Install Error

[BrendaLee1]

Hi!
When I tried to install vamos on linux platform, the following error occurred after I excute make:
In file included from vntr.h:12,
from main.cpp:6:
read.h:26:9: error: ‘uint16_t’ does not name a type
26 | uint16_t l_qname;
| ^~~~~~~~
read.h:1:1: note: ‘uint16_t’ is defined in header ‘’; did you forget to ‘#include ’?
+++ |+#include
1 | #ifndef READ_H_
read.h:28:9: error: ‘uint32_t’ does not name a type
28 | uint32_t len;
| ^~~~~~~~
read.h:28:9: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’?
read.h:34:9: error: ‘uint16_t’ does not name a type
34 | uint16_t flag=0;
| ^~~~~~~~
read.h:34:9: note: ‘uint16_t’ is defined in header ‘’; did you forget to ‘#include ’?
read.h:44:41: error: ‘uint32_t’ has not been declared
44 | READ (char * Qname, char * Chr, uint32_t Len) : qname(Qname), chr(Chr), len(Len) { seq = NULL;};
| ^~~~~~~~
read.h: In constructor ‘READ::READ()’:
read.h:38:17: error: ‘l_qname’ was not declared in this scope; did you mean ‘qname’?
38 | l_qname = 0;
| ^~~~~~~
| qname
read.h: In constructor ‘READ::READ(char*, char*, int)’:
read.h:44:81: error: class ‘READ’ does not have any field named ‘len’
44 | READ (char * Qname, char * Chr, uint32_t Len) : qname(Qname), chr(Chr), len(Len) { seq = NULL;};
| ^~~
read.h: In member function ‘bool less_than_key::operator()(READ*, READ*)’:
read.h:57:24: error: ‘class READ’ has no member named ‘len’
57 | return (read1->len < read2->len);
| ^~~
read.h:57:37: error: ‘class READ’ has no member named ‘len’
57 | return (read1->len < read2->len);
| ^~~
vntr.h: At global scope:
vntr.h:95:9: error: ‘uint32_t’ does not name a type
95 | uint32_t ref_start;
| ^~~~~~~~
vntr.h:14:1: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’?
13 | #include "option.h"
+++ |+#include
14 |
vntr.h:96:9: error: ‘uint32_t’ does not name a type
96 | uint32_t ref_end;
| ^~~~~~~~
vntr.h:96:9: note: ‘uint32_t’ is defined in header ‘’; did you forget to ‘#include ’?
vntr.h:103:23: error: ‘uint8_t’ was not declared in this scope
103 | vector<vector<uint8_t>> annos; // the motif annotation for each read sequence
| ^~~~~~~
vntr.h:103:23: note: ‘uint8_t’ is defined in header ‘’; did you forget to ‘#include ’?
vntr.h:103:23: error: template argument 1 is invalid
vntr.h:103:23: error: template argument 2 is invalid
vntr.h:103:30: error: template argument 1 is invalid
103 | vector<vector<uint8_t>> annos; // the motif annotation for each read sequence
| ^~
vntr.h:103:30: error: template argument 2 is invalid
vntr.h:118:23: error: ‘uint8_t’ was not declared in this scope
118 | vector<vector<uint8_t>> consensus;
| ^~~~~~~
vntr.h:118:23: note: ‘uint8_t’ is defined in header ‘’; did you forget to ‘#include ’?
vntr.h:118:23: error: template argument 1 is invalid
vntr.h:118:23: error: template argument 2 is invalid
vntr.h:118:30: error: template argument 1 is invalid
118 | vector<vector<uint8_t>> consensus;
| ^~
vntr.h:118:30: error: template argument 2 is invalid
vntr.h:129:27: error: ‘uint32_t’ has not been declared
129 | VNTR (string Chr, uint32_t Start, uint32_t End, uint32_t Len) : chr(Chr), ref_start(Start), ref_end(End), len(Len)
| ^~~~~~~~
vntr.h:129:43: error: ‘uint32_t’ has not been declared
129 | VNTR (string Chr, uint32_t Start, uint32_t End, uint32_t Len) : chr(Chr), ref_start(Start), ref_end(End), len(Len)
| ^~~~~~~~
vntr.h:129:57: error: ‘uint32_t’ has not been declared
129 | VNTR (string Chr, uint32_t Start, uint32_t End, uint32_t Len) : chr(Chr), ref_start(Start), ref_end(End), len(Len)
| ^~~~~~~~
vntr.h: In constructor ‘VNTR::VNTR(std::string, int, int, int)’:
vntr.h:129:83: error: class ‘VNTR’ does not have any field named ‘ref_start’
129 | VNTR (string Chr, uint32_t Start, uint32_t End, uint32_t Len) : chr(Chr), ref_start(Start), ref_end(End), len(Len)
| ^~~~~~~~~
vntr.h:129:101: error: class ‘VNTR’ does not have any field named ‘ref_end’
129 | VNTR (string Chr, uint32_t Start, uint32_t End, uint32_t Len) : chr(Chr), ref_start(Start), ref_end(End), len(Len)
| ^~~~~~~
vntr.h:131:44: error: ‘ref_start’ was not declared in this scope; did you mean ‘va_start’?
131 | string s = ":" + to_string(ref_start);
| ^~~~~~~~~
| va_start
vntr.h:132:44: error: ‘ref_end’ was not declared in this scope
132 | string e = "-" + to_string(ref_end);
| ^~~~~~~
vntr.h: At global scope:
vntr.h:189:30: error: ‘uint8_t’ was not declared in this scope
189 | void outputConsensus (vector<uint8_t> &consensus);
| ^~~~~~~
vntr.h:189:30: note: ‘uint8_t’ is defined in header ‘’; did you forget to ‘#include ’?
vntr.h:189:37: error: template argument 1 is invalid
189 | void outputConsensus (vector<uint8_t> &consensus);
| ^
vntr.h:189:37: error: template argument 2 is invalid
main.cpp: In function ‘int main(int, char**)’:
main.cpp:538:51: error: ‘class READ’ has no member named ‘l_qname’; did you mean ‘qname’?
538 | cout.write(read->qname, read->l_qname);
| ^~~~~~~
| qname
main.cpp:540:49: error: ‘class READ’ has no member named ‘len’
540 | cout.write(read->seq, read->len);
| ^~~
make: *** [Makefile:37: main.o] Error 1
Do you have any idea?

I changed to version 1.3.8, and installed libdeflate but new error occured:
anaconda2/envs/vamos/lib/libhts.so: undefined reference to `libdeflate_gzip_compress'

[mchaisso]

what version of gcc are you using?

[mchaisso]

I tried adding inttypes.h to define uint16_t, but these should have been available through your stdint.h include. You can pull a new version and try building again.

[BrendaLee1]

Hi mchaisso,
Thank you for your quick replay, I tried the new version, still can't install successfully. gcc version is 13.2.0. The error information below:
make[1]: Leaving directory 'soft/vamos/abPOA-1.4.1'
g++ -O3 -DNDEBUG -o vamos main.o io.o vcf.o vntr.o acc_lookup_table.o phase.o msa.o -L soft/anaconda2/envs/vamos/lib -lhts -lz -lpthread -L ../abPOA-1.4.1/lib -labpoa
/usr/bin/ld: warning: libdeflate.so.0, needed by soft/anaconda2/envs/vamos/lib/libhts.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libbz2.so.1.0, needed by soft/anaconda2/envs/vamos/lib/libhts.so, not found (try using -rpath or -rpath-link)
soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to libdeflate_free_compressor' soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to libdeflate_deflate_decompress'
soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to libdeflate_alloc_compressor' soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to BZ2_bzBuffToBuffCompress'
soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to libdeflate_gzip_decompress' soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to libdeflate_free_decompressor'
soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to BZ2_bzBuffToBuffDecompress' soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to libdeflate_crc32'
soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to libdeflate_deflate_compress' soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to libdeflate_gzip_compress'
soft/anaconda2/envs/vamos/lib/libhts.so: undefined reference to `libdeflate_alloc_decompressor'
collect2: error: ld returned 1 exit status
make: *** [Makefile:61: vamos] Error 1

[BrendaLee1]

Hi,

I installed vamos successfully use conda.