I ran into an issue when running "make" for demuxlet, I'm trying to install demuxlet locally, since I don't have "sudo" privilege on our cluster. I have htslib 1.11 installed in the same folder with demuxlet folder. The error is below:
make all-am make[1]: Entering directory/home/lbui/Softwares/demuxlet'
g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT filter.o -MD -MP -MF .deps/filter.Tpo -c -o filter.o filter.cpp
filter.cpp: In function ‘void filters_set_info(filter_t, bcf1_t, token_t)’:
filter.cpp:408:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
408 | if ( n >= tok->str_value.m )
| ^~~~~
filter.cpp: In function ‘void filters_set_format_int(filter_t, bcf1_t, token_t)’:
filter.cpp:705:58: error: expected ‘)’ before ‘PRId64’
705 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
| ~ ^~~
| )
filter.cpp:705:56: warning: spurious trailing ‘%’ in format [-Wformat=]
705 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
| ^
filter.cpp:705:15: warning: too many arguments for format [-Wformat-extra-args]
705 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
| ^~~~~~~~~~~
filter.cpp: In function ‘void filters_set_format_float(filter_t, bcf1_t, token_t)’:
filter.cpp:768:58: error: expected ‘)’ before ‘PRId64’
768 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
| ~ ^~~
| )
filter.cpp:768:56: warning: spurious trailing ‘%’ in format [-Wformat=]
768 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
| ^
filter.cpp:768:15: warning: too many arguments for format [-Wformat-extra-args]
768 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
| ^~~~~~~~~~~
filter.cpp: In function ‘void filters_set_format_string(filter_t, bcf1_t, token_t)’:
filter.cpp:831:58: error: expected ‘)’ before ‘PRId64’
831 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
| ~ ^~~
| )
filter.cpp:831:56: warning: spurious trailing ‘%’ in format [-Wformat=]
831 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
| ^
filter.cpp:831:15: warning: too many arguments for format [-Wformat-extra-args]
831 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
| ^~~~~~~~~~~
filter.cpp: In function ‘void _filters_set_genotype(filter_t, bcf1_t, token_t, int)’:
filter.cpp:888:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
888 | if ( tok->str_value.m <= nvals1nsmpl )
| ~~~^~~~~
filter.cpp:951:68: error: expected ‘)’ before ‘PRId64’
951 | default: error("The GT type is not lineognised: %d at %s:%" PRId64 "\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break;
| ~ ^~~
| )
filter.cpp:951:66: warning: spurious trailing ‘%’ in format [-Wformat=]
951 | default: error("The GT type is not lineognised: %d at %s:%" PRId64 "\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break;
| ^
filter.cpp:951:24: warning: too many arguments for format [-Wformat-extra-args]
951 | default: error("The GT type is not lineognised: %d at %s:%" PRId64 "\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break;
| ^~~~~~~~~~~~
filter.cpp: In function ‘void filters_set_genotype_string(filter_t, bcf1_t, token_t)’:
filter.cpp:980:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
980 | if ( tok->str_value.l - plen > blen )
| ~~~~~~^~~~
filter.cpp:989:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
989 | while ( plen < blen )
| ~^~
filter.cpp: In function ‘int func_count(filter_t, bcf1_t, token_t, token_t, int)’:
filter.cpp:1546:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1546 | for (i=0; istr_value.l; i++) if ( tok->str_value.s[i]==',' ) cnt++;
| ~^~~~~
filter.cpp: In function ‘int func_binom(filter_t, bcf1_t, token_t*, token_t*, int)’:
filter.cpp:1671:83: error: expected ‘)’ before ‘PRId64’
1671 | if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
| ~ ^~~
| )
filter.cpp:1671:81: warning: spurious trailing ‘%’ in format [-Wformat=]
1671 | if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
| ^
filter.cpp:1671:51: warning: too many arguments for format [-Wformat-extra-args]
1671 | if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
| ^~~~~~~~
filter.cpp:1672:83: error: expected ‘)’ before ‘PRId64’
1672 | if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
| ~ ^~~
| )
filter.cpp:1672:81: warning: spurious trailing ‘%’ in format [-Wformat=]
1672 | if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
| ^
filter.cpp:1672:51: warning: too many arguments for format [-Wformat-extra-args]
1672 | if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
| ^~~~~~~~
filter.cpp:1692:89: error: expected ‘)’ before ‘PRId64’
1692 | error("Expected one value per binom() argument, found %d and %d at %s:%" PRId64 "\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1);
| ~ ^~~
| )
filter.cpp:1692:87: warning: spurious trailing ‘%’ in format [-Wformat=]
1692 | error("Expected one value per binom() argument, found %d and %d at %s:%" PRId64 "\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1);
| ^
filter.cpp:1692:23: warning: too many arguments for format [-Wformat-extra-args]
1692 | error("Expected one value per binom() argument, found %d and %d at %s:%" PRId64 "\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1);
| ^~~~~~~~~~~~~~
In file included from ../htslib/htslib/vcf.h:45,
from ../htslib/htslib/vcfutils.h:29,
from filter.cpp:45:
filter.cpp: In function ‘void cmp_vector_strings(token_t, token_t, token_t)’:
filter.cpp:2162:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
2162 | assert( atok->nvalues==atok->str_value.l && btok->nvalues==btok->str_value.l );
| ~~~^~~~~
filter.cpp:2162:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
2162 | assert( atok->nvalues==atok->str_value.l && btok->nvalues==btok->str_value.l );
| ~~~^~~~~
filter.cpp: In function ‘int filters_init1(filter_t, char, int, token_t)’:
filter.cpp:2570:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
2570 | for (i=0; i<tmp.l; i++)
| ~^~
filter.cpp:2720:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
2720 | if ( end - tmp.s != strlen(tmp.s) )
| ~~^~~~~~
make[1]: [filter.o] Error 1
make[1]: Leaving directory /home/lbui/Softwares/demuxlet' make: *** [all] Error 2
Hi,
I ran into an issue when running "make" for demuxlet, I'm trying to install demuxlet locally, since I don't have "sudo" privilege on our cluster. I have htslib 1.11 installed in the same folder with demuxlet folder. The error is below:
make all-am make[1]: Entering directory/home/lbui/Softwares/demuxlet' g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT filter.o -MD -MP -MF .deps/filter.Tpo -c -o filter.o filter.cpp filter.cpp: In function ‘void filters_set_info(filter_t, bcf1_t, token_t)’: filter.cpp:408:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 408 | if ( n >= tok->str_value.m ) |^~~~~ filter.cpp: In function ‘void filters_set_format_int(filter_t, bcf1_t, token_t)’: filter.cpp:705:58: error: expected ‘)’ before ‘PRId64’ 705 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); | ~ ^~~ | ) filter.cpp:705:56: warning: spurious trailing ‘%’ in format [-Wformat=] 705 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); | ^ filter.cpp:705:15: warning: too many arguments for format [-Wformat-extra-args] 705 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); | ^~~~~~~~~~~ filter.cpp: In function ‘void filters_set_format_float(filter_t, bcf1_t, token_t)’: filter.cpp:768:58: error: expected ‘)’ before ‘PRId64’ 768 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); | ~ ^~~ | ) filter.cpp:768:56: warning: spurious trailing ‘%’ in format [-Wformat=] 768 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); | ^ filter.cpp:768:15: warning: too many arguments for format [-Wformat-extra-args] 768 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); | ^~~~~~~~~~~ filter.cpp: In function ‘void filters_set_format_string(filter_t, bcf1_t, token_t)’: filter.cpp:831:58: error: expected ‘)’ before ‘PRId64’ 831 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); | ~ ^~~ | ) filter.cpp:831:56: warning: spurious trailing ‘%’ in format [-Wformat=] 831 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); | ^ filter.cpp:831:15: warning: too many arguments for format [-Wformat-extra-args] 831 | error("Incorrect number of FORMAT fields at %s:%" PRId64 " .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples); | ^~~~~~~~~~~ filter.cpp: In function ‘void _filters_set_genotype(filter_t, bcf1_t, token_t, int)’: filter.cpp:888:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 888 | if ( tok->str_value.m <= nvals1nsmpl ) |~~~^~~~~ filter.cpp:951:68: error: expected ‘)’ before ‘PRId64’ 951 | default: error("The GT type is not lineognised: %d at %s:%" PRId64 "\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break; | ~ ^~~ | ) filter.cpp:951:66: warning: spurious trailing ‘%’ in format [-Wformat=] 951 | default: error("The GT type is not lineognised: %d at %s:%" PRId64 "\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break; | ^ filter.cpp:951:24: warning: too many arguments for format [-Wformat-extra-args] 951 | default: error("The GT type is not lineognised: %d at %s:%" PRId64 "\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break; | ^~~~~~~~~~~~ filter.cpp: In function ‘void filters_set_genotype_string(filter_t, bcf1_t, token_t)’: filter.cpp:980:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 980 | if ( tok->str_value.l - plen > blen ) |~~~~~~^~~~ filter.cpp:989:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 989 | while ( plen < blen ) |~^~filter.cpp: In function ‘int func_count(filter_t, bcf1_t, token_t, token_t, int)’: filter.cpp:1546:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1546 | for (i=0; i~~~~ filter.cpp: In function ‘int func_binom(filter_t, bcf1_t, token_t*, token_t*, int)’: filter.cpp:1671:83: error: expected ‘)’ before ‘PRId64’ 1671 | if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); | ~ ^~~ | ) filter.cpp:1671:81: warning: spurious trailing ‘%’ in format [-Wformat=] 1671 | if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); | ^ filter.cpp:1671:51: warning: too many arguments for format [-Wformat-extra-args] 1671 | if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); | ^~~~~~~~ filter.cpp:1672:83: error: expected ‘)’ before ‘PRId64’ 1672 | if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); | ~ ^~~ | ) filter.cpp:1672:81: warning: spurious trailing ‘%’ in format [-Wformat=] 1672 | if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); | ^ filter.cpp:1672:51: warning: too many arguments for format [-Wformat-extra-args] 1672 | if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%" PRId64 ", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]); | ^~~~~~~~ filter.cpp:1692:89: error: expected ‘)’ before ‘PRId64’ 1692 | error("Expected one value per binom() argument, found %d and %d at %s:%" PRId64 "\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); | ~ ^~~ | ) filter.cpp:1692:87: warning: spurious trailing ‘%’ in format [-Wformat=] 1692 | error("Expected one value per binom() argument, found %d and %d at %s:%" PRId64 "\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); | ^ filter.cpp:1692:23: warning: too many arguments for format [-Wformat-extra-args] 1692 | error("Expected one value per binom() argument, found %d and %d at %s:%" PRId64 "\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); | ^~~~~~~~~~~~~~In file included from ../htslib/htslib/vcf.h:45, from ../htslib/htslib/vcfutils.h:29, from filter.cpp:45: filter.cpp: In function ‘void cmp_vector_strings(token_t, token_t, token_t)’: filter.cpp:2162:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2162 | assert( atok->nvalues==atok->str_value.l && btok->nvalues==btok->str_value.l ); |~~~^~~~~ filter.cpp:2162:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2162 | assert( atok->nvalues==atok->str_value.l && btok->nvalues==btok->str_value.l ); |~~~^~~~~ filter.cpp: In function ‘int filters_init1(filter_t, char, int, token_t)’: filter.cpp:2570:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2570 | for (i=0; i<tmp.l; i++) | ~^~filter.cpp:2720:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2720 | if ( end - tmp.s != strlen(tmp.s) ) |~~^~~~~~ make[1]:/home/lbui/Softwares/demuxlet' make: *** [all] Error 2