[Debian-med-packaging] Bug#966868: igor: FTBFS: CDR3SeqData.h:20:10: error: ‘string’ in namespace ‘std’ does not name a type

[Lucas Nussbaum]

Source: igor
Version: 1.4.0+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++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.cpp
> In file included from ExtractFeatures.h:30,
>                  from ExtractFeatures.cpp:26:
> CDR3SeqData.h:20:10: error: ‘string’ in namespace ‘std’ does not name a type
>    20 |     std::string CDR3nt;
>       |          ^~~~~~
> CDR3SeqData.h:1:1: note: ‘std::string’ is defined in header ‘<string>’; did you forget to ‘#include <string>’?
>   +++ |+#include <string>
>     1 | 
> CDR3SeqData.h:21:10: error: ‘string’ in namespace ‘std’ does not name a type
>    21 |     std::string CDR3aa;
>       |          ^~~~~~
> CDR3SeqData.h:21:5: note: ‘std::string’ is defined in header ‘<string>’; did you forget to ‘#include <string>’?
>    21 |     std::string CDR3aa;
>       |     ^~~
> CDR3SeqData.h:22:10: error: ‘string’ in namespace ‘std’ does not name a type
>    22 |     std::string strData();
>       |          ^~~~~~
> CDR3SeqData.h:22:5: note: ‘std::string’ is defined in header ‘<string>’; did you forget to ‘#include <string>’?
>    22 |     std::string strData();
>       |     ^~~
> g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp
> g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp
> make[3]: *** [Makefile:635: igor-ExtractFeatures.o] Error 1

The full build log is available from:
   http://qa-logs.debian.net/2020/08/02/igor_1.4.0+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.