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a few issues with the generated unix man(ual) pages #124
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I think this is the part of seqan that needs fixing:
https://github.com/seqan/seqan/blob/develop/include/seqan/arg_parse/tool_doc.h#L1555
Are these things still a problem with the SeqAn3 argument parser?
Closing this. If it still exists with the lambda3 branch, please reopen.
@h-2 I can't get the
lambda3branch to buildFrom a fresh checkout today:
-- These dependencies were found: OPENMP TRUE -fopenmp ZLIB TRUE 1.2.11 BZIP2 TRUE 1.0.8 SEQAN TRUE 2.4.1 SEQAN3 TRUE 3.3.0-rc.1 -- The requirements were met. -- The C compiler identification is GNU 12.2.0 […] In file included from /home/michael/src/lambda/submodules/seqan/include/seqan/basic/basic_fundamental.h:82, from /home/michael/src/lambda/submodules/seqan/include/seqan/basic.h:58, from /home/michael/src/lambda/submodules/seqan/include/seqan/align.h:55, from /home/michael/src/lambda/src/seqan2seqan3.hpp:55: /home/michael/src/lambda/submodules/seqan/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator) [with TIterator = std::ranges::take_view<std::ranges::drop_view<seqan3::detail::view_translate_single<std::ranges::ref_view<std::vector<seqan3::dna5> > > > >*]’: /home/michael/src/lambda/submodules/seqan/include/seqan/basic/array_construct_destruct.h:286:28: required from ‘void seqan::valueConstruct(TIterator) [with TIterator = std::ranges::take_view<std::ranges::drop_view<seqan3::detail::view_translate_single<std::ranges::ref_view<std::vector<seqan3::dna5> > > > >*]’ /home/michael/src/lambda/submodules/seqan/include/seqan/basic/holder_tristate.h:589:27: required from ‘void seqan::create(Holder<TValue, Tag<Tristate_> >&) [with TValue = std::ranges::take_view<std::ranges::drop_view<seqan3::detail::view_translate_single<std::ranges::ref_view<std::vector<seqan3::dna5> > > > >]’ /home/michael/src/lambda/submodules/seqan/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tag<seqan::Tristate_> > >::Type seqan::value(Holder<TValue, Tag<Tristate_> >&) [with TValue = std::ranges::take_view<std::ranges::drop_view<seqan3::detail::view_translate_single<std::ranges::ref_view<std::vector<seqan3::dna5> > > > >; typename Reference<Holder<TValue, Tag<Tristate_> > >::Type = std::ranges::take_view<std::ranges::drop_view<seqan3::detail::view_translate_single<std::ranges::ref_view<std::vector<seqan3::dna5> > > > >&]’ /home/michael/src/lambda/submodules/seqan/include/seqan/align/gaps_array.h:427:10: required from ‘void seqan::assignSource(Gaps<TSequence, Tag<ArrayGaps_> >&, const TSequence2&) [with TSequence = std::ranges::take_view<std::ranges::drop_view<seqan3::detail::view_translate_single<std::ranges::ref_view<std::vector<seqan3::dna5> > > > >; TSequence2 = std::ranges::take_view<std::ranges::drop_view<seqan3::detail::view_translate_single<std::ranges::ref_view<std::vector<seqan3::dna5> > > > >]’ /home/michael/src/lambda/src/search_algo.hpp:863:24: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /home/michael/src/lambda/src/search_algo.hpp:1275:27: required from ‘void iterateMatches(TLocalHolder&) [with TLocalHolder = LocalDataHolder<GlobalDataHolder<DbIndexType::FM_INDEX, AlphabetEnum::DNA5, AlphabetEnum::AMINO_ACID, AlphabetEnum::AMINO_ACID, AlphabetEnum::DNA5> >]’ /home/michael/src/lambda/src/search.cpp:395:31: required from ‘void realMain(const LambdaOptions&) [with DbIndexType c_indexType = DbIndexType::FM_INDEX; AlphabetEnum c_origSbjAlph = AlphabetEnum::DNA5; AlphabetEnum c_transAlph = AlphabetEnum::AMINO_ACID; AlphabetEnum c_redAlph = AlphabetEnum::AMINO_ACID; AlphabetEnum c_origQryAlph = AlphabetEnum::DNA5]’ /home/michael/src/lambda/src/search.cpp:314:100: required from ‘void argConv3(const LambdaOptions&) [with DbIndexType c_indexType = DbIndexType::FM_INDEX; AlphabetEnum c_origSbjAlph = AlphabetEnum::DNA5; AlphabetEnum c_transAlph = AlphabetEnum::AMINO_ACID; AlphabetEnum c_redAlph = AlphabetEnum::AMINO_ACID]’ /home/michael/src/lambda/src/search.cpp:297:108: required from ‘void argConv2b(const LambdaOptions&) [with DbIndexType c_indexType = DbIndexType::FM_INDEX; AlphabetEnum c_origSbjAlph = AlphabetEnum::DNA5]’ /home/michael/src/lambda/src/search.cpp:261:66: required from ‘void argConv1(const LambdaOptions&) [with DbIndexType c_indexType = DbIndexType::FM_INDEX]’ /home/michael/src/lambda/src/search.cpp:241:51: required from here /home/michael/src/lambda/submodules/seqan/include/seqan/basic/array_construct_destruct.h:244:9: error: no matching function for call to ‘std::ranges::take_view<std::ranges::drop_view<seqan3::detail::view_translate_single<std::ranges::ref_view<std::vector<seqan3::dna5> > > > >::take_view()’ 244 | new( (void*) & value(it) ) TNonConstValue; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Okay, compiling with gcc 11 works; and there is still a problem
Here are my recommended fixes, using
lambda3 searchp --export-help man$ diff ./lambda3_searchp.1 ./lambda3_searchp.fixed.1 1c1 < .TH LAMBDA3-SEARCHP 1 "Sep 20 2022" "lambda3-searchp 3.0.0" "" --- > .TH LAMBDA3_SEARCHP 1 "Sep 20 2022" "lambda3-searchp 3.0.0" "" 3c3 < lambda3-searchp \- the Local Aligner for Massive Biological DatA --- > lambda3_searchp \- the Local Aligner for Massive Biological DatA 5c5 < \fB[\fIOPTIONS\fP]\fP \fI-q QUERY.fasta\fP \fI-i INDEX.lambda\fP [\fI-o output.m8\fP] --- > \fIlambda2 searchp\fP \fB[\fIOPTIONS\fP]\fP \fI-q QUERY.fasta\fP \fI-i INDEX.lambda\fP [\fI-o output.m8\fP]
Reacted by Hannes HauswedellI'll have a look sometime this week!
Reacted by Michael R. CrusoeTo be honest, I have no clue about the man-page formats. We are just using the seqan3 argument parser as recommend. The main problem seems to be
-instead of_... ?Would the following changes fix this for you:
https://github.com/seqan/lambda/blob/lambda3/src/search_options.hpp#L115
- std::string programName = "lambda3-" + std::string(argv[0]); + std::string programName = "lambda3_" + std::string(argv[0]);
https://github.com/seqan/lambda/blob/lambda3/src/search_options.hpp#L126
- parser.info.synopsis.push_back( + parser.info.synopsis.push_back(std::string{"\\fIlambda3 "} + std::string(argv[0]) + "\\fP " "[\\fIOPTIONS\\fP] \\fI-q QUERY.fasta\\fP \\fI-i INDEX.lambda\\fP [\\fI-o output.m8\\fP]");
Can you still reproduce the problems with the current lambda3-branch? Does it build for you now?
The search* manpages are warning/error-free; thanks!
The
mkindex*manpages have some issues withparagraph filling. They are usually related to long lines. Justifying text on the left hand side can help with adjustments. Hyphenation can help with breaks.
For more information, please see "Manipulating Filling and Adjusting" and "Manipulating Hyphenation" in the Groff manualLC_ALL=C.UTF-8 MANROFFSEQ='' MANWIDTH=80 man --warnings -E UTF-8 -l -Tutf8 -Z ./lambda3_mkindexn.1 >/dev/null troff: <standard input>:38: warning [p 1, 8.7i]: cannot adjust lineHi - could this link be the problem by chance?
lambda/src/mkindex_options.hpp
Line 120 in cf59351
At least it is longer than 80 char and can't just be split. If so, do you have a recommendation how you usually handle this?
Thank you for the unix man(ual) pages!
The Debian linter found a few issues with them. This might be more of a seqan issue, though.
https://lintian.debian.org/maintainer/debian-med-packaging@lists.alioth.debian.org.html#lambda-align2
1st issue:
using
lambda2-mkindexn.1.gzas an example:should be
The
NAMEcan't have spaces between the subcommand parts but they are allowed in theSYNOPSIS2nd issue:
In the example above we have
.TH LAMBDA2 MKINDEXN 1 "Jan 22 2019" "lambda2 mkindexn 2.0.0" "", and again the space betweenLAMBDA2andMKINDEXNshouldn't be there. Makes it look as if the section is "MKINDEXN" instead of section 1.