2023-06-27T16:28:36,698 Created temporary directory: /tmp/pip-build-tracker-llb0vzf9 2023-06-27T16:28:36,700 Initialized build tracking at /tmp/pip-build-tracker-llb0vzf9 2023-06-27T16:28:36,700 Created build tracker: /tmp/pip-build-tracker-llb0vzf9 2023-06-27T16:28:36,700 Entered build tracker: /tmp/pip-build-tracker-llb0vzf9 2023-06-27T16:28:36,700 Created temporary directory: /tmp/pip-wheel-4uwh6b7w 2023-06-27T16:28:36,703 Created temporary directory: /tmp/pip-ephem-wheel-cache-3wjga3nk 2023-06-27T16:28:36,730 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-06-27T16:28:36,733 2 location(s) to search for versions of splam: 2023-06-27T16:28:36,733 * https://pypi.org/simple/splam/ 2023-06-27T16:28:36,733 * https://www.piwheels.org/simple/splam/ 2023-06-27T16:28:36,734 Fetching project page and analyzing links: https://pypi.org/simple/splam/ 2023-06-27T16:28:36,734 Getting page https://pypi.org/simple/splam/ 2023-06-27T16:28:36,736 Found index url https://pypi.org/simple/ 2023-06-27T16:28:36,796 Fetched page https://pypi.org/simple/splam/ as application/vnd.pypi.simple.v1+json 2023-06-27T16:28:36,798 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) 2023-06-27T16:28:36,798 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 2023-06-27T16:28:36,799 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 2023-06-27T16:28:36,799 Fetching project page and analyzing links: https://www.piwheels.org/simple/splam/ 2023-06-27T16:28:36,800 Getting page https://www.piwheels.org/simple/splam/ 2023-06-27T16:28:36,801 Found index url https://www.piwheels.org/simple/ 2023-06-27T16:28:36,976 Fetched page https://www.piwheels.org/simple/splam/ as text/html 2023-06-27T16:28:36,977 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) 2023-06-27T16:28:36,977 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) 2023-06-27T16:28:36,978 Skipping link: not a file: https://www.piwheels.org/simple/splam/ 2023-06-27T16:28:36,978 Skipping link: not a file: https://pypi.org/simple/splam/ 2023-06-27T16:28:36,995 Given no hashes to check 1 links for project 'splam': discarding no candidates 2023-06-27T16:28:37,012 Collecting splam==0.2.9 2023-06-27T16:28:37,014 Created temporary directory: /tmp/pip-unpack-ch1i2h4x 2023-06-27T16:28:37,069 Downloading splam-0.2.9.tar.gz (20.3 MB) 2023-06-27T16:28:42,938 Added splam==0.2.9 from https://files.pythonhosted.org/packages/ba/e8/4cf0f802bf26fd6587829e3688109caef6d26e13d19ce003ac876212da15/splam-0.2.9.tar.gz to build tracker '/tmp/pip-build-tracker-llb0vzf9' 2023-06-27T16:28:42,940 Running setup.py (path:/tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/setup.py) egg_info for package splam 2023-06-27T16:28:42,941 Created temporary directory: /tmp/pip-pip-egg-info-cuu82r74 2023-06-27T16:28:42,941 Preparing metadata (setup.py): started 2023-06-27T16:28:42,942 Running command python setup.py egg_info 2023-06-27T16:28:43,731 running egg_info 2023-06-27T16:28:43,732 creating /tmp/pip-pip-egg-info-cuu82r74/splam.egg-info 2023-06-27T16:28:43,761 writing /tmp/pip-pip-egg-info-cuu82r74/splam.egg-info/PKG-INFO 2023-06-27T16:28:43,763 writing dependency_links to /tmp/pip-pip-egg-info-cuu82r74/splam.egg-info/dependency_links.txt 2023-06-27T16:28:43,765 writing entry points to /tmp/pip-pip-egg-info-cuu82r74/splam.egg-info/entry_points.txt 2023-06-27T16:28:43,766 writing requirements to /tmp/pip-pip-egg-info-cuu82r74/splam.egg-info/requires.txt 2023-06-27T16:28:43,767 writing top-level names to /tmp/pip-pip-egg-info-cuu82r74/splam.egg-info/top_level.txt 2023-06-27T16:28:43,768 writing manifest file '/tmp/pip-pip-egg-info-cuu82r74/splam.egg-info/SOURCES.txt' 2023-06-27T16:28:43,855 reading manifest file '/tmp/pip-pip-egg-info-cuu82r74/splam.egg-info/SOURCES.txt' 2023-06-27T16:28:43,857 reading manifest template 'MANIFEST.in' 2023-06-27T16:28:44,083 adding license file 'LICENSE' 2023-06-27T16:28:44,126 writing manifest file '/tmp/pip-pip-egg-info-cuu82r74/splam.egg-info/SOURCES.txt' 2023-06-27T16:28:44,197 Preparing metadata (setup.py): finished with status 'done' 2023-06-27T16:28:44,202 Source in /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409 has version 0.2.9, which satisfies requirement splam==0.2.9 from https://files.pythonhosted.org/packages/ba/e8/4cf0f802bf26fd6587829e3688109caef6d26e13d19ce003ac876212da15/splam-0.2.9.tar.gz 2023-06-27T16:28:44,203 Removed splam==0.2.9 from https://files.pythonhosted.org/packages/ba/e8/4cf0f802bf26fd6587829e3688109caef6d26e13d19ce003ac876212da15/splam-0.2.9.tar.gz from build tracker '/tmp/pip-build-tracker-llb0vzf9' 2023-06-27T16:28:44,209 Created temporary directory: /tmp/pip-unpack-qqb03i3f 2023-06-27T16:28:44,210 Building wheels for collected packages: splam 2023-06-27T16:28:44,214 Created temporary directory: /tmp/pip-wheel-fxe1x5yv 2023-06-27T16:28:44,214 Building wheel for splam (setup.py): started 2023-06-27T16:28:44,215 Destination directory: /tmp/pip-wheel-fxe1x5yv 2023-06-27T16:28:44,215 Running command python setup.py bdist_wheel 2023-06-27T16:28:45,029 running bdist_wheel 2023-06-27T16:28:45,110 running build 2023-06-27T16:28:45,111 running build_py 2023-06-27T16:28:45,140 creating build 2023-06-27T16:28:45,141 creating build/lib.linux-armv7l-cpython-39 2023-06-27T16:28:45,141 creating build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,143 copying splam/prediction.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,145 copying splam/extract_gff.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,147 copying splam/config.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,148 copying splam/helper.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,150 copying splam/chr_size.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,152 copying splam/__init__.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,154 copying splam/parse.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,156 copying splam/splam.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,158 copying splam/test.py -> build/lib.linux-armv7l-cpython-39/splam 2023-06-27T16:28:45,160 running build_ext 2023-06-27T16:28:45,492 -- The C compiler identification is GNU 10.2.1 2023-06-27T16:28:45,819 -- The CXX compiler identification is GNU 10.2.1 2023-06-27T16:28:45,865 -- Detecting C compiler ABI info 2023-06-27T16:28:46,207 -- Detecting C compiler ABI info - done 2023-06-27T16:28:46,286 -- Check for working C compiler: /usr/bin/cc - skipped 2023-06-27T16:28:46,288 -- Detecting C compile features 2023-06-27T16:28:46,292 -- Detecting C compile features - done 2023-06-27T16:28:46,329 -- Detecting CXX compiler ABI info 2023-06-27T16:28:46,727 -- Detecting CXX compiler ABI info - done 2023-06-27T16:28:46,789 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-06-27T16:28:46,790 -- Detecting CXX compile features 2023-06-27T16:28:46,793 -- Detecting CXX compile features - done 2023-06-27T16:28:46,820 -- pybind11 v2.11.0 dev1 2023-06-27T16:28:46,882 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-06-27T16:28:47,394 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-06-27T16:28:47,401 -- Performing Test HAS_FLTO 2023-06-27T16:28:48,018 -- Performing Test HAS_FLTO - Success 2023-06-27T16:28:48,058 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") 2023-06-27T16:28:48,060 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/htslib 2023-06-27T16:28:48,194 -- Configuring done 2023-06-27T16:28:48,279 -- Generating done 2023-06-27T16:28:48,292 -- Build files have been written to: /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/build/temp.linux-armv7l-cpython-39/splam_extract 2023-06-27T16:28:48,355 gmake: Warning: File 'Makefile' has modification time 1.4 s in the future 2023-06-27T16:28:48,446 gmake[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 1.4 s in the future 2023-06-27T16:28:48,453 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-27T16:28:48,495 Scanning dependencies of target htslib 2023-06-27T16:28:48,498 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:28:48,505 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-27T16:28:48,545 [ 2%] Creating directories for 'htslib' 2023-06-27T16:28:48,966 [ 5%] No download step for 'htslib' 2023-06-27T16:28:49,124 [ 8%] No update step for 'htslib' 2023-06-27T16:28:49,251 [ 11%] No patch step for 'htslib' 2023-06-27T16:28:49,369 [ 13%] Performing configure step for 'htslib' 2023-06-27T16:28:54,737 checking for gcc... gcc 2023-06-27T16:28:55,028 checking whether the C compiler works... yes 2023-06-27T16:28:55,029 checking for C compiler default output file name... a.out 2023-06-27T16:28:55,189 checking for suffix of executables... 2023-06-27T16:28:55,372 checking whether we are cross compiling... no 2023-06-27T16:28:55,459 checking for suffix of object files... o 2023-06-27T16:28:55,536 checking whether we are using the GNU C compiler... yes 2023-06-27T16:28:55,613 checking whether gcc accepts -g... yes 2023-06-27T16:28:55,736 checking for gcc option to accept ISO C89... none needed 2023-06-27T16:28:55,739 checking for ranlib... ranlib 2023-06-27T16:28:55,751 checking for grep that handles long lines and -e... /usr/bin/grep 2023-06-27T16:28:55,858 checking for C compiler warning flags... -Wall 2023-06-27T16:28:55,916 checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no 2023-06-27T16:28:55,965 checking whether C compiler accepts -mavx2... no 2023-06-27T16:28:56,015 checking whether C compiler accepts -mavx512f... no 2023-06-27T16:28:56,368 checking whether C compiler supports ARM Neon... no 2023-06-27T16:28:56,370 checking for pkg-config... /usr/bin/pkg-config 2023-06-27T16:28:56,376 checking pkg-config is at least version 0.9.0... yes 2023-06-27T16:28:56,378 checking for special C compiler options needed for large files... no 2023-06-27T16:28:56,566 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-06-27T16:28:56,583 checking shared library type for unknown-Linux... plain .so 2023-06-27T16:28:56,753 checking whether the linker supports versioned symbols... yes 2023-06-27T16:28:56,921 checking whether the compiler accepts -fvisibility=hidden... yes 2023-06-27T16:28:57,027 checking how to run the C preprocessor... gcc -E 2023-06-27T16:28:57,140 checking for egrep... /usr/bin/grep -E 2023-06-27T16:28:57,630 checking for ANSI C header files... yes 2023-06-27T16:28:57,750 checking for sys/types.h... yes 2023-06-27T16:28:57,885 checking for sys/stat.h... yes 2023-06-27T16:28:58,016 checking for stdlib.h... yes 2023-06-27T16:28:58,192 checking for string.h... yes 2023-06-27T16:28:58,334 checking for memory.h... yes 2023-06-27T16:28:58,474 checking for strings.h... yes 2023-06-27T16:28:58,618 checking for inttypes.h... yes 2023-06-27T16:28:58,760 checking for stdint.h... yes 2023-06-27T16:28:58,949 checking for unistd.h... yes 2023-06-27T16:28:58,978 checking for stdlib.h... (cached) yes 2023-06-27T16:28:59,002 checking for unistd.h... (cached) yes 2023-06-27T16:28:59,177 checking for sys/param.h... yes 2023-06-27T16:28:59,368 checking for getpagesize... yes 2023-06-27T16:28:59,694 checking for working mmap... yes 2023-06-27T16:28:59,929 checking for gmtime_r... yes 2023-06-27T16:29:00,131 checking for fsync... yes 2023-06-27T16:29:00,331 checking for drand48... yes 2023-06-27T16:29:00,551 checking for srand48_deterministic... no 2023-06-27T16:29:00,754 checking whether fdatasync is declared... yes 2023-06-27T16:29:00,928 checking for fdatasync... yes 2023-06-27T16:29:01,579 checking for library containing log... -lm 2023-06-27T16:29:01,681 checking for zlib.h... yes 2023-06-27T16:29:01,856 checking for inflate in -lz... yes 2023-06-27T16:29:02,036 checking for library containing recv... none required 2023-06-27T16:29:02,123 checking for bzlib.h... yes 2023-06-27T16:29:02,327 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-06-27T16:29:02,340 checking whether htscodecs files are present... yes 2023-06-27T16:29:02,341 configure: WARNING: GCS support not enabled: requires libcurl support 2023-06-27T16:29:02,342 configure: WARNING: S3 support not enabled: requires libcurl support 2023-06-27T16:29:02,522 checking for library containing regcomp... none required 2023-06-27T16:29:02,642 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2023-06-27T16:29:02,708 configure: creating ./config.status 2023-06-27T16:29:03,025 config.status: creating config.mk 2023-06-27T16:29:03,090 config.status: creating htslib.pc.tmp 2023-06-27T16:29:03,157 config.status: creating config.h 2023-06-27T16:29:03,203 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-06-27T16:29:03,434 [ 16%] Performing build step for 'htslib' 2023-06-27T16:29:03,457 fatal: not a git repository: /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/htslib/../../../.git/modules/SPLAM_C++/include/htslib 2023-06-27T16:29:03,466 fatal: not a git repository: /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/htslib/../../../.git/modules/SPLAM_C++/include/htslib 2023-06-27T16:29:03,509 make[3]: Warning: File 'config.mk' has modification time 1.1 s in the future 2023-06-27T16:29:17,047 fatal: not a git repository: /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/htslib/htscodecs/../../../../.git/modules/SPLAM_C++/include/htslib/modules/htscodecs 2023-06-27T16:29:17,055 Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "" 2023-06-27T16:33:15,867 make[3]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:33:15,951 [ 19%] No install step for 'htslib' 2023-06-27T16:33:16,070 [ 22%] Completed 'htslib' 2023-06-27T16:33:16,184 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:33:16,227 [ 22%] Built target htslib 2023-06-27T16:33:16,462 Scanning dependencies of target splam_clean 2023-06-27T16:33:16,477 gmake[2]: Warning: File 'CMakeFiles/splam_clean.dir/depend.make' has modification time 1.5 s in the future 2023-06-27T16:33:16,516 [ 25%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-06-27T16:33:21,732 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-06-27T16:33:21,732 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:319:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,733 319 | 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()}; 2023-06-27T16:33:21,733 | ^~~~~~~~~~ 2023-06-27T16:33:21,733 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:319:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,733 319 | 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()}; 2023-06-27T16:33:21,733 | ^~~~~~ 2023-06-27T16:33:21,733 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:319:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,734 319 | 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()}; 2023-06-27T16:33:21,734 | ^~~~ 2023-06-27T16:33:21,734 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:319:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,734 319 | 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()}; 2023-06-27T16:33:21,734 | ^~~~ 2023-06-27T16:33:21,734 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:329:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,735 329 | 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()}; 2023-06-27T16:33:21,735 | ^~~~~~~~~~ 2023-06-27T16:33:21,735 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:329:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,735 329 | 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()}; 2023-06-27T16:33:21,735 | ^~~~~~ 2023-06-27T16:33:21,735 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:329:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,736 329 | 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()}; 2023-06-27T16:33:21,736 | ^~~~ 2023-06-27T16:33:21,736 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:329:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,736 329 | 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()}; 2023-06-27T16:33:21,736 | ^~~~ 2023-06-27T16:33:21,736 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,736 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:33:21,736 | ^~~~~~~~~~ 2023-06-27T16:33:21,737 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,737 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:33:21,737 | ^~~~~~~ 2023-06-27T16:33:21,737 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,737 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:33:21,737 | ^~~~ 2023-06-27T16:33:21,737 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,737 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:33:21,738 | ^~~~ 2023-06-27T16:33:21,738 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,738 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:33:21,738 | ^~~~ 2023-06-27T16:33:21,738 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,738 354 | 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()}; 2023-06-27T16:33:21,738 | ^~~~~~~~~~ 2023-06-27T16:33:21,739 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,739 354 | 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()}; 2023-06-27T16:33:21,739 | ^~~~~~~ 2023-06-27T16:33:21,739 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,739 354 | 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()}; 2023-06-27T16:33:21,739 | ^~~~ 2023-06-27T16:33:21,739 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,740 354 | 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()}; 2023-06-27T16:33:21,740 | ^~~~ 2023-06-27T16:33:21,740 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:33:21,740 354 | 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()}; 2023-06-27T16:33:21,740 | ^~~~ 2023-06-27T16:33:26,701 [ 27%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-06-27T16:33:34,789 [ 30%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-06-27T16:33:35,275 [ 33%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-06-27T16:33:35,816 [ 36%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-06-27T16:33:36,127 [ 38%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-06-27T16:33:37,904 [ 41%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-06-27T16:33:40,612 [ 44%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-06-27T16:33:44,620 [ 47%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/predict.cpp.o 2023-06-27T16:33:48,718 [ 50%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-06-27T16:33:53,245 [ 52%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-06-27T16:33:57,449 [ 55%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-06-27T16:34:01,505 [ 58%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-06-27T16:34:04,991 [ 61%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-06-27T16:34:07,185 [ 63%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-06-27T16:34:08,265 [ 66%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-06-27T16:34:09,055 [ 69%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-06-27T16:34:10,013 [ 72%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so 2023-06-27T16:34:30,895 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:34:30,950 [ 72%] Built target splam_clean 2023-06-27T16:34:31,104 Scanning dependencies of target splam_extract 2023-06-27T16:34:31,119 gmake[2]: Warning: File 'CMakeFiles/splam_extract.dir/depend.make' has modification time 1.5 s in the future 2023-06-27T16:34:31,160 [ 75%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-06-27T16:34:41,319 [ 77%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-06-27T16:34:45,277 [ 80%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-06-27T16:34:47,960 [ 83%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-06-27T16:34:51,975 [ 86%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-06-27T16:34:55,463 [ 88%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-06-27T16:34:57,649 [ 91%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-06-27T16:34:58,721 [ 94%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-06-27T16:34:59,504 [ 97%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-06-27T16:35:00,453 [100%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so 2023-06-27T16:35:14,570 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-06-27T16:35:14,570 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/gclib/GVec.hh:107:14: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-06-27T16:35:14,571 107 | fArray=new OBJ[NewCapacity]; 2023-06-27T16:35:14,571 | ^ 2023-06-27T16:35:14,571 /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-06-27T16:35:14,571 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-06-27T16:35:14,571 | ^ 2023-06-27T16:35:22,702 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:35:22,747 [100%] Built target splam_extract 2023-06-27T16:35:22,750 gmake[1]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:35:22,799 gmake: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:35:23,129 -- The C compiler identification is GNU 10.2.1 2023-06-27T16:35:23,450 -- The CXX compiler identification is GNU 10.2.1 2023-06-27T16:35:23,495 -- Detecting C compiler ABI info 2023-06-27T16:35:23,854 -- Detecting C compiler ABI info - done 2023-06-27T16:35:23,922 -- Check for working C compiler: /usr/bin/cc - skipped 2023-06-27T16:35:23,923 -- Detecting C compile features 2023-06-27T16:35:23,925 -- Detecting C compile features - done 2023-06-27T16:35:23,949 -- Detecting CXX compiler ABI info 2023-06-27T16:35:24,345 -- Detecting CXX compiler ABI info - done 2023-06-27T16:35:24,408 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-06-27T16:35:24,409 -- Detecting CXX compile features 2023-06-27T16:35:24,412 -- Detecting CXX compile features - done 2023-06-27T16:35:24,439 -- pybind11 v2.11.0 dev1 2023-06-27T16:35:24,509 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-06-27T16:35:25,054 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-06-27T16:35:25,062 -- Performing Test HAS_FLTO 2023-06-27T16:35:25,655 -- Performing Test HAS_FLTO - Success 2023-06-27T16:35:25,696 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") 2023-06-27T16:35:25,697 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/htslib 2023-06-27T16:35:25,834 -- Configuring done 2023-06-27T16:35:25,915 -- Generating done 2023-06-27T16:35:25,926 -- Build files have been written to: /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/build/temp.linux-armv7l-cpython-39/splam_clean 2023-06-27T16:35:25,986 gmake: Warning: File 'Makefile' has modification time 1.4 s in the future 2023-06-27T16:35:26,074 gmake[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 1.4 s in the future 2023-06-27T16:35:26,081 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-27T16:35:26,130 Scanning dependencies of target htslib 2023-06-27T16:35:26,135 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:35:26,144 gmake[2]: Warning: File 'CMakeFiles/htslib.dir/progress.make' has modification time 1.3 s in the future 2023-06-27T16:35:26,198 [ 2%] Creating directories for 'htslib' 2023-06-27T16:35:26,538 [ 5%] No download step for 'htslib' 2023-06-27T16:35:26,653 [ 8%] No update step for 'htslib' 2023-06-27T16:35:26,765 [ 11%] No patch step for 'htslib' 2023-06-27T16:35:26,878 [ 13%] Performing configure step for 'htslib' 2023-06-27T16:35:31,372 checking for gcc... gcc 2023-06-27T16:35:31,703 checking whether the C compiler works... yes 2023-06-27T16:35:31,704 checking for C compiler default output file name... a.out 2023-06-27T16:35:31,860 checking for suffix of executables... 2023-06-27T16:35:32,037 checking whether we are cross compiling... no 2023-06-27T16:35:32,123 checking for suffix of object files... o 2023-06-27T16:35:32,200 checking whether we are using the GNU C compiler... yes 2023-06-27T16:35:32,277 checking whether gcc accepts -g... yes 2023-06-27T16:35:32,435 checking for gcc option to accept ISO C89... none needed 2023-06-27T16:35:32,437 checking for ranlib... ranlib 2023-06-27T16:35:32,444 checking for grep that handles long lines and -e... /usr/bin/grep 2023-06-27T16:35:32,524 checking for C compiler warning flags... -Wall 2023-06-27T16:35:32,583 checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no 2023-06-27T16:35:32,632 checking whether C compiler accepts -mavx2... no 2023-06-27T16:35:32,684 checking whether C compiler accepts -mavx512f... no 2023-06-27T16:35:33,029 checking whether C compiler supports ARM Neon... no 2023-06-27T16:35:33,031 checking for pkg-config... /usr/bin/pkg-config 2023-06-27T16:35:33,037 checking pkg-config is at least version 0.9.0... yes 2023-06-27T16:35:33,039 checking for special C compiler options needed for large files... no 2023-06-27T16:35:33,219 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-06-27T16:35:33,235 checking shared library type for unknown-Linux... plain .so 2023-06-27T16:35:33,406 checking whether the linker supports versioned symbols... yes 2023-06-27T16:35:33,572 checking whether the compiler accepts -fvisibility=hidden... yes 2023-06-27T16:35:33,677 checking how to run the C preprocessor... gcc -E 2023-06-27T16:35:33,790 checking for egrep... /usr/bin/grep -E 2023-06-27T16:35:34,283 checking for ANSI C header files... yes 2023-06-27T16:35:34,407 checking for sys/types.h... yes 2023-06-27T16:35:34,545 checking for sys/stat.h... yes 2023-06-27T16:35:34,710 checking for stdlib.h... yes 2023-06-27T16:35:34,859 checking for string.h... yes 2023-06-27T16:35:35,006 checking for memory.h... yes 2023-06-27T16:35:35,153 checking for strings.h... yes 2023-06-27T16:35:35,297 checking for inttypes.h... yes 2023-06-27T16:35:35,443 checking for stdint.h... yes 2023-06-27T16:35:35,628 checking for unistd.h... yes 2023-06-27T16:35:35,655 checking for stdlib.h... (cached) yes 2023-06-27T16:35:35,680 checking for unistd.h... (cached) yes 2023-06-27T16:35:35,856 checking for sys/param.h... yes 2023-06-27T16:35:36,054 checking for getpagesize... yes 2023-06-27T16:35:36,404 checking for working mmap... yes 2023-06-27T16:35:36,598 checking for gmtime_r... yes 2023-06-27T16:35:36,801 checking for fsync... yes 2023-06-27T16:35:37,006 checking for drand48... yes 2023-06-27T16:35:37,270 checking for srand48_deterministic... no 2023-06-27T16:35:37,440 checking whether fdatasync is declared... yes 2023-06-27T16:35:37,616 checking for fdatasync... yes 2023-06-27T16:35:38,009 checking for library containing log... -lm 2023-06-27T16:35:38,112 checking for zlib.h... yes 2023-06-27T16:35:38,289 checking for inflate in -lz... yes 2023-06-27T16:35:38,475 checking for library containing recv... none required 2023-06-27T16:35:38,563 checking for bzlib.h... yes 2023-06-27T16:35:38,770 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-06-27T16:35:38,782 checking whether htscodecs files are present... yes 2023-06-27T16:35:38,783 configure: WARNING: GCS support not enabled: requires libcurl support 2023-06-27T16:35:38,784 configure: WARNING: S3 support not enabled: requires libcurl support 2023-06-27T16:35:38,965 checking for library containing regcomp... none required 2023-06-27T16:35:39,087 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2023-06-27T16:35:39,152 configure: creating ./config.status 2023-06-27T16:35:39,515 config.status: creating config.mk 2023-06-27T16:35:39,581 config.status: creating htslib.pc.tmp 2023-06-27T16:35:39,656 config.status: creating config.h 2023-06-27T16:35:39,685 config.status: config.h is unchanged 2023-06-27T16:35:39,695 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-06-27T16:35:39,928 [ 16%] Performing build step for 'htslib' 2023-06-27T16:35:39,952 fatal: not a git repository: /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/htslib/../../../.git/modules/SPLAM_C++/include/htslib 2023-06-27T16:35:39,961 fatal: not a git repository: /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/htslib/../../../.git/modules/SPLAM_C++/include/htslib 2023-06-27T16:35:40,003 make[3]: Warning: File 'config.mk' has modification time 1.1 s in the future 2023-06-27T16:35:40,020 fatal: not a git repository: /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/htslib/htscodecs/../../../../.git/modules/SPLAM_C++/include/htslib/modules/htscodecs 2023-06-27T16:35:40,075 make[3]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:35:40,156 [ 19%] No install step for 'htslib' 2023-06-27T16:35:40,280 [ 22%] Completed 'htslib' 2023-06-27T16:35:40,395 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:35:40,441 [ 22%] Built target htslib 2023-06-27T16:35:40,648 Scanning dependencies of target splam_clean 2023-06-27T16:35:40,672 gmake[2]: Warning: File 'CMakeFiles/splam_clean.dir/depend.make' has modification time 1.5 s in the future 2023-06-27T16:35:40,718 [ 25%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/splam_clean.cpp.o 2023-06-27T16:35:45,934 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp: In function ‘int splam_clean(pybind11::list)’: 2023-06-27T16:35:45,934 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:319:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,934 319 | 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()}; 2023-06-27T16:35:45,934 | ^~~~~~~~~~ 2023-06-27T16:35:45,935 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:319:44: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,935 319 | 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()}; 2023-06-27T16:35:45,935 | ^~~~~~ 2023-06-27T16:35:45,935 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:319:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,936 319 | 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()}; 2023-06-27T16:35:45,936 | ^~~~ 2023-06-27T16:35:45,936 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:319:129: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,936 319 | 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()}; 2023-06-27T16:35:45,936 | ^~~~ 2023-06-27T16:35:45,937 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:329:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,937 329 | 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()}; 2023-06-27T16:35:45,938 | ^~~~~~~~~~ 2023-06-27T16:35:45,938 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:329:45: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,938 329 | 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()}; 2023-06-27T16:35:45,938 | ^~~~~~ 2023-06-27T16:35:45,938 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:329:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,939 329 | 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()}; 2023-06-27T16:35:45,939 | ^~~~ 2023-06-27T16:35:45,939 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:329:142: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,939 329 | 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()}; 2023-06-27T16:35:45,939 | ^~~~ 2023-06-27T16:35:45,940 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,940 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:35:45,941 | ^~~~~~~~~~ 2023-06-27T16:35:45,941 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:43: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,941 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:35:45,941 | ^~~~~~~ 2023-06-27T16:35:45,941 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,942 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:35:45,942 | ^~~~ 2023-06-27T16:35:45,942 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:58: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,942 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:35:45,942 | ^~~~ 2023-06-27T16:35:45,942 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:336:91: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,943 336 | char *merge_argv[] = {"samtools", "merge", "-f", "-@", (char*)thread_num.chars(), "-o", (char*)outfname_cleaned.chars(), 2023-06-27T16:35:45,943 | ^~~~ 2023-06-27T16:35:45,944 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,944 354 | 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()}; 2023-06-27T16:35:45,944 | ^~~~~~~~~~ 2023-06-27T16:35:45,944 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:37: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,945 354 | 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()}; 2023-06-27T16:35:45,945 | ^~~~~~~ 2023-06-27T16:35:45,945 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:46: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,945 354 | 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()}; 2023-06-27T16:35:45,945 | ^~~~ 2023-06-27T16:35:45,945 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,945 354 | 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()}; 2023-06-27T16:35:45,946 | ^~~~ 2023-06-27T16:35:45,946 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/splam/module/splam_clean.cpp:354:85: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 2023-06-27T16:35:45,946 354 | 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()}; 2023-06-27T16:35:45,946 | ^~~~ 2023-06-27T16:35:50,899 [ 27%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam_sort.c.o 2023-06-27T16:35:58,936 [ 30%] Building C object CMakeFiles/splam_clean.dir/splam/module/bam.c.o 2023-06-27T16:35:59,416 [ 33%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_utils.c.o 2023-06-27T16:35:59,919 [ 36%] Building C object CMakeFiles/splam_clean.dir/splam/module/sam_opts.c.o 2023-06-27T16:36:00,229 [ 38%] Building C object CMakeFiles/splam_clean.dir/splam/module/bedidx.c.o 2023-06-27T16:36:02,003 [ 41%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/junc_func.cpp.o 2023-06-27T16:36:04,678 [ 44%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/extract.cpp.o 2023-06-27T16:36:08,625 [ 47%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/predict.cpp.o 2023-06-27T16:36:12,675 [ 50%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/clean.cpp.o 2023-06-27T16:36:17,212 [ 52%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/update.cpp.o 2023-06-27T16:36:21,346 [ 55%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/util.cpp.o 2023-06-27T16:36:25,364 [ 58%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/tmerge.cpp.o 2023-06-27T16:36:28,847 [ 61%] Building CXX object CMakeFiles/splam_clean.dir/splam/module/GSam.cpp.o 2023-06-27T16:36:31,041 [ 63%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GStr.cpp.o 2023-06-27T16:36:32,134 [ 66%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GArgs.cpp.o 2023-06-27T16:36:32,946 [ 69%] Building CXX object CMakeFiles/splam_clean.dir/include/gclib/GBase.cpp.o 2023-06-27T16:36:33,892 [ 72%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so 2023-06-27T16:36:54,756 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:36:54,812 [ 72%] Built target splam_clean 2023-06-27T16:36:54,966 Scanning dependencies of target splam_extract 2023-06-27T16:36:54,980 gmake[2]: Warning: File 'CMakeFiles/splam_extract.dir/depend.make' has modification time 1.5 s in the future 2023-06-27T16:36:55,022 [ 75%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/splam_extract.cpp.o 2023-06-27T16:37:05,148 [ 77%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/extract.cpp.o 2023-06-27T16:37:09,122 [ 80%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/junc_func.cpp.o 2023-06-27T16:37:11,841 [ 83%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/util.cpp.o 2023-06-27T16:37:15,870 [ 86%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/tmerge.cpp.o 2023-06-27T16:37:19,360 [ 88%] Building CXX object CMakeFiles/splam_extract.dir/splam/module/GSam.cpp.o 2023-06-27T16:37:21,530 [ 91%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GStr.cpp.o 2023-06-27T16:37:22,620 [ 94%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GArgs.cpp.o 2023-06-27T16:37:23,423 [ 97%] Building CXX object CMakeFiles/splam_extract.dir/include/gclib/GBase.cpp.o 2023-06-27T16:37:24,380 [100%] Linking CXX shared module ../../lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so 2023-06-27T16:37:38,625 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/gclib/GVec.hh: In member function ‘setCapacity’: 2023-06-27T16:37:38,626 /tmp/pip-wheel-4uwh6b7w/splam_3318731d72ce4affa78eac042ebf7409/include/gclib/GVec.hh:107:14: warning: argument 1 value ‘4294967295’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-06-27T16:37:38,626 107 | fArray=new OBJ[NewCapacity]; 2023-06-27T16:37:38,626 | ^ 2023-06-27T16:37:38,626 /usr/include/c++/10/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 2023-06-27T16:37:38,626 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) 2023-06-27T16:37:38,627 | ^ 2023-06-27T16:37:46,817 gmake[2]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:37:46,862 [100%] Built target splam_extract 2023-06-27T16:37:46,865 gmake[1]: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:37:46,911 gmake: warning: Clock skew detected. Your build may be incomplete. 2023-06-27T16:37:46,965 /home/piwheels/.local/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-06-27T16:37:46,965 !! 2023-06-27T16:37:46,966 ******************************************************************************** 2023-06-27T16:37:46,966 Please avoid running ``setup.py`` directly. 2023-06-27T16:37:46,966 Instead, use pypa/build, pypa/installer, pypa/build or 2023-06-27T16:37:46,966 other standards-based tools. 2023-06-27T16:37:46,966 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-06-27T16:37:46,967 ******************************************************************************** 2023-06-27T16:37:46,967 !! 2023-06-27T16:37:46,967 self.initialize_options() 2023-06-27T16:37:46,993 installing to build/bdist.linux-armv7l/wheel 2023-06-27T16:37:46,994 running install 2023-06-27T16:37:47,019 running install_lib 2023-06-27T16:37:47,048 creating build/bdist.linux-armv7l 2023-06-27T16:37:47,049 creating build/bdist.linux-armv7l/wheel 2023-06-27T16:37:47,050 copying build/lib.linux-armv7l-cpython-39/splam_clean.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-06-27T16:37:47,057 copying build/lib.linux-armv7l-cpython-39/splam_extract.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-06-27T16:37:47,064 creating build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,065 copying build/lib.linux-armv7l-cpython-39/splam/prediction.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,068 copying build/lib.linux-armv7l-cpython-39/splam/extract_gff.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,070 copying build/lib.linux-armv7l-cpython-39/splam/config.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,072 copying build/lib.linux-armv7l-cpython-39/splam/helper.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,074 copying build/lib.linux-armv7l-cpython-39/splam/chr_size.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,077 copying build/lib.linux-armv7l-cpython-39/splam/__init__.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,080 copying build/lib.linux-armv7l-cpython-39/splam/parse.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,082 copying build/lib.linux-armv7l-cpython-39/splam/splam.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,085 copying build/lib.linux-armv7l-cpython-39/splam/test.py -> build/bdist.linux-armv7l/wheel/splam 2023-06-27T16:37:47,087 running install_egg_info 2023-06-27T16:37:47,158 running egg_info 2023-06-27T16:37:47,193 writing splam.egg-info/PKG-INFO 2023-06-27T16:37:47,196 writing dependency_links to splam.egg-info/dependency_links.txt 2023-06-27T16:37:47,199 writing entry points to splam.egg-info/entry_points.txt 2023-06-27T16:37:47,202 writing requirements to splam.egg-info/requires.txt 2023-06-27T16:37:47,204 writing top-level names to splam.egg-info/top_level.txt 2023-06-27T16:37:47,246 reading manifest file 'splam.egg-info/SOURCES.txt' 2023-06-27T16:37:47,441 reading manifest template 'MANIFEST.in' 2023-06-27T16:37:47,696 adding license file 'LICENSE' 2023-06-27T16:37:47,761 writing manifest file 'splam.egg-info/SOURCES.txt' 2023-06-27T16:37:47,765 Copying splam.egg-info to build/bdist.linux-armv7l/wheel/splam-0.2.9-py3.9.egg-info 2023-06-27T16:37:47,778 running install_scripts 2023-06-27T16:37:47,829 creating build/bdist.linux-armv7l/wheel/splam-0.2.9.dist-info/WHEEL 2023-06-27T16:37:47,832 creating '/tmp/pip-wheel-fxe1x5yv/splam-0.2.9-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-06-27T16:37:47,913 adding 'splam_clean.cpython-39-arm-linux-gnueabihf.so' 2023-06-27T16:37:47,968 adding 'splam_extract.cpython-39-arm-linux-gnueabihf.so' 2023-06-27T16:37:47,972 adding 'splam/__init__.py' 2023-06-27T16:37:47,976 adding 'splam/chr_size.py' 2023-06-27T16:37:47,978 adding 'splam/config.py' 2023-06-27T16:37:47,980 adding 'splam/extract_gff.py' 2023-06-27T16:37:47,981 adding 'splam/helper.py' 2023-06-27T16:37:47,983 adding 'splam/parse.py' 2023-06-27T16:37:47,985 adding 'splam/prediction.py' 2023-06-27T16:37:47,988 adding 'splam/splam.py' 2023-06-27T16:37:47,989 adding 'splam/test.py' 2023-06-27T16:37:47,992 adding 'splam-0.2.9.dist-info/LICENSE' 2023-06-27T16:37:47,993 adding 'splam-0.2.9.dist-info/METADATA' 2023-06-27T16:37:47,994 adding 'splam-0.2.9.dist-info/WHEEL' 2023-06-27T16:37:47,996 adding 'splam-0.2.9.dist-info/entry_points.txt' 2023-06-27T16:37:47,997 adding 'splam-0.2.9.dist-info/top_level.txt' 2023-06-27T16:37:47,998 adding 'splam-0.2.9.dist-info/RECORD' 2023-06-27T16:37:48,003 removing build/bdist.linux-armv7l/wheel 2023-06-27T16:37:48,094 Building wheel for splam (setup.py): finished with status 'done' 2023-06-27T16:37:48,101 Created wheel for splam: filename=splam-0.2.9-cp39-cp39-linux_armv7l.whl size=294160 sha256=434410fd7dfc947ef68b0c85650d0b6930abcf1fc52e3a4db0fde3c579d0530c 2023-06-27T16:37:48,102 Stored in directory: /tmp/pip-ephem-wheel-cache-3wjga3nk/wheels/92/e5/bc/fed16dc0e4bdc89c64bb5554ea9a3e40815378bc51599099d7 2023-06-27T16:37:48,113 Successfully built splam 2023-06-27T16:37:48,128 Removed build tracker: '/tmp/pip-build-tracker-llb0vzf9'