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.