xlan
commented
3 months ago Hi Shitong,
I appreciate your interest in our study. Keyong will be able to help you with the issue you encountered.
Keyong,
Please see the message below,
Best,
Xun
On Wed, Jul 17, 2024 at 10:22 PM ς (>‿<.) @.***> wrote:
Hi, I downloaded your pipeline to process the data. But I met a problem when downloading the dependency fastx_toolkit. When I downloaded the libgtextutils, a dependency of fastx_toolkit, I had a bad make result. The process before make is normal. Because of the lack of it, I can't download and use the fastx_trimmer properly.
make all-recursive make[1]: Entering directory '/mnt/data/home/d/libgtextutils-0.7' Making all in m4 make[2]: Entering directory '/mnt/data/home/d/libgtextutils-0.7/m4' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/mnt/data/home/d/libgtextutils-0.7/m4' Making all in src make[2]: Entering directory '/mnt/data/home/d/libgtextutils-0.7/src' Making all in gtextutils make[3]: Entering directory '/mnt/data/home/d/libgtextutils-0.7/src/gtextutils' /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -MT stream_wrapper.lo -MD -MP -MF .deps/stream_wrapper.Tpo -c -o stream_wrapper.lo stream_wrapper.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -MT stream_wrapper.lo -MD -MP -MF .deps/stream_wrapper.Tpo -c stream_wrapper.cpp -fPIC -DPIC -o .libs/stream_wrapper.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -MT stream_wrapper.lo -MD -MP -MF .deps/stream_wrapper.Tpo -c stream_wrapper.cpp -o stream_wrapper.o >/dev/null 2>&1 mv -f .deps/stream_wrapper.Tpo .deps/stream_wrapper.Plo /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -MT text_line_reader.lo -MD -MP -MF .deps/text_line_reader.Tpo -c -o text_line_reader.lo text_line_reader.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -MT text_line_reader.lo -MD -MP -MF .deps/text_line_reader.Tpo -c text_line_reader.cpp -fPIC -DPIC -o .libs/text_line_reader.o text_line_reader.cpp: In member function ‘bool TextLineReader::next_line()’: text_line_reader.cpp:47:16: error: cannot convert ‘std::istream’ {aka ‘std::basic_istream ’} to ‘bool’ in return 47 return input_stream ; ^ ~~~std::istream {aka std::basic_istream } make[3]: [Makefile:495: text_line_reader.lo] Error 1 make[3]: Leaving directory '/mnt/data/home/d/libgtextutils-0.7/src/gtextutils' make[2]: [Makefile:352: all-recursive] Error 1 make[2]: Leaving directory '/mnt/data/home/d/libgtextutils-0.7/src' make[1]: [Makefile:466: all-recursive] Error 1 make[1]: Leaving directory '/mnt/data/home/d/libgtextutils-0.7' make: [Makefile:374: all] Error 2
And this is the config outpot below:
checking for a BSD-compatible install... /bin/install -c checking whether build environment is sane... yes /mnt/data/home/tycloud/libgtextutils-0.7/config/missing: Unknown
--is-lightweight' option Try/mnt/data/home/d/libgtextutils-0.7/config/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /bin/ld checking if the linker (/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B checking the name lister (/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /bin/nm -B output from gcc object... ok checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld used by g++... /bin/ld -m elf_x86_64 checking if the linker (/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/gtextutils/Makefile config.status: creating gtextutils.pc config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commandsI think this may caused by software version conflict, but I can't know whether the fastx-toolkit is still upgrading. I wonder whether you met the same problem when you use this tool.
Sincerely, Shitong
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dstyaaaaaa
Hi, I downloaded your pipeline to process the data. But I met a problem when downloading the dependency fastx_toolkit. When I downloaded the libgtextutils, a dependency of fastx_toolkit, I had a bad make result. The process before make is normal. Because of the lack of it, I can't download and use the fastx_trimmer properly.
And this is the config outpot below:
I think this may caused by software version conflict, but I can't know whether the fastx-toolkit is still upgrading. I wonder whether you met the same problem when you use this tool.
Sincerely, Shitong