[BUG] extend_right/left() needs `char const *` overload #1588

Irallia · 2020-02-11T18:01:23Z

Resolves #1473.

Test case added.

include/seqan3/search/fm_index/bi_fm_index_cursor.hpp

CHANGELOG.md

SGSSGene · 2020-02-12T16:40:36Z

Wow, any one knows why std::ranges::range includes the \0 at the end of a char*?

Also I wanted to point out that the same issue should exists with bi_fm_index_cursor.

codecov · 2020-02-13T12:11:07Z

Codecov Report

Merging #1588 into master will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master    #1588   +/-   ##
=======================================
  Coverage   97.68%   97.68%           
=======================================
  Files         237      237           
  Lines        9057     9063    +6     
=======================================
+ Hits         8847     8853    +6     
  Misses        210      210

Impacted Files	Coverage Δ
...lude/seqan3/search/fm_index/bi_fm_index_cursor.hpp	`100.00% <100.00%> (ø)`
include/seqan3/search/fm_index/fm_index_cursor.hpp	`100.00% <100.00%> (ø)`
...e/seqan3/alignment/pairwise/detail/type_traits.hpp	`100.00% <0.00%> (ø)`

Continue to review full report at Codecov.

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eseiler · 2020-02-13T12:54:36Z

Wow, any one knows why std::ranges::range includes the \0 at the end of a char*?

char const * models std::ranges::range and it always includes a \0 as terminator (C-Style string). Also, the size of the char const * includes the terminator, so it's natural to include the terminator when you look at it as a range. If you do not want the terminator, you need to explicitly do something to get rid of it. For example, constructing a string_view which is aware that the \0 isn't part of the acutal string, but more like an implementation detail, and acts this way, i.e. as a range it does not include the \0 and the size also does not include the terminator.

Also I wanted to point out that the same issue should exists with bi_fm_index_cursor.

Yes it should; for extend_left and extend_right

marehr

Can you add the overloads and test cases for extend_left, too?

Thank you!

test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp

SGSSGene · 2020-02-13T16:30:54Z

Wow, any one knows why std::ranges::range includes the \0 at the end of a char*?

char const * models std::ranges::range and it always includes a \0 as terminator (C-Style string). Also, the size of the char const * includes the terminator, so it's natural to include the terminator when you look at it as a range. If you do not want the terminator, you need to explicitly do something to get rid of it. For example, constructing a string_view which is aware that the \0 isn't part of the acutal string, but more like an implementation detail, and acts this way, i.e. as a range it does not include the \0 and the size also does not include the terminator.

I know that std::ranges::range includes the \0 ;-) I was more wondering, why does it?
If I look at C and functions like strlen it doesn't include the \0. Also std::ranges::range assumes that a char const* is a C-Style string. This seems counter intuitive since char const* is often used for just data. But even assuming it is a C-Style string, in which cases do I want to manipulate the terminator? I can think of many cases were are \0 should be ignored, but non were it could be useful.

marehr · 2020-02-13T23:08:55Z

I know that std::ranges::range includes the \0 ;-) I was more wondering, why does it?
If I look at C and functions like strlen it doesn't include the \0. Also std::ranges::range assumes that a char const* is a C-Style string. This seems counter intuitive since char const* is often used for just data. But even assuming it is a C-Style string, in which cases do I want to manipulate the terminator? I can think of many cases were are \0 should be ignored, but non were it could be useful.

In this case the string is not of type char const * (char pointer, which is not a range), but of type char [] (bounded char array, which is a range). (See https://en.cppreference.com/w/cpp/language/array)

Only a bounded array can be a range, because it knows its start and its end position (start + array size). Here an example: https://godbolt.org/z/zt-Aga

You can argue why char[] should be always a range with size - 1, but I guess that this is more error prone (on some platforms is uint8_t = char so a sequence of numbers might be misinterpreted as a cstring and would truncate data) than to accept that char literals always include \0. An easy fix to convert a classic cstr is to use string_view.

SGSSGene · 2020-02-13T23:15:19Z

I know that std::ranges::range includes the \0 ;-) I was more wondering, why does it?
If I look at C and functions like strlen it doesn't include the \0. Also std::ranges::range assumes that a char const* is a C-Style string. This seems counter intuitive since char const* is often used for just data. But even assuming it is a C-Style string, in which cases do I want to manipulate the terminator? I can think of many cases were are \0 should be ignored, but non were it could be useful.

In this case the string is not of type char const * (char pointer, which is not a range), but of type char [] (bounded char array, which is a range). (See https://en.cppreference.com/w/cpp/language/array)

Only a bounded array can be a range, because it knows its start and its end position (start + array size). Here an example: https://godbolt.org/z/zt-Aga

Ah it is a char [], I wasn't aware of that. Now the puzzle comes together. I have no experience with ranges and couldn't find anything on this particular issue. Thank you

marehr

lgtm :)

Irallia · 2020-04-07T09:02:32Z

@smehringer after this long time, I had some merging problems. I solved everything, but some includes poped up witch are not mine I think.. Can you please check with me again if there are still open comments and if these includes are useful?

smehringer

I caught some things :)

smehringer · 2020-04-07T09:13:55Z

CHANGELOG.md

@@ -56,6 +56,8 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele

 * Added `seqan3::interleaved_bloom_filter`, a data structure that efficiently answers set-membership queries for
  multiple bins ([\#920](https://github.com/seqan/seqan3/pull/920)).
+*  The `extend_right()` function can now also handle `char const *`.


this can be removed because there is a note under bug fixes below

smehringer · 2020-04-07T09:15:13Z

test/unit/search/fm_index/bi_fm_index_aa27_test.cpp

@@ -10,6 +10,8 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"

+#include <seqan3/alphabet/aminoacid/aa27.hpp>


remove this

smehringer · 2020-04-07T09:15:32Z

test/unit/search/fm_index/bi_fm_index_char_test.cpp

@@ -8,6 +8,8 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"

+#include <seqan3/alphabet/adaptation/uint.hpp>


remove this

smehringer · 2020-04-07T09:15:45Z

test/unit/search/fm_index/bi_fm_index_dna4_test.cpp

@@ -10,6 +10,8 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"

+#include <seqan3/alphabet/nucleotide/dna4.hpp>


remove this

smehringer · 2020-04-07T09:15:58Z

test/unit/search/fm_index/fm_index_dna4_test.cpp

@@ -11,6 +11,9 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"

+#include <seqan3/alphabet/nucleotide/dna4.hpp>


remove this

test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp

smehringer

tiny tiny thing

smehringer · 2020-04-08T14:06:27Z

test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test_template.hpp

@@ -222,5 +222,38 @@ TYPED_TEST_P(bi_fm_index_cursor_collection_test, to_rev_cursor)
    }
 }

+TYPED_TEST_P(bi_fm_index_cursor_collection_test, locate_char_string)


Suggested change

TYPED_TEST_P(bi_fm_index_cursor_collection_test, locate_char_string)

TYPED_TEST_P(bi_fm_index_cursor_collection_test, extend_const_char_pointer)

💅 Since it is not about locate but about extend_left/right :)

marehr · 2020-04-09T10:40:53Z

Travis fails:

In file included from /home/travis/build/seqan/seqan3/include/seqan3/search/fm_index/fm_index.hpp:24,

                 from /home/travis/build/seqan/seqan3/include/seqan3/search/fm_index/bi_fm_index.hpp:20,

                 from /home/travis/build/seqan/seqan3/include/seqan3/search/fm_index/all.hpp:48,

                 from /home/travis/build/seqan/seqan3/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp:12,

                 from /home/travis/build/seqan/seqan3/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test.cpp:16:

/home/travis/build/seqan/seqan3/include/seqan3/search/fm_index/fm_index_cursor.hpp: In member function ‘void gtest_suite_fm_index_cursor_collection_test_::locate_char_string<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = seqan3::fm_index_cursor<seqan3::fm_index<char, (seqan3::text_layout)1> >]’:

/home/travis/build/seqan/seqan3/include/seqan3/search/fm_index/fm_index_cursor.hpp:331:19: error: ‘it1.seqan3::fm_index_cursor<seqan3::fm_index<char, (seqan3::text_layout)1> >::parent_lb’ may be used uninitialized in this function [-Werror=maybe-uninitialized]

         size_type new_parent_lb = parent_lb, new_parent_rb = parent_rb;

                   ^~~~~~~~~~~~~

/home/travis/build/seqan/seqan3/include/seqan3/search/fm_index/fm_index_cursor.hpp:331:46: error: ‘it1.seqan3::fm_index_cursor<seqan3::fm_index<char, (seqan3::text_layout)1> >::parent_rb’ may be used uninitialized in this function [-Werror=maybe-uninitialized]

         size_type new_parent_lb = parent_lb, new_parent_rb = parent_rb;

                                              ^~~~~~~~~~~~~

cc1plus: all warnings being treated as errors

rrahn · 2020-04-15T10:48:06Z

It seems that these here are not initialised:

seqan3/include/seqan3/search/fm_index/fm_index_cursor.hpp

Lines 91 to 93 in 332f4b3

    
           size_type parent_lb; 
        
           //!\brief Right suffix array interval of the parent node. Needed for cycle_back(). 
        
           size_type parent_rb;

So you need to change the initialisers:

    //!\brief Underlying FM index.
    index_type const * index{nullptr};
    //!\brief Left suffix array interval of the parent node. Needed for cycle_back().
    size_type parent_lb{};
    //!\brief Right suffix array interval of the parent node. Needed for cycle_back().
    size_type parent_rb{};
    //!\brief Underlying index from the SDSL.
    node_type node{};
    //!\brief Alphabet size of the index without delimiters
    sdsl_sigma_type sigma{};

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

…elease

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

…udes Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

Irallia · 2020-04-17T09:35:55Z

@rrahn, thanks for your help! It seems that your suggestion helped a bit. Travis is running through now, but Jenkins still shows some problems with the osx_g++-9_cereal-true_Release:
99% tests passed, 3 tests failed out of 6419
The following tests FAILED:
5930 - search_collection_test_NOT_BUILT (Not Run)
5963 - search_scheme_algorithm_test_NOT_BUILT (Not Run)
5964 - search_scheme_test_NOT_BUILT (Not Run)

I still cannot reconstruct the errors.
Log file:

[ 91%] Linking CXX executable search_collection_test
g++-9: error: CMakeFiles/search_collection_test.dir/search_collection_test.cpp.o: No such file or directory
CMake Error at /usr/local/Cellar/cmake/3.15.3/share/cmake/Modules/GoogleTestAddTests.cmake:26 (message):
  Specified test executable does not exist.

    Path: '/Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/build/search/search_collection_test'

[ 91%] Built target search_collection_test

smehringer · 2020-04-17T20:30:03Z

Jenkins currently fails on every PR with this error :( I think @rrahn is working on it already

marehr · 2020-04-20T11:23:22Z

Current build failure:

[ 89%] Building CXX object search/CMakeFiles/search_scheme_test.dir/search_scheme_test.cpp.o
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/wait.h:110,
                 from /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdlib.h:66,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cstdlib:75,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/stl_algo.h:59,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/algorithm:62,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:8:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/resource.h:443:34: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  443 | int     getiopolicy_np(int, int) __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_2_0);
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/resource.h:449:39: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  449 | int     setiopolicy_np(int, int, int) __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_2_0);
      |                                       ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdlib.h:128,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cstdlib:75,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/stl_algo.h:59,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/algorithm:62,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:8:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/malloc/_malloc.h:52:74: error: expected initializer before '__OSX_AVAILABLE_STARTING'
   52 | int   posix_memalign(void **__memptr, size_t __alignment, size_t __size) __OSX_AVAILABLE_STARTING(__MAC_10_6, __IPHONE_3_0);
      |                                                                          ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cstdlib:75,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/stl_algo.h:59,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/algorithm:62,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:8:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdlib.h:270:53: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  270 | void  arc4random_buf(void * __buf, size_t __nbytes) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                     ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdlib.h:273:46: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  273 |   arc4random_uniform(uint32_t __upper_bound) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                              ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cstdlib:75,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/stl_algo.h:59,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/algorithm:62,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:8:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdlib.h:292:45: error: expected initializer before '__OSX_AVAILABLE_BUT_DEPRECATED_MSG'
  292 | int  daemon(int, int) __DARWIN_1050(daemon) __OSX_AVAILABLE_BUT_DEPRECATED_MSG(__MAC_10_0, __MAC_10_5, __IPHONE_2_0, __IPHONE_2_0, "Use posix_spawn APIs instead.") __WATCHOS_PROHIBITED __TVOS_PROHIBITED;
      |                                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdlib.h:325:6: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  325 |      __OSX_AVAILABLE_STARTING(__MAC_10_6, __IPHONE_3_2);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/stdlib.h:333:6: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  333 |      __OSX_AVAILABLE_STARTING(__MAC_10_6, __IPHONE_3_2);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/_stdio.h:79,
                 from /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin19/9.3.0/include-fixed/stdio.h:78,
                 from /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:90,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cwchar:44,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/postypes.h:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/char_traits.h:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/string:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/stdexcept:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/array:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/tuple:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/functional:54,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/pstl/glue_algorithm_defs.h:13,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/algorithm:71,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:8:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/sys/stdio.h:39:56: error: expected initializer before '__OSX_AVAILABLE_STARTING'
   39 | int     renameat(int, const char *, int, const char *) __OSX_AVAILABLE_STARTING(__MAC_10_10, __IPHONE_8_0);
      |                                                        ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:90,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cwchar:44,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/postypes.h:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/char_traits.h:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/string:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/stdexcept:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/array:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/tuple:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/functional:54,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/pstl/glue_algorithm_defs.h:13,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/algorithm:71,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:8:
/usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin19/9.3.0/include-fixed/stdio.h:366:67: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  366 | int dprintf(int, const char * __restrict, ...) __printflike(2, 3) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                                   ^~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin19/9.3.0/include-fixed/stdio.h:367:79: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  367 | int vdprintf(int, const char * __restrict, __gnuc_va_list) __printflike(2, 0) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                                               ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:90,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cwchar:44,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/postypes.h:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/char_traits.h:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/string:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/stdexcept:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/array:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/tuple:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/functional:54,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/pstl/glue_algorithm_defs.h:13,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/algorithm:71,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:8:
/usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin19/9.3.0/include-fixed/stdio.h:368:123: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  368 | ssize_t getdelim(char ** __restrict __linep, size_t * __restrict __linecapp, int __delimiter, FILE * __restrict __stream) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                                                                                           ^~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin19/9.3.0/include-fixed/stdio.h:369:105: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  369 | ssize_t getline(char ** __restrict __linep, size_t * __restrict __linecapp, FILE * __restrict __stream) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cwchar:44,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/postypes.h:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/bits/char_traits.h:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/string:40,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/stdexcept:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/array:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/tuple:39,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/functional:54,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/pstl/glue_algorithm_defs.h:13,
                 from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/algorithm:71,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:8:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:197:67: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  197 | wchar_t *wcpcpy(wchar_t * __restrict, const wchar_t * __restrict) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                                   ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:198:76: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  198 | wchar_t *wcpncpy(wchar_t * __restrict, const wchar_t * __restrict, size_t) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                                            ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:199:34: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  199 | wchar_t *wcsdup(const wchar_t *) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:200:54: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  200 | int     wcscasecmp(const wchar_t *, const wchar_t *) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                      ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:201:65: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  201 | int     wcsncasecmp(const wchar_t *, const wchar_t *, size_t n) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:202:49: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  202 | size_t  wcsnlen(const wchar_t *, size_t) __pure __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/wchar.h:215:47: error: expected initializer before '__OSX_AVAILABLE_STARTING'
  215 | wchar_t *fgetwln(FILE * __restrict, size_t *) __OSX_AVAILABLE_STARTING(__MAC_10_7, __IPHONE_4_3);
      |                                               ^~~~~~~~~~~~~~~~~~~~~~~~
[ 89%] Linking CXX executable view_translate_test
In file included from /usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cinttypes:46,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/include/seqan3/core/platform.hpp:10,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/include/seqan3/search/detail/search_scheme_precomputed.hpp:18,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/helper_search_scheme.hpp:13,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:11:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/inttypes.h:234:25: error: expected constructor, destructor, or type conversion before '(' token
  234 | __OSX_AVAILABLE_STARTING(__MAC_10_4, __IPHONE_2_0)
      |                         ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/inttypes.h:244:25: error: expected constructor, destructor, or type conversion before '(' token
  244 | __OSX_AVAILABLE_STARTING(__MAC_10_4, __IPHONE_2_0)
      |                         ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/inttypes.h:249:25: error: expected constructor, destructor, or type conversion before '(' token
  249 | __OSX_AVAILABLE_STARTING(__MAC_10_4, __IPHONE_2_0)
      |                         ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/inttypes.h:255:25: error: expected constructor, destructor, or type conversion before '(' token
  255 | __OSX_AVAILABLE_STARTING(__MAC_10_4, __IPHONE_2_0)
      |                         ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/inttypes.h:262:25: error: expected constructor, destructor, or type conversion before '(' token
  262 | __OSX_AVAILABLE_STARTING(__MAC_10_4, __IPHONE_2_0)
      |                         ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/inttypes.h:268:25: error: expected constructor, destructor, or type conversion before '(' token
  268 | __OSX_AVAILABLE_STARTING(__MAC_10_4, __IPHONE_2_0)
      |                         ^
In file included from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/include/seqan3/core/platform.hpp:10,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/include/seqan3/search/detail/search_scheme_precomputed.hpp:18,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/helper_search_scheme.hpp:13,
                 from /Users/builder/jenkins/ws/seqan3_build_pipeline_PR-1588/checkout/test/unit/search/search_scheme_test.cpp:11:
/usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cinttypes:61:11: error: '::imaxabs' has not been declared
   61 |   using ::imaxabs;
      |           ^~~~~~~
/usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cinttypes:62:11: error: '::imaxdiv' has not been declared
   62 |   using ::imaxdiv;
      |           ^~~~~~~
/usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cinttypes:68:11: error: '::strtoimax' has not been declared
   68 |   using ::strtoimax;
      |           ^~~~~~~~~
/usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cinttypes:69:11: error: '::strtoumax' has not been declared
   69 |   using ::strtoumax;
      |           ^~~~~~~~~
/usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cinttypes:72:11: error: '::wcstoimax' has not been declared
   72 |   using ::wcstoimax;
      |           ^~~~~~~~~
/usr/local/Cellar/gcc/9.3.0/include/c++/9.3.0/cinttypes:73:11: error: '::wcstoumax' has not been declared
   73 |   using ::wcstoumax;
      |           ^~~~~~~~~

smehringer · 2020-04-20T16:46:31Z

Since the error is not related to this PR I'll merge this

Irallia requested review from a team, wvdtoorn, simonsasse and marehr and removed request for a team, wvdtoorn and simonsasse February 11, 2020 18:01

marehr reviewed Feb 11, 2020

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Irallia requested a review from marehr February 13, 2020 10:48

Irallia force-pushed the BUG/search/extend_right_needs_overload branch from 295b32a to 67e065c Compare February 13, 2020 12:11

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marehr changed the title ~~[BUG] extend_right() needs char const * overload~~ [BUG] extend_right/left() needs char const * overload Feb 13, 2020

Irallia requested a review from marehr February 14, 2020 14:33

marehr approved these changes Feb 17, 2020

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Irallia requested a review from a team February 17, 2020 12:09

Irallia force-pushed the BUG/search/extend_right_needs_overload branch 2 times, most recently from 28c5a57 to a4d3e06 Compare March 3, 2020 11:22

Irallia force-pushed the BUG/search/extend_right_needs_overload branch from ffd0ba3 to 4d6bc09 Compare April 6, 2020 15:00

Irallia requested a review from smehringer April 7, 2020 08:59

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Irallia force-pushed the BUG/search/extend_right_needs_overload branch 2 times, most recently from a04799c to 941d650 Compare April 8, 2020 13:43

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Irallia force-pushed the BUG/search/extend_right_needs_overload branch from 941d650 to d61a120 Compare April 11, 2020 11:58

rrahn added this to the Sprint 2 milestone Apr 15, 2020

Irallia added 10 commits April 16, 2020 13:45

[FIX] extend_right() needs char const * overload

f19304e

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

[FIX] change changelog

84c20e0

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

[TEST] add test case

2c37e11

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

[FIX] shorten the function with a redirect; move log to the correct r…

217552f

…elease

[FIX] add extend_left() overload

792e946

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

[DOC] generalized extend-functions; expand the changelog; update incl…

ccdde98

…udes Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

[FIX] fix merge conflicts

1139714

[TEST] add tests for issue seqan#1473

7f4ecd0

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

[TEST] renaming

72c11c5

[FIX] missing initialisation added

1e7cd7d

Irallia force-pushed the BUG/search/extend_right_needs_overload branch from d61a120 to 1e7cd7d Compare April 16, 2020 11:47

smehringer merged commit d921134 into seqan:master Apr 20, 2020

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[BUG] extend_right/left() needs `char const *` overload #1588

[BUG] extend_right/left() needs `char const *` overload #1588

Irallia commented Feb 11, 2020

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smehringer commented Apr 20, 2020

	TYPED_TEST_P(bi_fm_index_cursor_collection_test, locate_char_string)
	TYPED_TEST_P(bi_fm_index_cursor_collection_test, extend_const_char_pointer)

[BUG] extend_right/left() needs char const * overload #1588

[BUG] extend_right/left() needs char const * overload #1588

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[BUG] extend_right/left() needs `char const *` overload #1588

[BUG] extend_right/left() needs `char const *` overload #1588

codecov bot commented Feb 13, 2020 •

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eseiler commented Feb 13, 2020 •

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