Issue with make & install

[SihuiZhu0927]

command in Ubuntu: make -j 4 && make install

[ 3%] Built target generated
[ 6%] Built target ffindex
[ 8%] Built target hhviterbialgorithm_with_celloff_and_ss
[ 10%] Built target hhviterbialgorithm_with_celloff
[ 12%] Built target hhviterbialgorithm_and_ss
[ 12%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o
[ 14%] Built target ffindex_apply
[ 22%] Built target CS_OBJECTS
[ 24%] Built target ffindex_reduce
[ 26%] Built target ffindex_build
[ 28%] Built target ffindex_from_fasta
[ 30%] Built target ffindex_get
[ 32%] Built target ffindex_modify
[ 34%] Built target ffindex_unpack
[ 36%] Built target ffindex_order
[ 38%] Built target ffindex_from_fasta_with_split
[ 68%] Built target HH_OBJECTS
[ 70%] Built target hhfilter
[ 72%] Built target hhmake
[ 74%] Built target hhblits
[ 76%] Built target hhsearch
[ 78%] Built target hhalign
[ 80%] Built target hhconsensus
[ 82%] Built target hhblits_omp
[ 84%] Built target hhsearch_omp
[ 86%] Built target hhalign_omp
In file included from /mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp:8:
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.h:37:37: error: ‘uint16_t’ has not been declared
37 | void writeU16(std::ostream& file, uint16_t);
| ^~~~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.h:38:28: error: ‘uint16_t’ has not been declared
38 | void readU16(char** ptr, uint16_t &result);
| ^~~~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.h:40:37: error: ‘uint32_t’ has not been declared
40 | void writeU32(std::ostream& file, uint32_t);
| ^~~~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.h:41:27: error: ‘uint32_t’ has not been declared
41 | void readU32(charptr, uint32_t &result);
| ^~~~~~~~
[ 88%] Built target hhblits_ca3m
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp: In function ‘void compressed_a3m::extract_a3m(char*, size_t, ffindex_index_t*, char*, ffindex_index_t*, char*, std::ostream*)’:
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp:293:20: error: cannot bind non-const lvalue reference of type ‘int&’ to a value of type ‘unsigned int’
293 | readU32(&data, entry_index);
| ^~~~~~~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.h:41:37: note: initializing argument 2 of ‘void compressed_a3m::readU32(char, int&)’
41 | void readU32(charptr, uint32_t &result);
| ~~~~~~~~~~^~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp:310:20: error: cannot bind non-const lvalue reference of type ‘int&’ to a value of type ‘short unsigned int’
310 | readU16(&data, start_pos);
| ^~~~~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.h:38:38: note: initializing argument 2 of ‘void compressed_a3m::readU16(char, int&)’
38 | void readU16(char** ptr, uint16_t &result);
| ~~~~~~~~~~^~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp:313:20: error: cannot bind non-const lvalue reference of type ‘int&’ to a value of type ‘short unsigned int’
313 | readU16(&data, nr_blocks);
| ^~~~~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.h:38:38: note: initializing argument 2 of ‘void compressed_a3m::readU16(char**, int&)’
38 | void readU16(char** ptr, uint16_t &result);
| ~~~~~~~~~~^~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’:
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp:504:43: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result ()(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
504 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from /mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.h:11:
/usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (__x)(_Arg))
| ^~~~~~~
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp: At global scope:
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp:548:63: error: ‘void compressed_a3m::writeU16(std::ostream&, uint16_t)’ should have been declared inside ‘compressed_a3m’
548 | void compressed_a3m::writeU16(std::ostream& file, uint16_t val) {
| ^
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp:559:58: error: ‘void compressed_a3m::readU16(char**, uint16_t&)’ should have been declared inside ‘compressed_a3m’
559 | void compressed_a3m::readU16(char** ptr, uint16_t &result) {
| ^
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp:570:63: error: ‘void compressed_a3m::writeU32(std::ostream&, uint32_t)’ should have been declared inside ‘compressed_a3m’
570 | void compressed_a3m::writeU32(std::ostream& file, uint32_t val) {
| ^
/mnt/T38/bioinf/zsh/hh-suite/src/a3m_compress.cpp:583:58: error: ‘void compressed_a3m::readU32(char**, uint32_t&)’ should have been declared inside ‘compressed_a3m’
583 | void compressed_a3m::readU32(char** ptr, uint32_t &result) {
| ^
make[2]: *** [src/CMakeFiles/A3M_COMPRESS.dir/build.make:76: src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:840: src/CMakeFiles/A3M_COMPRESS.dir/all] Error 2
make: *** [Makefile:156: all] Error 2

How should I do to solve the Error?

Thank you for your help.

[streptomyces]

For me it got resolved by adding

#include <cstdint>

to the includes in src/a3m_compress.h.