Hi Filippo,
this is extremely unfortunate. However, I guess the alternative would
have been to keep some RC buggy seqan-dev which would not have helped
openms as well. I tried the same as Peter and replaced the
Build-Depends seqan-dev by libseqan2-dev.
I can confirm the observation from Peter about the missing header file.
I simply tried to comment those missing headers (next one is also
missing):
// #include <seqan/seq_io/guess_stream_format.h>
// #include <seqan/seq_io/read_fasta_fastq.h>
This leaded to:
...
cd /build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openms && /usr/bin/c++
-DBOOST_ALL_NO_LIB -DOpenMS_EXPORTS -DQT_CORE_LIB -DQT_NETWORK_LIB
-DQT_NO_DEBUG -I/build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openms
-I/build/openms-2.6.0+cleaned1/src/openms
-I/build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openms/OpenMS_autogen/include
-I/build/openms-2.6.0+cleaned1/src/openms/include
-I/build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openms/include -isystem
/usr/lib -isystem /usr/lib/x86_64-linux-gnu/include -isystem
/build/openms-2.6.0+cleaned1/src/openms/thirdparty/evergreen/src -isystem
/usr/include/hdf5/serial -isystem /usr/include/libsvm -isystem
/usr/include/eigen3 -isystem /usr/include/libwildmagic -isystem
/build/openms-2.6.0+cleaned1/src/openswathalgo/include -isystem
/build/openms-2.6.0+cleaned1/obj-x86_64-linux-gnu/src/openswathalgo/include
-isystem
/build/openms-2.6.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include
-isystem
/build/openms-2.6.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src
-isystem /usr/include/x86_64-linux-gnu/qt5 -isystem
/usr/include/x86_64-linux-gnu/qt5/QtCore -isystem
/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem
/usr/include/x86_64-linux-gnu/qt5/QtNetwork -isystem
/build/openms-2.6.0+cleaned1/src/openms/thirdparty/eol-bspline -isystem
/build/openms-2.6.0+cleaned1/src/openms/thirdparty/IsoSpec -isystem
/build/openms-2.6.0+cleaned1/src/openms/thirdparty/json -g -O2
-ffile-prefix-map=/build/openms-2.6.0+cleaned1=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3
-DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -Wall -Wextra
-Wno-non-virtual-dtor -Wno-unknown-pragmas -Wno-long-long -Wno-unused-function
-Wno-variadic-macros -fPIC -fopenmp -o
CMakeFiles/OpenMS.dir/source/FORMAT/FASTAFile.cpp.o -c
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:50:18:
error: 'RecordReader' in namespace 'seqan' does not name a template type
50 | typedef seqan::RecordReader<std::fstream, seqan::SinglePass<> >
FASTARecordReader;
| ^~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In member
function 'void OpenMS::FASTAFile::readStart(const OpenMS::String&)':
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:93:66:
error: expected primary-expression before '(' token
93 | reader_ = std::unique_ptr<void, std::function<void(void*) > >(new
FASTARecordReader(infile_),
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:93:71:
error: expected type-specifier before 'FASTARecordReader'
93 | reader_ = std::unique_ptr<void, std::function<void(void*) > >(new
FASTARecordReader(infile_),
|
^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In lambda
function:
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:26:
error: 'FASTARecordReader' does not name a type
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:43:
error: expected '>' before '*' token
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:43:
error: expected '(' before '*' token
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^
| (
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:44:
error: expected primary-expression before '>' token
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:96:50:
error: expected ')' before ';' token
96 | delete static_cast<FASTARecordReader*>(ptr);
| ^
| )
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In member
function 'bool OpenMS::FASTAFile::readNext(OpenMS::FASTAFile::FASTAEntry&)':
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:35:
error: 'FASTARecordReader' does not name a type
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:52:
error: expected '>' before '*' token
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:52:
error: expected '(' before '*' token
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ^
| (
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:53:
error: expected primary-expression before '>' token
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:104:71:
error: expected ')' before '{' token
104 | if (seqan::atEnd(*static_cast<FASTARecordReader*>(reader_.get())))
| ~ ^
| )
105 | {
| ~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:109:17:
warning: suggest braces around empty body in an 'if' statement [-Wempty-body]
109 | String id, s;
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:20:
error: 'id' was not declared in this scope
110 | if (readRecord(id, s,
*static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:24:
error: 's' was not declared in this scope
110 | if (readRecord(id, s,
*static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:40:
error: 'FASTARecordReader' does not name a type
110 | if (readRecord(id, s,
*static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:57:
error: expected '>' before '*' token
110 | if (readRecord(id, s,
*static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:57:
error: expected '(' before '*' token
110 | if (readRecord(id, s,
*static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^
| (
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:58:
error: expected primary-expression before '>' token
110 | if (readRecord(id, s,
*static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:83:
error: 'Fasta' is not a member of 'seqan'
110 | if (readRecord(id, s,
*static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
|
^~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:9:
error: 'readRecord' was not declared in this scope; did you mean 'reader_'?
110 | if (readRecord(id, s,
*static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ^~~~~~~~~~
| reader_
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:110:97:
error: expected ')' before '{' token
110 | if (readRecord(id, s,
*static_cast<FASTARecordReader*>(reader_.get()), seqan::Fasta()) != 0)
| ~
^
|
)
111 | {
| ~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:116:20:
warning: suggest braces around empty body in an 'if' statement [-Wempty-body]
116 | ++entries_read_;
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:117:5:
error: 's' was not declared in this scope
117 | s.removeWhitespaces();
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:121:5:
error: 'id' was not declared in this scope
121 | id.trim();
| ^~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In member
function 'std::streampos OpenMS::FASTAFile::position() const':
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:139:41:
error: 'FASTARecordReader' does not name a type
139 | return
seqan::position(*static_cast<FASTARecordReader*>(reader_.get()));
| ^~~~~~~~~~~~~~~~~
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:139:58:
error: expected '>' before '*' token
139 | return
seqan::position(*static_cast<FASTARecordReader*>(reader_.get()));
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:139:58:
error: expected '(' before '*' token
139 | return
seqan::position(*static_cast<FASTARecordReader*>(reader_.get()));
| ^
| (
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:139:59:
error: expected primary-expression before '>' token
139 | return
seqan::position(*static_cast<FASTARecordReader*>(reader_.get()));
| ^
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp: In member
function 'bool OpenMS::FASTAFile::setPosition(const streampos&)':
/build/openms-2.6.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:144:45:
error: 'FASTARecordReader' does not name a type
144 | return
(seqan::setPosition(*static_cast<FASTARecordReader*>(reader_.get()), pos) == 0);
| ^~~~~~~~~~~~~~~~~
So it seems we need to seek for that missing function inside
libseqan2-dev and replace the include by a new one. Hopefully
it is that simple and we can save the case.
Kind regards
Andreas.
--
http://fam-tille.de
