[Debian-med-packaging] Bug#966876: trinityrnaseq: FTBFS: sift_bam_max_cov.cpp:99:10: error: ‘string’ is not a member of ‘std’

[Lucas Nussbaum]

Source: trinityrnaseq
Version: 2.10.0+dfsg-1
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200802 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now sift_bam_max_cov.cpp -Wall -lhts -O2 -o bamsifter
> sift_bam_max_cov.cpp: In function ‘int main(int, char**)’:
> sift_bam_max_cov.cpp:99:10: error: ‘string’ is not a member of ‘std’
>    99 |     std::string tmp_text(input_header->text, input_header->l_text);
>       |          ^~~~~~
> sift_bam_max_cov.cpp:16:1: note: ‘std::string’ is defined in header ‘<string>’; did you forget to ‘#include <string>’?
>    15 | #include "htslib/bgzf.h"
>   +++ |+#include <string>
>    16 | 
> sift_bam_max_cov.cpp:100:24: error: ‘tmp_text’ was not declared in this scope
>   100 |     size_t start_pos = tmp_text.find("@HD");
>       |                        ^~~~~~~~
> sift_bam_max_cov.cpp:101:27: error: ‘std::string’ has not been declared
>   101 |     if (start_pos == std::string::npos) {
>       |                           ^~~~~~
> sift_bam_max_cov.cpp:106:25: error: ‘std::string’ has not been declared
>   106 |     if (end_pos == std::string::npos) {
>       |                         ^~~~~~
> sift_bam_max_cov.cpp:111:27: error: ‘std::string’ has not been declared
>   111 |     if (start_pos == std::string::npos) {
>       |                           ^~~~~~
> sift_bam_max_cov.cpp:116:27: error: ‘std::string’ has not been declared
>   116 |     if (start_pos == std::string::npos) {
>       |                           ^~~~~~
> sift_bam_max_cov.cpp:144:19: error: ‘string’ is not a member of ‘std’
>   144 |     std::set<std::string> mates_to_keep[input_header->n_targets];
>       |                   ^~~~~~
> sift_bam_max_cov.cpp:144:19: note: ‘std::string’ is defined in header ‘<string>’; did you forget to ‘#include <string>’?
> sift_bam_max_cov.cpp:144:19: error: ‘string’ is not a member of ‘std’
> sift_bam_max_cov.cpp:144:19: note: ‘std::string’ is defined in header ‘<string>’; did you forget to ‘#include <string>’?
> sift_bam_max_cov.cpp:144:25: error: template argument 1 is invalid
>   144 |     std::set<std::string> mates_to_keep[input_header->n_targets];
>       |                         ^
> sift_bam_max_cov.cpp:144:25: error: template argument 2 is invalid
> sift_bam_max_cov.cpp:144:25: error: template argument 3 is invalid
> sift_bam_max_cov.cpp:160:48: error: request for member ‘clear’ in ‘mates_to_keep[current_rname_index]’, which is of non-class type ‘int’
>   160 |             mates_to_keep[current_rname_index].clear();
>       |                                                ^~~~~
> sift_bam_max_cov.cpp:205:43: error: request for member ‘find’ in ‘mates_to_keep[aln->bam1_t::core.bam1_core_t::tid]’, which is of non-class type ‘int’
>   205 |             (mates_to_keep[aln->core.tid].find(bam_get_qname(aln)) != mates_to_keep[aln->core.tid].end())) {
>       |                                           ^~~~
> sift_bam_max_cov.cpp:205:100: error: request for member ‘end’ in ‘mates_to_keep[aln->bam1_t::core.bam1_core_t::tid]’, which is of non-class type ‘int’
>   205 |             (mates_to_keep[aln->core.tid].find(bam_get_qname(aln)) != mates_to_keep[aln->core.tid].end())) {
>       |                                                                                                    ^~~
> sift_bam_max_cov.cpp:249:47: error: request for member ‘insert’ in ‘mates_to_keep[aln->bam1_t::core.bam1_core_t::mtid]’, which is of non-class type ‘int’
>   249 |                 mates_to_keep[aln->core.mtid].insert(bam_get_qname(aln));
>       |                                               ^~~~~~
> make[2]: *** [Makefile:3: sift_bam_max_cov] Error 1

The full build log is available from:
   http://qa-logs.debian.net/2020/08/02/trinityrnaseq_2.10.0+dfsg-1_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.