

    **Action:** build-and-test (macos-14, xcode, 15.0.1)
    **Failed stage:** [Build](https://github.com/OpenMS/OpenMS/actions/runs/10698094887/job/29656710726) [❌]
    **Failed test name:** ""
    **Failure summary:** The action failed due to the following reasons:
  • There was an error during the build process, indicated by the message "Error(s) when building
    project".
  • A specific error occurred because the file 'build.ninja' could not be found, as indicated by the
    message "ninja: error: loading 'build.ninja': No such file or directory".
  • The process completed with exit code 255, which typically indicates a failure in the build or
    execution process.
    • Relevant error logs: ```yaml 1: ##[group]Operating System 2: macOS ... 212: ##[endgroup] 213: ##[group]Run DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 214: DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 215: echo $DO_PACKAGE 216: if [[ "macos-14" == ubuntu-* ]]; then 217:  echo "tp_folder=Linux" >> $GITHUB_OUTPUT 218:  echo "xvfb=xvfb-run -a" >> $GITHUB_OUTPUT 219:  echo "static_boost=OFF" >> $GITHUB_OUTPUT 220:  # always run doxygen on Ubuntu (because its fast), to detect Doxygen errors ... 279:  sudo add-apt-repository universe 280:  sudo apt update  281:  sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache 282:  sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev 283:  sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \ 284:  libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev 285:  286:  echo "cmake_prefix=" >> $GITHUB_OUTPUT 287:  ## always run doxygen on Ubuntu to detect Doxygen errors ... 662: shell: /bin/bash --noprofile --norc -e -o pipefail {0} 663: env: 664: TERM: xterm-256color 665: Qt5_DIR: /opt/homebrew/opt/qt@5/lib/cmake/Qt5 666: ##[endgroup] 667: Submodule 'THIRDPARTY' (https://github.com/OpenMS/THIRDPARTY) registered for path 'THIRDPARTY' 668: Cloning into '/Users/runner/work/OpenMS/OpenMS/OpenMS/THIRDPARTY'... 669: Submodule path 'THIRDPARTY': checked out 'd6594eb775ebca0255f0129d946d7e582b37ac37' 670: ##[group]Run # do not fail immediately 671: # do not fail immediately 672: set +e 673: mkdir $GITHUB_WORKSPACE/OpenMS/bld/ 674:  ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake 675: retVal=$? 676: if [ $retVal -ne 0 ]; then 677:  echo -e "\033[0;31m Errors in build:" ... 691: CI_PROVIDER: GitHub-Actions 692: CMAKE_GENERATOR: Ninja 693: SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 694: BUILD_NAME: 7573-MacOS-ARM64-xcode-15.0.1-class-topp-1716 695: ENABLE_STYLE_TESTING: OFF 696: ENABLE_TOPP_TESTING: ON 697: ENABLE_CLASS_TESTING: ON 698: ENABLE_DOCS: OFF 699: ENABLE_GCC_WERROR: OFF ... 711: CCACHE_COMPRESS: true 712: CCACHE_COMPRESSLEVEL: 12 713: CCACHE_MAXSIZE: 400M 714: CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime 715: CCACHE_COMPILERCHECK: content 716: WITH_THERMORAWFILEPARSER_TEST: OFF 717: Eigen3_DIR: 718: ##[endgroup] 719: tools/ci/cibuild.cmake: Loading the following vars from ENV if available: ADDRESS_SANITIZER;CMAKE_PREFIX_PATH;CMAKE_BUILD_TYPE;CMAKE_GENERATOR_PLATFORM;Boost_DEBUG;BOOST_USE_STATIC;OPENMS_CONTRIB_LIBS;ENABLE_CLASS_TESTING;ENABLE_GCC_WERROR;ENABLE_STYLE_TESTING;ENABLE_TOPP_TESTING;ENABLE_TUTORIALS;ENABLE_UPDATE_CHECK;MT_ENABLE_OPENMP;SEARCH_ENGINES_DIRECTORY;PACKAGE_TYPE;PYOPENMS;PY_MEMLEAK_DISABLE;PY_NO_OPTIMIZATION;PY_NO_OUTPUT;PY_NUM_MODULES;PY_NUM_THREADS;WITH_GUI;WITH_THERMORAWFILEPARSER_TEST 720: -- CTEST_SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 721: tools/ci/cibuild.cmake: Found ADDRESS_SANITIZER with value Off 722: -- CTEST_BINARY_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld 723: tools/ci/cibuild.cmake: Found CMAKE_PREFIX_PATH with value /opt/homebrew/opt/qt@5/lib/cmake;/opt/homebrew/opt/qt@5 724: tools/ci/cibuild.cmake: Found BOOST_USE_STATIC with value OFF 725: tools/ci/cibuild.cmake: Found OPENMS_CONTRIB_LIBS with value /Users/runner/work/OpenMS/OpenMS/OpenMS/contrib 726: tools/ci/cibuild.cmake: Found ENABLE_CLASS_TESTING with value ON 727: tools/ci/cibuild.cmake: Found ENABLE_GCC_WERROR with value OFF ... 741: -- Found Git: /opt/homebrew/bin/git (found version "2.46.0") 742: Updating the repository: /Users/runner/work/OpenMS/OpenMS/OpenMS 743: Use GIT repository type 744: New revision of repository is: 29a779f0a6b551e6265bf805e0cadf6f0de3678e 745: Gathering version information (one . per revision): 746: Configure project 747: Each . represents 1024 bytes of output 748: ... Size of output: 2K 749: Error(s) when configuring the project 750: Submit files 751: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 752: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240904-0838/Update.xml 753: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240904-0838/Configure.xml 754: Submission successful 755: Build project 756: Each symbol represents 1024 bytes of output. 757: '!' represents an error and '*' a warning. 758: ! Size of output: 0K 759: Error(s) when building project 760: 1 Compiler errors 761: 1 Compiler warnings 762: Submit files 763: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 764: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240904-0838/Build.xml 765: Submission successful 766: CMake Error at /Users/runner/work/OpenMS/OpenMS/OpenMS/tools/ci/cibuild.cmake:175 (message): 767: There were errors: Please check the build results at: 768: https://cdash.openms.de/index.php?project=OpenMS&begin=2023-01-01&end=2030-01-01&filtercount=1&field1=buildname&compare1=63&value1=7573-MacOS-ARM64-xcode-15%2E0%2E1-class-topp-1716 769:  Errors in build: 770: ninja: error: loading 'build.ninja': No such file or directory 771: ##[error]Process completed with exit code 255. ```
    ✨ CI feedback usage guide:
    The CI feedback tool (`/checks)` automatically triggers when a PR has a failed check. The tool analyzes the failed checks and provides several feedbacks: - Failed stage - Failed test name - Failure summary - Relevant error logs In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR: ``` /checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}" ``` where `{repo_name}` is the name of the repository, `{run_number}` is the run number of the failed check, and `{job_number}` is the job number of the failed check. #### Configuration options - `enable_auto_checks_feedback` - if set to true, the tool will automatically provide feedback when a check is failed. Default is true. - `excluded_checks_list` - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list. - `enable_help_text` - if set to true, the tool will provide a help message with the feedback. Default is true. - `persistent_comment` - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true. - `final_update_message` - if `persistent_comment` is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true. See more information about the `checks` tool in the [docs](https://pr-agent-docs.codium.ai/tools/ci_feedback/).
    codiumai-pr-agent-pro[bot] commented 3 weeks ago

    PR-Agent was enabled for this repository. To continue using it, please link your git user with your CodiumAI identity here.

    CI Failure Feedback 🧐

    **Action:** build-and-test (macos-13, xcode, 14.2)
    **Failed stage:** [Build](https://github.com/OpenMS/OpenMS/actions/runs/10698094887/job/29656710138) [❌]
    **Failed test name:** ""
    **Failure summary:** The action failed due to the following reasons:
  • There was an error during the build process, as indicated by the message "Error(s) when building
    project".
  • A specific error occurred because the 'build.ninja' file could not be found, as indicated by the
    message "ninja: error: loading 'build.ninja': No such file or directory".
  • The process completed with exit code 255, which typically indicates a failure in the script or
    command execution.
    • Relevant error logs: ```yaml 1: ##[group]Operating System 2: macOS ... 225: ##[endgroup] 226: ##[group]Run DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 227: DO_PACKAGE=$( [[ ( "" || "7573" == "nightly" || "7573" =~ release/* ) && "xcode" != "clang++" ]] && echo true || echo false) 228: echo $DO_PACKAGE 229: if [[ "macos-13" == ubuntu-* ]]; then 230:  echo "tp_folder=Linux" >> $GITHUB_OUTPUT 231:  echo "xvfb=xvfb-run -a" >> $GITHUB_OUTPUT 232:  echo "static_boost=OFF" >> $GITHUB_OUTPUT 233:  # always run doxygen on Ubuntu (because its fast), to detect Doxygen errors ... 292:  sudo add-apt-repository universe 293:  sudo apt update  294:  sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache 295:  sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev 296:  sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \ 297:  libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev 298:  299:  echo "cmake_prefix=" >> $GITHUB_OUTPUT 300:  ## always run doxygen on Ubuntu to detect Doxygen errors ... 619: shell: /bin/bash --noprofile --norc -e -o pipefail {0} 620: env: 621: TERM: xterm-256color 622: Qt5_DIR: /usr/local/opt/qt@5/lib/cmake/Qt5 623: ##[endgroup] 624: Submodule 'THIRDPARTY' (https://github.com/OpenMS/THIRDPARTY) registered for path 'THIRDPARTY' 625: Cloning into '/Users/runner/work/OpenMS/OpenMS/OpenMS/THIRDPARTY'... 626: Submodule path 'THIRDPARTY': checked out 'd6594eb775ebca0255f0129d946d7e582b37ac37' 627: ##[group]Run # do not fail immediately 628: # do not fail immediately 629: set +e 630: mkdir $GITHUB_WORKSPACE/OpenMS/bld/ 631:  ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake 632: retVal=$? 633: if [ $retVal -ne 0 ]; then 634:  echo -e "\033[0;31m Errors in build:" ... 648: CI_PROVIDER: GitHub-Actions 649: CMAKE_GENERATOR: Ninja 650: SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 651: BUILD_NAME: 7573-MacOS-X64-xcode-14.2-class-topp-1716 652: ENABLE_STYLE_TESTING: OFF 653: ENABLE_TOPP_TESTING: ON 654: ENABLE_CLASS_TESTING: ON 655: ENABLE_DOCS: OFF 656: ENABLE_GCC_WERROR: OFF ... 668: CCACHE_COMPRESS: true 669: CCACHE_COMPRESSLEVEL: 12 670: CCACHE_MAXSIZE: 400M 671: CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime 672: CCACHE_COMPILERCHECK: content 673: WITH_THERMORAWFILEPARSER_TEST: OFF 674: Eigen3_DIR: 675: ##[endgroup] 676: tools/ci/cibuild.cmake: Loading the following vars from ENV if available: ADDRESS_SANITIZER;CMAKE_PREFIX_PATH;CMAKE_BUILD_TYPE;CMAKE_GENERATOR_PLATFORM;Boost_DEBUG;BOOST_USE_STATIC;OPENMS_CONTRIB_LIBS;ENABLE_CLASS_TESTING;ENABLE_GCC_WERROR;ENABLE_STYLE_TESTING;ENABLE_TOPP_TESTING;ENABLE_TUTORIALS;ENABLE_UPDATE_CHECK;MT_ENABLE_OPENMP;SEARCH_ENGINES_DIRECTORY;PACKAGE_TYPE;PYOPENMS;PY_MEMLEAK_DISABLE;PY_NO_OPTIMIZATION;PY_NO_OUTPUT;PY_NUM_MODULES;PY_NUM_THREADS;WITH_GUI;WITH_THERMORAWFILEPARSER_TEST 677: -- CTEST_SOURCE_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS 678: -- CTEST_BINARY_DIRECTORY: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld 679: tools/ci/cibuild.cmake: Found ADDRESS_SANITIZER with value Off 680: tools/ci/cibuild.cmake: Found CMAKE_PREFIX_PATH with value /usr/local/opt/qt@5/lib/cmake;/usr/local/opt/qt@5 681: tools/ci/cibuild.cmake: Found BOOST_USE_STATIC with value OFF 682: tools/ci/cibuild.cmake: Found OPENMS_CONTRIB_LIBS with value /Users/runner/work/OpenMS/OpenMS/OpenMS/contrib 683: tools/ci/cibuild.cmake: Found ENABLE_CLASS_TESTING with value ON 684: tools/ci/cibuild.cmake: Found ENABLE_GCC_WERROR with value OFF ... 698: -- Found Git: /usr/local/bin/git (found version "2.46.0") 699: Updating the repository: /Users/runner/work/OpenMS/OpenMS/OpenMS 700: Use GIT repository type 701: New revision of repository is: 29a779f0a6b551e6265bf805e0cadf6f0de3678e 702: Gathering version information (one . per revision): 703: Configure project 704: Each . represents 1024 bytes of output 705: ... Size of output: 2K 706: Error(s) when configuring the project 707: Submit files 708: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 709: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240904-0841/Update.xml 710: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240904-0841/Configure.xml 711: Submission successful 712: Build project 713: Each symbol represents 1024 bytes of output. 714: '!' represents an error and '*' a warning. 715: ! Size of output: 0K 716: Error(s) when building project 717: 1 Compiler errors 718: 1 Compiler warnings 719: Submit files 720: SubmitURL: https://cdash.openms.de/submit.php?project=OpenMS 721: Uploaded: /Users/runner/work/OpenMS/OpenMS/OpenMS/bld/Testing/20240904-0841/Build.xml 722: CMake Error at /Users/runner/work/OpenMS/OpenMS/OpenMS/tools/ci/cibuild.cmake:175 (message): 723: Submission successful 724: There were errors: Please check the build results at: 725: https://cdash.openms.de/index.php?project=OpenMS&begin=2023-01-01&end=2030-01-01&filtercount=1&field1=buildname&compare1=63&value1=7573-MacOS-X64-xcode-14%2E2-class-topp-1716 726:  Errors in build: 727: ninja: error: loading 'build.ninja': No such file or directory 728: ##[error]Process completed with exit code 255. ```
    ✨ CI feedback usage guide:
    The CI feedback tool (`/checks)` automatically triggers when a PR has a failed check. The tool analyzes the failed checks and provides several feedbacks: - Failed stage - Failed test name - Failure summary - Relevant error logs In addition to being automatically triggered, the tool can also be invoked manually by commenting on a PR: ``` /checks "https://github.com/{repo_name}/actions/runs/{run_number}/job/{job_number}" ``` where `{repo_name}` is the name of the repository, `{run_number}` is the run number of the failed check, and `{job_number}` is the job number of the failed check. #### Configuration options - `enable_auto_checks_feedback` - if set to true, the tool will automatically provide feedback when a check is failed. Default is true. - `excluded_checks_list` - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list. - `enable_help_text` - if set to true, the tool will provide a help message with the feedback. Default is true. - `persistent_comment` - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true. - `final_update_message` - if `persistent_comment` is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true. See more information about the `checks` tool in the [docs](https://pr-agent-docs.codium.ai/tools/ci_feedback/).