2023-06-27T16:42:59,236 Created temporary directory: /tmp/pip-build-tracker-nxzwd3uj 2023-06-27T16:42:59,237 Initialized build tracking at /tmp/pip-build-tracker-nxzwd3uj 2023-06-27T16:42:59,237 Created build tracker: /tmp/pip-build-tracker-nxzwd3uj 2023-06-27T16:42:59,237 Entered build tracker: /tmp/pip-build-tracker-nxzwd3uj 2023-06-27T16:42:59,238 Created temporary directory: /tmp/pip-wheel-mhtyhf8h 2023-06-27T16:42:59,241 Created temporary directory: /tmp/pip-ephem-wheel-cache-qhhgjr3x 2023-06-27T16:42:59,267 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-06-27T16:42:59,271 2 location(s) to search for versions of splam: 2023-06-27T16:42:59,271 * https://pypi.org/simple/splam/ 2023-06-27T16:42:59,271 * https://www.piwheels.org/simple/splam/ 2023-06-27T16:42:59,271 Fetching project page and analyzing links: https://pypi.org/simple/splam/ 2023-06-27T16:42:59,271 Getting page https://pypi.org/simple/splam/ 2023-06-27T16:42:59,273 Found index url https://pypi.org/simple/ 2023-06-27T16:42:59,333 Fetched page https://pypi.org/simple/splam/ as application/vnd.pypi.simple.v1+json 2023-06-27T16:42:59,335 Skipping link: No binaries permitted for splam: https://files.pythonhosted.org/packages/57/2a/d68f86c46b3152c9072975cb1c8b3f2345e0f71cea763c0635ca8c5e0261/splam-0.2.9-cp38-cp38-macosx_13_0_arm64.whl (from https://pypi.org/simple/splam/) (requires-python:>=3.6) 2023-06-27T16:42:59,335 Found link https://files.pythonhosted.org/packages/ba/e8/4cf0f802bf26fd6587829e3688109caef6d26e13d19ce003ac876212da15/splam-0.2.9.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.9 2023-06-27T16:42:59,336 Found link https://files.pythonhosted.org/packages/72/d1/671663c98d0cfca3218b880633390493fcebf9972175a7c4d2752259f2ea/splam-0.2.10.tar.gz (from https://pypi.org/simple/splam/) (requires-python:>=3.6), version: 0.2.10 2023-06-27T16:42:59,336 Fetching project page and analyzing links: https://www.piwheels.org/simple/splam/ 2023-06-27T16:42:59,336 Getting page https://www.piwheels.org/simple/splam/ 2023-06-27T16:42:59,337 Found index url https://www.piwheels.org/simple/ 2023-06-27T16:42:59,514 Fetched page https://www.piwheels.org/simple/splam/ as text/html 2023-06-27T16:42:59,517 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.10-cp37-cp37m-linux_armv7l.whl#sha256=177b04f8ab6035570b2a34ff26f1903996d7f554131eaaddd22614d25e474b0c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-06-27T16:42:59,517 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.10-cp37-cp37m-linux_armv6l.whl#sha256=177b04f8ab6035570b2a34ff26f1903996d7f554131eaaddd22614d25e474b0c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-06-27T16:42:59,518 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.9-cp39-cp39-linux_armv7l.whl#sha256=434410fd7dfc947ef68b0c85650d0b6930abcf1fc52e3a4db0fde3c579d0530c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-06-27T16:42:59,518 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.9-cp39-cp39-linux_armv6l.whl#sha256=434410fd7dfc947ef68b0c85650d0b6930abcf1fc52e3a4db0fde3c579d0530c (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-06-27T16:42:59,518 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.9-cp37-cp37m-linux_armv7l.whl#sha256=c68c4cf3ddbbeac64db06ce5656b1f5ec7df1d53684b7ece65ce366d235c82a1 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-06-27T16:42:59,518 Skipping link: No binaries permitted for splam: https://www.piwheels.org/simple/splam/splam-0.2.9-cp37-cp37m-linux_armv6l.whl#sha256=c68c4cf3ddbbeac64db06ce5656b1f5ec7df1d53684b7ece65ce366d235c82a1 (from https://www.piwheels.org/simple/splam/) (requires-python:>=3.6) 2023-06-27T16:42:59,518 Skipping link: not a file: https://www.piwheels.org/simple/splam/ 2023-06-27T16:42:59,519 Skipping link: not a file: https://pypi.org/simple/splam/ 2023-06-27T16:42:59,536 Given no hashes to check 1 links for project 'splam': discarding no candidates 2023-06-27T16:42:59,553 Collecting splam==0.2.10 2023-06-27T16:42:59,555 Created temporary directory: /tmp/pip-unpack-mybxyknr 2023-06-27T16:42:59,621 Downloading splam-0.2.10.tar.gz (40.6 MB) 2023-06-27T16:43:05,735 Added splam==0.2.10 from https://files.pythonhosted.org/packages/72/d1/671663c98d0cfca3218b880633390493fcebf9972175a7c4d2752259f2ea/splam-0.2.10.tar.gz to build tracker '/tmp/pip-build-tracker-nxzwd3uj' 2023-06-27T16:43:05,738 Running setup.py (path:/tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/setup.py) egg_info for package splam 2023-06-27T16:43:05,739 Created temporary directory: /tmp/pip-pip-egg-info-ek7b2qe5 2023-06-27T16:43:05,739 Preparing metadata (setup.py): started 2023-06-27T16:43:05,741 Running command python setup.py egg_info 2023-06-27T16:43:06,552 running egg_info 2023-06-27T16:43:06,553 creating /tmp/pip-pip-egg-info-ek7b2qe5/splam.egg-info 2023-06-27T16:43:06,581 writing /tmp/pip-pip-egg-info-ek7b2qe5/splam.egg-info/PKG-INFO 2023-06-27T16:43:06,583 writing dependency_links to /tmp/pip-pip-egg-info-ek7b2qe5/splam.egg-info/dependency_links.txt 2023-06-27T16:43:06,585 writing entry points to /tmp/pip-pip-egg-info-ek7b2qe5/splam.egg-info/entry_points.txt 2023-06-27T16:43:06,586 writing requirements to /tmp/pip-pip-egg-info-ek7b2qe5/splam.egg-info/requires.txt 2023-06-27T16:43:06,587 writing top-level names to /tmp/pip-pip-egg-info-ek7b2qe5/splam.egg-info/top_level.txt 2023-06-27T16:43:06,589 writing manifest file '/tmp/pip-pip-egg-info-ek7b2qe5/splam.egg-info/SOURCES.txt' 2023-06-27T16:43:06,673 reading manifest file '/tmp/pip-pip-egg-info-ek7b2qe5/splam.egg-info/SOURCES.txt' 2023-06-27T16:43:06,674 reading manifest template 'MANIFEST.in' 2023-06-27T16:43:06,909 adding license file 'LICENSE' 2023-06-27T16:43:06,950 writing manifest file '/tmp/pip-pip-egg-info-ek7b2qe5/splam.egg-info/SOURCES.txt' 2023-06-27T16:43:07,023 Preparing metadata (setup.py): finished with status 'done' 2023-06-27T16:43:07,028 Source in /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e has version 0.2.10, which satisfies requirement splam==0.2.10 from https://files.pythonhosted.org/packages/72/d1/671663c98d0cfca3218b880633390493fcebf9972175a7c4d2752259f2ea/splam-0.2.10.tar.gz 2023-06-27T16:43:07,029 Removed splam==0.2.10 from https://files.pythonhosted.org/packages/72/d1/671663c98d0cfca3218b880633390493fcebf9972175a7c4d2752259f2ea/splam-0.2.10.tar.gz from build tracker '/tmp/pip-build-tracker-nxzwd3uj' 2023-06-27T16:43:07,035 Created temporary directory: /tmp/pip-unpack-er39fn3n 2023-06-27T16:43:07,035 Building wheels for collected packages: splam 2023-06-27T16:43:07,040 Created temporary directory: /tmp/pip-wheel-2u0gjzqn 2023-06-27T16:43:07,040 Building wheel for splam (setup.py): started 2023-06-27T16:43:07,041 Destination directory: /tmp/pip-wheel-2u0gjzqn 2023-06-27T16:43:07,041 Running command python setup.py bdist_wheel 2023-06-27T16:43:07,840 running bdist_wheel 2023-06-27T16:43:07,920 running build 2023-06-27T16:43:07,920 running build_py 2023-06-27T16:43:07,949 creating build 2023-06-27T16:43:07,950 creating build/lib.linux-armv7l-cpython-39 2023-06-27T16:43:07,951 creating build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,952 copying splam/prediction.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,955 copying splam/splam.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,957 copying splam/config.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,959 copying splam/extract_gff.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,960 copying splam/parse.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,963 copying splam/__init__.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,964 copying splam/helper.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,966 copying splam/chr_size.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,969 copying splam/test.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:43:07,971 running build_ext 2023-06-27T16:43:08,326 -- The C compiler identification is GNU 10.2.1 2023-06-27T16:43:08,655 -- The CXX compiler identification is GNU 10.2.1 2023-06-27T16:43:08,721 -- Detecting C compiler ABI info 2023-06-27T16:43:09,079 -- Detecting C compiler ABI info - done 2023-06-27T16:43:09,139 -- Check for working C compiler: /usr/bin/cc - skipped 2023-06-27T16:43:09,140 -- Detecting C compile features 2023-06-27T16:43:09,142 -- Detecting C compile features - done 2023-06-27T16:43:09,167 -- Detecting CXX compiler ABI info 2023-06-27T16:43:09,605 -- Detecting CXX compiler ABI info - done 2023-06-27T16:43:09,668 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-06-27T16:43:09,669 -- Detecting CXX compile features 2023-06-27T16:43:09,673 -- Detecting CXX compile features - done 2023-06-27T16:43:09,699 -- pybind11 v2.11.0 dev1 2023-06-27T16:43:09,762 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-06-27T16:43:10,233 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-06-27T16:43:10,240 -- Performing Test HAS_FLTO 2023-06-27T16:43:10,826 -- Performing Test HAS_FLTO - Success 2023-06-27T16:43:10,869 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") 2023-06-27T16:43:10,870 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/include/htslib 2023-06-27T16:43:11,005 -- Configuring done 2023-06-27T16:43:11,083 -- Generating done 2023-06-27T16:43:11,095 -- Build files have been written to: /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/build/temp.linux-armv7l-cpython-39/splam_extract 2023-06-27T16:43:11,156 gmake: Warning: File 'Makefile' has modification time 1.4 s in the future 2023-06-27T16:43:11,246 gmake[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 1.4 s in the future 2023-06-27T16:43:11,253 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-27T16:43:11,294 Scanning dependencies of target htslib 2023-06-27T16:43:11,297 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:43:11,305 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-27T16:43:11,344 [ 2%] Creating directories for 'htslib' 2023-06-27T16:43:11,686 [ 5%] No download step for 'htslib' 2023-06-27T16:43:11,834 [ 8%] No update step for 'htslib' 2023-06-27T16:43:11,950 [ 11%] No patch step for 'htslib' 2023-06-27T16:43:12,066 [ 13%] Performing configure step for 'htslib' 2023-06-27T16:43:18,302 checking for gcc... gcc 2023-06-27T16:43:18,572 checking whether the C compiler works... yes 2023-06-27T16:43:18,575 checking for C compiler default output file name... a.out 2023-06-27T16:43:18,748 checking for suffix of executables... 2023-06-27T16:43:18,930 checking whether we are cross compiling... no 2023-06-27T16:43:19,018 checking for suffix of object files... o 2023-06-27T16:43:19,095 checking whether we are using the GNU C compiler... yes 2023-06-27T16:43:19,171 checking whether gcc accepts -g... yes 2023-06-27T16:43:19,290 checking for gcc option to accept ISO C89... none needed 2023-06-27T16:43:19,293 checking for ranlib... ranlib 2023-06-27T16:43:19,301 checking for grep that handles long lines and -e... /usr/bin/grep 2023-06-27T16:43:19,416 checking for C compiler warning flags... -Wall 2023-06-27T16:43:19,570 checking how to run the C preprocessor... gcc -E 2023-06-27T16:43:19,695 checking for egrep... /usr/bin/grep -E 2023-06-27T16:43:20,141 checking for ANSI C header files... yes 2023-06-27T16:43:20,260 checking for sys/types.h... yes 2023-06-27T16:43:20,418 checking for sys/stat.h... yes 2023-06-27T16:43:20,557 checking for stdlib.h... yes 2023-06-27T16:43:20,699 checking for string.h... yes 2023-06-27T16:43:20,839 checking for memory.h... yes 2023-06-27T16:43:20,980 checking for strings.h... yes 2023-06-27T16:43:21,126 checking for inttypes.h... yes 2023-06-27T16:43:21,299 checking for stdint.h... yes 2023-06-27T16:43:21,459 checking for unistd.h... yes 2023-06-27T16:43:21,629 checking whether _XOPEN_SOURCE is declared... no 2023-06-27T16:43:21,799 checking C compiler flags needed for ssse3... none 2023-06-27T16:43:21,981 checking C compiler flags needed for popcnt... none 2023-06-27T16:43:22,200 checking C compiler flags needed for sse4.1... none 2023-06-27T16:43:22,365 checking C compiler flags needed for avx2... none 2023-06-27T16:43:22,530 checking C compiler flags needed for avx512f... none 2023-06-27T16:43:22,533 checking for pkg-config... /usr/bin/pkg-config 2023-06-27T16:43:22,539 checking pkg-config is at least version 0.9.0... yes 2023-06-27T16:43:22,541 checking for special C compiler options needed for large files... no 2023-06-27T16:43:22,720 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-06-27T16:43:22,735 checking shared library type for unknown-Linux... plain .so 2023-06-27T16:43:22,922 checking whether the linker supports versioned symbols... yes 2023-06-27T16:43:23,099 checking whether the compiler accepts -fvisibility=hidden... yes 2023-06-27T16:43:23,111 checking for stdlib.h... (cached) yes 2023-06-27T16:43:23,136 checking for unistd.h... (cached) yes 2023-06-27T16:43:23,300 checking for sys/param.h... yes 2023-06-27T16:43:23,489 checking for getpagesize... yes 2023-06-27T16:43:23,832 checking for working mmap... yes 2023-06-27T16:43:24,022 checking for gmtime_r... yes 2023-06-27T16:43:24,222 checking for fsync... yes 2023-06-27T16:43:24,420 checking for drand48... yes 2023-06-27T16:43:24,673 checking for srand48_deterministic... no 2023-06-27T16:43:24,832 checking whether fdatasync is declared... yes 2023-06-27T16:43:25,011 checking for fdatasync... yes 2023-06-27T16:43:25,436 checking for library containing log... -lm 2023-06-27T16:43:25,538 checking for zlib.h... yes 2023-06-27T16:43:25,715 checking for inflate in -lz... yes 2023-06-27T16:43:25,896 checking for library containing recv... none required 2023-06-27T16:43:25,982 checking for bzlib.h... yes 2023-06-27T16:43:26,188 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-06-27T16:43:26,203 checking whether htscodecs files are present... yes 2023-06-27T16:43:26,205 configure: WARNING: GCS support not enabled: requires libcurl support 2023-06-27T16:43:26,205 configure: WARNING: S3 support not enabled: requires libcurl support 2023-06-27T16:43:26,382 checking for library containing regcomp... none required 2023-06-27T16:43:26,447 configure: creating ./config.status 2023-06-27T16:43:26,754 config.status: creating config.mk 2023-06-27T16:43:26,797 config.status: creating htslib.pc.tmp 2023-06-27T16:43:26,844 config.status: creating config.h 2023-06-27T16:43:26,877 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-06-27T16:43:27,100 [ 16%] Performing build step for 'htslib' 2023-06-27T16:43:27,349 make[3]: Warning: File 'config.mk' has modification time 0.94 s in the future 2023-06-27T16:43:40,759 Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "1.5.0-5-g109f069" 2023-06-27T16:47:41,290 make[3]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:47:41,376 [ 19%] No install step for 'htslib' 2023-06-27T16:47:41,494 [ 22%] Completed 'htslib' 2023-06-27T16:47:41,604 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:47:41,644 [ 22%] Built target htslib 2023-06-27T16:47:41,845 Scanning dependencies of target splam_clean 2023-06-27T16:47:41,860 gmake[2]: Warning: File 'CMakeFiles/splam_clean.dir/depend.make' has modification time 1.5 s in the future 2023-06-27T16:47:41,900 [ 25%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-06-27T16:47:47,198 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-06-27T16:47:47,198 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:319:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,198 319 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-06-27T16:47:47,198 | ^~~~~~~~~~ 2023-06-27T16:47:47,199 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:319:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,199 319 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-06-27T16:47:47,199 | ^~~~~~ 2023-06-27T16:47:47,199 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:319:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,199 319 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-06-27T16:47:47,199 | ^~~~ 2023-06-27T16:47:47,200 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:319:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,200 319 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-06-27T16:47:47,200 | ^~~~ 2023-06-27T16:47:47,200 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:329:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,200 329 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-06-27T16:47:47,200 | ^~~~~~~~~~ 2023-06-27T16:47:47,201 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:329:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,201 329 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-06-27T16:47:47,201 | ^~~~~~ 2023-06-27T16:47:47,201 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:329:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,201 329 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-06-27T16:47:47,201 | ^~~~ 2023-06-27T16:47:47,201 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:329:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,202 329 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-06-27T16:47:47,202 | ^~~~ 2023-06-27T16:47:47,202 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,202 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:47:47,202 | ^~~~~~~~~~ 2023-06-27T16:47:47,202 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,202 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:47:47,203 | ^~~~~~~ 2023-06-27T16:47:47,203 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,203 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:47:47,203 | ^~~~ 2023-06-27T16:47:47,203 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,203 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:47:47,203 | ^~~~ 2023-06-27T16:47:47,203 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,203 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:47:47,204 | ^~~~ 2023-06-27T16:47:47,204 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,204 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:47:47,204 | ^~~~~~~~~~ 2023-06-27T16:47:47,204 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,204 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:47:47,204 | ^~~~~~~ 2023-06-27T16:47:47,205 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,205 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:47:47,205 | ^~~~ 2023-06-27T16:47:47,205 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,205 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:47:47,205 | ^~~~ 2023-06-27T16:47:47,206 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:47:47,206 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:47:47,206 | ^~~~ 2023-06-27T16:47:52,209 [ 27%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-06-27T16:48:00,238 [ 30%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-06-27T16:48:00,715 [ 33%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-06-27T16:48:01,225 [ 36%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-06-27T16:48:01,530 [ 38%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-06-27T16:48:03,306 [ 41%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-06-27T16:48:06,012 [ 44%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-06-27T16:48:09,994 [ 47%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/predict.cpp.o 2023-06-27T16:48:14,105 [ 50%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-06-27T16:48:18,677 [ 52%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-06-27T16:48:22,837 [ 55%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-06-27T16:48:26,941 [ 58%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-06-27T16:48:30,440 [ 61%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-06-27T16:48:32,628 [ 63%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-06-27T16:48:33,712 [ 66%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-06-27T16:48:34,495 [ 69%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-06-27T16:48:35,444 [ 72%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so 2023-06-27T16:48:56,268 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:48:56,319 [ 72%] Built target splam_clean 2023-06-27T16:48:56,472 Scanning dependencies of target splam_extract 2023-06-27T16:48:56,486 gmake[2]: Warning: File 'CMakeFiles/splam_extract.dir/depend.make' has modification time 1.5 s in the future 2023-06-27T16:48:56,527 [ 75%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-06-27T16:49:06,707 [ 77%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-06-27T16:49:10,684 [ 80%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-06-27T16:49:13,383 [ 83%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-06-27T16:49:17,413 [ 86%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-06-27T16:49:20,937 [ 88%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-06-27T16:49:23,142 [ 91%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-06-27T16:49:24,218 [ 94%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-06-27T16:49:25,037 [ 97%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-06-27T16:49:25,986 [100%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so 2023-06-27T16:49:40,086 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-06-27T16:49:40,087 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/include/gclib/GVec.hh:107:14: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-06-27T16:49:40,087 107 | fArray=new OBJ[NewCapacity]; 2023-06-27T16:49:40,087 | ^ 2023-06-27T16:49:40,087 /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-06-27T16:49:40,087 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-06-27T16:49:40,088 | ^ 2023-06-27T16:49:48,222 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:49:48,265 [100%] Built target splam_extract 2023-06-27T16:49:48,268 gmake[1]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:49:48,315 gmake: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:49:48,641 -- The C compiler identification is GNU 10.2.1 2023-06-27T16:49:48,991 -- The CXX compiler identification is GNU 10.2.1 2023-06-27T16:49:49,037 -- Detecting C compiler ABI info 2023-06-27T16:49:49,385 -- Detecting C compiler ABI info - done 2023-06-27T16:49:49,446 -- Check for working C compiler: /usr/bin/cc - skipped 2023-06-27T16:49:49,447 -- Detecting C compile features 2023-06-27T16:49:49,449 -- Detecting C compile features - done 2023-06-27T16:49:49,474 -- Detecting CXX compiler ABI info 2023-06-27T16:49:49,905 -- Detecting CXX compiler ABI info - done 2023-06-27T16:49:49,968 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-06-27T16:49:49,969 -- Detecting CXX compile features 2023-06-27T16:49:49,972 -- Detecting CXX compile features - done 2023-06-27T16:49:49,998 -- pybind11 v2.11.0 dev1 2023-06-27T16:49:50,064 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-06-27T16:49:50,568 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-06-27T16:49:50,576 -- Performing Test HAS_FLTO 2023-06-27T16:49:51,189 -- Performing Test HAS_FLTO - Success 2023-06-27T16:49:51,229 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") 2023-06-27T16:49:51,230 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/include/htslib 2023-06-27T16:49:51,367 -- Configuring done 2023-06-27T16:49:51,452 -- Generating done 2023-06-27T16:49:51,464 -- Build files have been written to: /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/build/temp.linux-armv7l-cpython-39/splam_clean 2023-06-27T16:49:51,527 gmake: Warning: File 'Makefile' has modification time 1.4 s in the future 2023-06-27T16:49:51,618 gmake[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 1.3 s in the future 2023-06-27T16:49:51,626 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-27T16:49:51,669 Scanning dependencies of target htslib 2023-06-27T16:49:51,672 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:49:51,680 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-27T16:49:51,720 [ 2%] Creating directories for 'htslib' 2023-06-27T16:49:52,140 [ 5%] No download step for 'htslib' 2023-06-27T16:49:52,260 [ 8%] No update step for 'htslib' 2023-06-27T16:49:52,374 [ 11%] No patch step for 'htslib' 2023-06-27T16:49:52,488 [ 13%] Performing configure step for 'htslib' 2023-06-27T16:49:57,003 checking for gcc... gcc 2023-06-27T16:49:57,330 checking whether the C compiler works... yes 2023-06-27T16:49:57,331 checking for C compiler default output file name... a.out 2023-06-27T16:49:57,496 checking for suffix of executables... 2023-06-27T16:49:57,674 checking whether we are cross compiling... no 2023-06-27T16:49:57,761 checking for suffix of object files... o 2023-06-27T16:49:57,839 checking whether we are using the GNU C compiler... yes 2023-06-27T16:49:57,916 checking whether gcc accepts -g... yes 2023-06-27T16:49:58,074 checking for gcc option to accept ISO C89... none needed 2023-06-27T16:49:58,075 checking for ranlib... ranlib 2023-06-27T16:49:58,084 checking for grep that handles long lines and -e... /usr/bin/grep 2023-06-27T16:49:58,163 checking for C compiler warning flags... -Wall 2023-06-27T16:49:58,274 checking how to run the C preprocessor... gcc -E 2023-06-27T16:49:58,384 checking for egrep... /usr/bin/grep -E 2023-06-27T16:49:58,872 checking for ANSI C header files... yes 2023-06-27T16:49:58,992 checking for sys/types.h... yes 2023-06-27T16:49:59,127 checking for sys/stat.h... yes 2023-06-27T16:49:59,263 checking for stdlib.h... yes 2023-06-27T16:49:59,402 checking for string.h... yes 2023-06-27T16:49:59,543 checking for memory.h... yes 2023-06-27T16:49:59,743 checking for strings.h... yes 2023-06-27T16:49:59,895 checking for inttypes.h... yes 2023-06-27T16:50:00,041 checking for stdint.h... yes 2023-06-27T16:50:00,194 checking for unistd.h... yes 2023-06-27T16:50:00,365 checking whether _XOPEN_SOURCE is declared... no 2023-06-27T16:50:00,571 checking C compiler flags needed for ssse3... none 2023-06-27T16:50:00,739 checking C compiler flags needed for popcnt... none 2023-06-27T16:50:00,908 checking C compiler flags needed for sse4.1... none 2023-06-27T16:50:01,082 checking C compiler flags needed for avx2... none 2023-06-27T16:50:01,247 checking C compiler flags needed for avx512f... none 2023-06-27T16:50:01,250 checking for pkg-config... /usr/bin/pkg-config 2023-06-27T16:50:01,256 checking pkg-config is at least version 0.9.0... yes 2023-06-27T16:50:01,258 checking for special C compiler options needed for large files... no 2023-06-27T16:50:01,430 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-06-27T16:50:01,446 checking shared library type for unknown-Linux... plain .so 2023-06-27T16:50:01,616 checking whether the linker supports versioned symbols... yes 2023-06-27T16:50:01,786 checking whether the compiler accepts -fvisibility=hidden... yes 2023-06-27T16:50:01,800 checking for stdlib.h... (cached) yes 2023-06-27T16:50:01,824 checking for unistd.h... (cached) yes 2023-06-27T16:50:01,995 checking for sys/param.h... yes 2023-06-27T16:50:02,245 checking for getpagesize... yes 2023-06-27T16:50:02,549 checking for working mmap... yes 2023-06-27T16:50:02,737 checking for gmtime_r... yes 2023-06-27T16:50:02,954 checking for fsync... yes 2023-06-27T16:50:03,159 checking for drand48... yes 2023-06-27T16:50:03,382 checking for srand48_deterministic... no 2023-06-27T16:50:03,542 checking whether fdatasync is declared... yes 2023-06-27T16:50:03,725 checking for fdatasync... yes 2023-06-27T16:50:04,135 checking for library containing log... -lm 2023-06-27T16:50:04,235 checking for zlib.h... yes 2023-06-27T16:50:04,412 checking for inflate in -lz... yes 2023-06-27T16:50:04,629 checking for library containing recv... none required 2023-06-27T16:50:04,716 checking for bzlib.h... yes 2023-06-27T16:50:04,893 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-06-27T16:50:04,904 checking whether htscodecs files are present... yes 2023-06-27T16:50:04,905 configure: WARNING: GCS support not enabled: requires libcurl support 2023-06-27T16:50:04,906 configure: WARNING: S3 support not enabled: requires libcurl support 2023-06-27T16:50:05,084 checking for library containing regcomp... none required 2023-06-27T16:50:05,148 configure: creating ./config.status 2023-06-27T16:50:05,527 config.status: creating config.mk 2023-06-27T16:50:05,592 config.status: creating htslib.pc.tmp 2023-06-27T16:50:05,659 config.status: creating config.h 2023-06-27T16:50:05,686 config.status: config.h is unchanged 2023-06-27T16:50:05,694 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-06-27T16:50:05,923 [ 16%] Performing build step for 'htslib' 2023-06-27T16:50:06,174 make[3]: Warning: File 'config.mk' has modification time 0.9 s in the future 2023-06-27T16:50:06,241 make[3]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:50:06,316 [ 19%] No install step for 'htslib' 2023-06-27T16:50:06,433 [ 22%] Completed 'htslib' 2023-06-27T16:50:06,544 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:50:06,586 [ 22%] Built target htslib 2023-06-27T16:50:06,796 Scanning dependencies of target splam_clean 2023-06-27T16:50:06,812 gmake[2]: Warning: File 'CMakeFiles/splam_clean.dir/depend.make' has modification time 1.5 s in the future 2023-06-27T16:50:06,851 [ 25%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-06-27T16:50:12,051 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-06-27T16:50:12,051 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:319:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,052 319 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-06-27T16:50:12,052 | ^~~~~~~~~~ 2023-06-27T16:50:12,052 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:319:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,052 319 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-06-27T16:50:12,052 | ^~~~~~ 2023-06-27T16:50:12,053 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:319:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,053 319 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-06-27T16:50:12,053 | ^~~~ 2023-06-27T16:50:12,053 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:319:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,053 319 | char *s_uniq_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), "-o", (char*)outfname_s_uniq_map_cleaned_sort.chars()}; 2023-06-27T16:50:12,053 | ^~~~ 2023-06-27T16:50:12,053 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:329:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,054 329 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-06-27T16:50:12,054 | ^~~~~~~~~~ 2023-06-27T16:50:12,054 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:329:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,054 329 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-06-27T16:50:12,054 | ^~~~~~ 2023-06-27T16:50:12,054 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:329:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,055 329 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-06-27T16:50:12,055 | ^~~~ 2023-06-27T16:50:12,055 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:329:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,055 329 | char *s_multi_argv[] = {"samtools", "sort", "-@", (char*)thread_num.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars(), "-o", (char*)outfname_s_multi_map_cleaned_nh_updated_sort.chars()}; 2023-06-27T16:50:12,055 | ^~~~ 2023-06-27T16:50:12,055 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,055 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:50:12,055 | ^~~~~~~~~~ 2023-06-27T16:50:12,056 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,056 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:50:12,056 | ^~~~~~~ 2023-06-27T16:50:12,056 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,056 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:50:12,056 | ^~~~ 2023-06-27T16:50:12,056 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,056 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:50:12,057 | ^~~~ 2023-06-27T16:50:12,057 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:336:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,057 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:50:12,057 | ^~~~ 2023-06-27T16:50:12,057 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,057 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:50:12,057 | ^~~~~~~~~~ 2023-06-27T16:50:12,057 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,058 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:50:12,058 | ^~~~~~~ 2023-06-27T16:50:12,058 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,058 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:50:12,058 | ^~~~ 2023-06-27T16:50:12,058 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,059 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:50:12,059 | ^~~~ 2023-06-27T16:50:12,059 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/splam/module/splam_clean.cpp:354:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:50:12,059 354 | char *test[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), (char*)outfname_ns_uniq_map.chars(), (char*)outfname_ns_multi_map_nh_updated.chars(), (char*)outfname_s_uniq_map_cleaned.chars(), (char*)outfname_s_multi_map_cleaned_nh_updated.chars()}; 2023-06-27T16:50:12,059 | ^~~~ 2023-06-27T16:50:17,080 [ 27%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-06-27T16:50:25,207 [ 30%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-06-27T16:50:25,727 [ 33%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-06-27T16:50:26,289 [ 36%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-06-27T16:50:26,659 [ 38%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-06-27T16:50:28,437 [ 41%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-06-27T16:50:31,136 [ 44%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-06-27T16:50:35,124 [ 47%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/predict.cpp.o 2023-06-27T16:50:39,205 [ 50%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-06-27T16:50:43,853 [ 52%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-06-27T16:50:48,019 [ 55%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-06-27T16:50:52,053 [ 58%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-06-27T16:50:55,623 [ 61%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-06-27T16:50:57,816 [ 63%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-06-27T16:50:58,902 [ 66%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-06-27T16:50:59,724 [ 69%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-06-27T16:51:00,673 [ 72%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so 2023-06-27T16:51:21,522 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:51:21,578 [ 72%] Built target splam_clean 2023-06-27T16:51:21,722 Scanning dependencies of target splam_extract 2023-06-27T16:51:21,736 gmake[2]: Warning: File 'CMakeFiles/splam_extract.dir/depend.make' has modification time 1.5 s in the future 2023-06-27T16:51:21,776 [ 75%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-06-27T16:51:31,965 [ 77%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-06-27T16:51:35,957 [ 80%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-06-27T16:51:38,650 [ 83%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-06-27T16:51:42,703 [ 86%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-06-27T16:51:46,203 [ 88%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-06-27T16:51:48,418 [ 91%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-06-27T16:51:49,489 [ 94%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-06-27T16:51:50,275 [ 97%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-06-27T16:51:51,224 [100%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so 2023-06-27T16:52:05,362 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-06-27T16:52:05,363 /tmp/pip-wheel-mhtyhf8h/splam_78393191eae049e0a8ada4db7a76f41e/include/gclib/GVec.hh:107:14: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-06-27T16:52:05,363 107 | fArray=new OBJ[NewCapacity]; 2023-06-27T16:52:05,363 | ^ 2023-06-27T16:52:05,363 /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-06-27T16:52:05,363 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-06-27T16:52:05,364 | ^ 2023-06-27T16:52:13,563 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:52:13,609 [100%] Built target splam_extract 2023-06-27T16:52:13,612 gmake[1]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:52:13,660 gmake: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:52:13,713 /home/piwheels/.local/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-06-27T16:52:13,714 !! 2023-06-27T16:52:13,714 ******************************************************************************** 2023-06-27T16:52:13,714 Please avoid running ``setup.py`` directly. 2023-06-27T16:52:13,714 Instead, use pypa/build, pypa/installer, pypa/build or 2023-06-27T16:52:13,715 other standards-based tools. 2023-06-27T16:52:13,715 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-06-27T16:52:13,715 ******************************************************************************** 2023-06-27T16:52:13,715 !! 2023-06-27T16:52:13,715 self.initialize_options() 2023-06-27T16:52:13,742 installing to build/bdist.linux-armv7l/wheel 2023-06-27T16:52:13,742 running install 2023-06-27T16:52:13,768 running install_lib 2023-06-27T16:52:13,796 creating build/bdist.linux-armv7l 2023-06-27T16:52:13,796 creating build/bdist.linux-armv7l/wheel 2023-06-27T16:52:13,797 copying build/lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-06-27T16:52:13,804 copying build/lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-06-27T16:52:13,812 creating build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,813 copying build/lib.linux-armv7l-cpython-39/splam/prediction.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,816 copying build/lib.linux-armv7l-cpython-39/splam/splam.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,818 copying build/lib.linux-armv7l-cpython-39/splam/config.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,820 copying build/lib.linux-armv7l-cpython-39/splam/extract_gff.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,821 copying build/lib.linux-armv7l-cpython-39/splam/parse.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,824 copying build/lib.linux-armv7l-cpython-39/splam/__init__.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,825 copying build/lib.linux-armv7l-cpython-39/splam/helper.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,827 copying build/lib.linux-armv7l-cpython-39/splam/chr_size.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,830 copying build/lib.linux-armv7l-cpython-39/splam/test.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:52:13,831 running install_egg_info 2023-06-27T16:52:13,900 running egg_info 2023-06-27T16:52:13,925 writing splam.egg-info/PKG-INFO 2023-06-27T16:52:13,926 writing dependency_links to splam.egg-info/dependency_links.txt 2023-06-27T16:52:13,929 writing entry points to splam.egg-info/entry_points.txt 2023-06-27T16:52:13,930 writing requirements to splam.egg-info/requires.txt 2023-06-27T16:52:13,931 writing top-level names to splam.egg-info/top_level.txt 2023-06-27T16:52:13,961 reading manifest file 'splam.egg-info/SOURCES.txt' 2023-06-27T16:52:14,145 reading manifest template 'MANIFEST.in' 2023-06-27T16:52:14,437 adding license file 'LICENSE' 2023-06-27T16:52:14,503 writing manifest file 'splam.egg-info/SOURCES.txt' 2023-06-27T16:52:14,506 Copying splam.egg-info to build/bdist.linux-armv7l/wheel/splam-0.2.10-py3.9.egg-info 2023-06-27T16:52:14,518 running install_scripts 2023-06-27T16:52:14,566 creating build/bdist.linux-armv7l/wheel/splam-0.2.10.dist-info/WHEEL 2023-06-27T16:52:14,569 creating '/tmp/pip-wheel-2u0gjzqn/splam-0.2.10-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-06-27T16:52:14,650 adding 'splam_clean.cpython-39-arm-linux-gnueabihf.so' 2023-06-27T16:52:14,703 adding 'splam_extract.cpython-39-arm-linux-gnueabihf.so' 2023-06-27T16:52:14,706 adding 'splam/__init__.py' 2023-06-27T16:52:14,709 adding 'splam/chr_size.py' 2023-06-27T16:52:14,711 adding 'splam/config.py' 2023-06-27T16:52:14,712 adding 'splam/extract_gff.py' 2023-06-27T16:52:14,713 adding 'splam/helper.py' 2023-06-27T16:52:14,715 adding 'splam/parse.py' 2023-06-27T16:52:14,717 adding 'splam/prediction.py' 2023-06-27T16:52:14,718 adding 'splam/splam.py' 2023-06-27T16:52:14,720 adding 'splam/test.py' 2023-06-27T16:52:14,722 adding 'splam-0.2.10.dist-info/LICENSE' 2023-06-27T16:52:14,723 adding 'splam-0.2.10.dist-info/METADATA' 2023-06-27T16:52:14,724 adding 'splam-0.2.10.dist-info/WHEEL' 2023-06-27T16:52:14,725 adding 'splam-0.2.10.dist-info/entry_points.txt' 2023-06-27T16:52:14,726 adding 'splam-0.2.10.dist-info/top_level.txt' 2023-06-27T16:52:14,727 adding 'splam-0.2.10.dist-info/RECORD' 2023-06-27T16:52:14,733 removing build/bdist.linux-armv7l/wheel 2023-06-27T16:52:14,825 Building wheel for splam (setup.py): finished with status 'done' 2023-06-27T16:52:14,831 Created wheel for splam: filename=splam-0.2.10-cp39-cp39-linux_armv7l.whl size=294203 sha256=bc7a085b3f086edc5395dc060b95fe568bab61c94fd8cf56dc6f58b7e62442e3 2023-06-27T16:52:14,833 Stored in directory: /tmp/pip-ephem-wheel-cache-qhhgjr3x/wheels/0a/cb/4a/a9a82c606b89db228924dd4700ce0b0076c7736d320d3e8282 2023-06-27T16:52:14,844 Successfully built splam 2023-06-27T16:52:14,855 Removed build tracker: '/tmp/pip-build-tracker-nxzwd3uj'