Installation issue with arrow error and termination

[santoshbiowarrior333]

I am trying the github clone as its not possible to get singularity installed and i do not have admin privileges.

I get this error:

Conan version 1.65.0 Requirement already satisfied: setuptools_scm==7.1.0 in /mnt/beegfs/esashi/Santosh/python/venv/lib/python3.9/site-packages (7.1.0) Requirement already satisfied: packaging>=20.0 in /mnt/beegfs/esashi/Santosh/python/venv/lib/python3.9/site-packages (from setuptools_scm==7.1.0) (23.2) Requirement already satisfied: setuptools in /mnt/beegfs/esashi/Santosh/python/venv/lib/python3.9/site-packages (from setuptools_scm==7.1.0) (69.0.2) Requirement already satisfied: typing-extensions in /mnt/beegfs/esashi/Santosh/python/venv/lib/python3.9/site-packages (from setuptools_scm==7.1.0) (4.9.0) Requirement already satisfied: tomli>=1.0.0 in /mnt/beegfs/esashi/Santosh/python/venv/lib/python3.9/site-packages (from setuptools_scm==7.1.0) (2.0.1) 0.3.12 Writing POD5Version.cmake with version: 0.3.12 Copying _version.py into lib_pod5 and pod5 source directories mkdir: cannot create directory ‘build’: File exists

WARN: ** WARN: * Conan 1 is legacy and on a deprecation path ** WARN: ***** Please upgrade to Conan 2 **** WARN: ** Configuration: [settings] arch=x86_64 arch_build=x86_64 build_type=Release compiler=gcc compiler.libcxx=libstdc++ compiler.version=9 os=Linux os_build=Linux [options] [build_requires] [env]

WARN: boost/1.78.0: requirement zlib/[>=1.2.11 <2] overridden by pod5_file_format/None to zlib/1.2.13 arrow/12.0.0: WARN: Package binary is corrupted, removing: fb3e694494e879f7c5825e62fd1f053fed021e08 conanfile.py (pod5_file_format/None): Installing package Requirements arrow/12.0.0 from 'conancenter' - Cache boost/1.78.0 from 'conancenter' - Cache bzip2/1.0.8 from 'conancenter' - Cache flatbuffers/2.0.0 from 'conancenter' - Cache jemalloc/5.2.1 from 'conancenter' - Cache libbacktrace/cci.20210118 from 'conancenter' - Cache xsimd/9.0.1 from 'conancenter' - Cache zlib/1.2.13 from 'conancenter' - Cache zstd/1.5.5 from 'conancenter' - Cache Packages arrow/12.0.0:fb3e694494e879f7c5825e62fd1f053fed021e08 - Build boost/1.78.0:adf48b8e4446dcb68f440fe42ff08878d5c7feed - Cache bzip2/1.0.8:da606cf731e334010b0bf6e85a2a6f891b9f36b0 - Cache flatbuffers/2.0.0:50a5030bbbb13ae56bc4be41915ecd48549cb895 - Cache jemalloc/5.2.1:31d60acd62057f01d2e023493bbd556ef8ecceb8 - Cache libbacktrace/cci.20210118:6af9cc7cb931c5ad942174fd7838eb655717c709 - Cache xsimd/9.0.1:5ab84d6acfe1f23c4fae0ab88f26e3a396351ac9 - Cache zlib/1.2.13:6af9cc7cb931c5ad942174fd7838eb655717c709 - Cache zstd/1.5.5:9140b8c2655272e600ab5536dd4ea64a13cddb98 - Cache

Installing (downloading, building) binaries... bzip2/1.0.8: Already installed! flatbuffers/2.0.0: Already installed! flatbuffers/2.0.0: Appending PATH environment variable: /mnt/beegfs/esashi/Santosh/.conan/data/flatbuffers/2.0.0///package/50a5030bbbb13ae56bc4be41915ecd48549cb895/bin jemalloc/5.2.1: Already installed! libbacktrace/cci.20210118: Already installed! xsimd/9.0.1: Already installed! zlib/1.2.13: Already installed! zstd/1.5.5: Already installed! arrow/12.0.0: WARN: Build folder is dirty, removing it: /mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0///build/fb3e694494e879f7c5825e62fd1f053fed021e08 arrow/12.0.0: Copying sources to build folder arrow/12.0.0: Building your package in /mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0///build/fb3e694494e879f7c5825e62fd1f053fed021e08 arrow/12.0.0: Generator txt created conanbuildinfo.txt arrow/12.0.0: Calling generate() arrow/12.0.0: WARN: Using the new toolchains and generators without specifying a build profile (e.g: -pr:b=default) is discouraged and might cause failures and unexpected behavior arrow/12.0.0: Preset 'release' added to CMakePresets.json. Invoke it manually using 'cmake --preset release' arrow/12.0.0: If your CMake version is not compatible with CMakePresets (<3.19) call cmake like: 'cmake -G "Unix Makefiles" -DCMAKE_TOOLCHAINFILE=/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/build/fb3e694494e879f7c5825e62fd1f053fed021e08/build/Release/generators/conan_toolchain.cmake -DCMAKE_PROJECT_arrowINCLUDE=/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/build/fb3e694494e879f7c5825e62fd1f053fed021e08/src/conan_cmake_project_include.cmake -DCMAKE_POLICY_DEFAULT_CMP0091=NEW -DCMAKE_BUILD_TYPE=Release' arrow/12.0.0: WARN: Using the new toolchains and generators without specifying a build profile (e.g: -pr:b=default) is discouraged and might cause failures and unexpected behavior arrow/12.0.0: Aggregating env generators arrow/12.0.0: Calling build() arrow/12.0.0: apply_conandata_patches(): No patches defined in conandata arrow/12.0.0: CMake command: cmake -G "Unix Makefiles" -DCMAKE_TOOLCHAINFILE="/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/build/fb3e694494e879f7c5825e62fd1f053fed021e08/build/Release/generators/conan_toolchain.cmake" -DCMAKE_INSTALLPREFIX="/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/package/fb3e694494e879f7c5825e62fd1f053fed021e08" -DCMAKE_PROJECT_arrowINCLUDE="/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/build/fb3e694494e879f7c5825e62fd1f053fed021e08/src/conan_cmake_project_include.cmake" -DCMAKE_POLICY_DEFAULT_CMP0091="NEW" -DCMAKE_BUILDTYPE="Release" "/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0///build/fb3e694494e879f7c5825e62fd1f053fed021e08/src/cpp" /bin/sh: 1: cmake: not found arrow/12.0.0: arrow/12.0.0: ERROR: Package 'fb3e694494e879f7c5825e62fd1f053fed021e08' build failed arrow/12.0.0: WARN: Build folder /mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/build/fb3e694494e879f7c5825e62fd1f053fed021e08/build/Release ERROR: arrow/12.0.0: Error in build() method, line 414 cmake.configure(build_script_folder=os.path.join(self.source_folder, "cpp")) ConanException: Error 127 while executing cmake -G "Unix Makefiles" -DCMAKE_TOOLCHAINFILE="/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/build/fb3e694494e879f7c5825e62fd1f053fed021e08/build/Release/generators/conan_toolchain.cmake" -DCMAKE_INSTALLPREFIX="/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/package/fb3e694494e879f7c5825e62fd1f053fed021e08" -DCMAKE_PROJECT_arrowINCLUDE="/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/build/fb3e694494e879f7c5825e62fd1f053fed021e08/src/conan_cmake_project_include.cmake" -DCMAKE_POLICY_DEFAULT_CMP0091="NEW" -DCMAKE_BUILDTYPE="Release" "/mnt/beegfs/esashi/Santosh/.conan/data/arrow/12.0.0//_/build/fb3e694494e879f7c5825e62fd1f053fed021e08/src/cpp" rm -f ./.depend g++ -Wall -O2 -fopenmp -std=c++14 -I./hdf5-1.8.14/hdf5/include -I./htslib -I./fast5/include -I./tensorflow/include -I./pod5-file-format/build/c++ -MM src/htsInterface.cpp src/forkSense.cpp src/data_IO.cpp src/reads.cpp src/trainGMM.cpp src/tensor.cpp src/detect.cpp src/trainCNN.cpp src/event_handling.cpp src/fast5.cpp src/common.cpp src/pod5.cpp src/index.cpp src/alignment.cpp src/probability.cpp src/scrappie/event_detection.c src/scrappie/scrappie_common.c src/pfasta/pfasta.c > ./.depend; In file included from src/detect.cpp:28: src/../pod5-file-format/c++/pod5_format/c_api.h:3:10: fatal error: pod5_format/pod5_format_export.h: No such file or directory 3 | #include "pod5_format/pod5_format_export.h" | ^~~~~~~~~~ compilation terminated. In file included from src/trainCNN.cpp:22: src/../pod5-file-format/c++/pod5_format/c_api.h:3:10: fatal error: pod5_format/pod5_format_export.h: No such file or directory 3 | #include "pod5_format/pod5_format_export.h" | ^~~~~~~~~~ compilation terminated. In file included from src/pod5.cpp:12: src/../pod5-file-format/c++/pod5_format/c_api.h:3:10: fatal error: pod5_format/pod5_format_export.h: No such file or directory 3 | #include "pod5_format/pod5_format_export.h" | ^~~~~~~~~~ compilation terminated. In file included from src/alignment.cpp:21: src/../pod5-file-format/c++/pod5_format/c_api.h:3:10: fatal error: pod5_format/pod5_format_export.h: No such file or directory 3 | #include "pod5_format/pod5_format_export.h" | ^~~~~~~~~~ compilation terminated. make: *** [Makefile:113: .depend] Error 1