Charlotte Soneson
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/Rhisat2 |
| git_branch: devel |
| git_last_commit: b1ac924 |
| git_last_commit_date: 2025-04-15 11:40:26 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1759/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rhisat2 1.25.0 (landing page) Charlotte Soneson
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the Rhisat2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhisat2.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: Rhisat2 |
| Version: 1.25.0 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhisat2.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Rhisat2_1.25.0.tar.gz |
| StartedAt: 2025-08-15 07:04:47 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 07:10:17 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 330.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rhisat2.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhisat2.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Rhisat2_1.25.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/Rhisat2.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rhisat2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rhisat2' version '1.25.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rhisat2' can be installed ... WARNING
Found the following significant warnings:
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
hisat2.cpp:1823:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
hisat2.cpp:3167:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
hisat2.cpp:3168:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
hisat2.cpp:3189:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
hisat2.cpp:4035:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
splice_site.cpp:717:59: warning: '?:' using integer constants in boolean context, the expression will always evaluate to 'true' [-Wint-in-bool-context]
ds.h:663:28: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class Exon'; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'F:/biocbuild/bbs-3.22-bioc/meat/Rhisat2.Rcheck/00install.out' for details.
* checking installed package size ... INFO
installed size is 70.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'F:/biocbuild/bbs-3.22-bioc/meat/Rhisat2.Rcheck/00check.log'
for details.
Rhisat2.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL Rhisat2
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'Rhisat2' ...
** this is package 'Rhisat2' version '1.25.0'
** using staged installation
** libs
running 'src/Makefile.win' ...
g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"2.2.1\"" -DBUILD_HOST="\"palomino8\"" -DBUILD_TIME="\"Thu Aug 14 16:42:49 EDT 2025\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \
-I. -I third_party \
-o hisat2-build-s hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
In file included from hisat2_build.cpp:35:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h: In instantiation of 'void GFM<index_t>::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, bool) [with TStr = SString<char>; index_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ofstream = std::basic_ofstream<char>; uint32_t = unsigned int]':
gfm.h:1039:23: required from 'GFM<index_t>::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
1039 | initFromVector<TStr>(
| ~~~~~~~~~~~~~~~~~~~~^
1040 | s,
| ~~
1041 | snpfile,
| ~~~~~~~~
1042 | htfile,
| ~~~~~~~
1043 | ssfile,
| ~~~~~~~
1044 | exonfile,
| ~~~~~~~~~
1045 | svfile,
| ~~~~~~~
1046 | repeatfile,
| ~~~~~~~~~~~
1047 | is,
| ~~~
1048 | szs,
| ~~~~
1049 | sztot,
| ~~~~~~
1050 | refparams,
| ~~~~~~~~~~
1051 | fout1,
| ~~~~~~
1052 | fout2,
| ~~~~~~
1053 | outfile,
| ~~~~~~~~
1054 | useBlockwise,
| ~~~~~~~~~~~~~
1055 | bmax,
| ~~~~~
1056 | bmaxSqrtMult,
| ~~~~~~~~~~~~~
1057 | bmaxDivN,
| ~~~~~~~~~
1058 | dcv,
| ~~~~
1059 | parent_szs,
| ~~~~~~~~~~~
1060 | parent_refnames,
| ~~~~~~~~~~~~~~~~
1061 | seed,
| ~~~~~
1062 | verbose);
| ~~~~~~~~
hgfm.h:1989:14: required from 'HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = unsigned int; uint32_t = unsigned int]'
1989 | _in6(NULL)
| ^
hisat2_build.cpp:535:15: required from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
535 | gfm = new HGFM<TIndexOffU>(
| ^~~~~~~~~~~~~~~~~~~~~
536 | s,
| ~~
537 | packed,
| ~~~~~~~
538 | 1, // TODO: maybe not?
| ~~~~~~~~~~~~~~~~~~~~~~~
539 | lineRate,
| ~~~~~~~~~
540 | offRate, // suffix-array sampling rate
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
541 | ftabChars, // number of chars in initial arrow-pair calc
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
542 | localOffRate,
| ~~~~~~~~~~~~~
543 | localFtabChars,
| ~~~~~~~~~~~~~~~
544 | nthreads,
| ~~~~~~~~~
545 | snpfile,
| ~~~~~~~~
546 | htfile,
| ~~~~~~~
547 | ssfile,
| ~~~~~~~
548 | exonfile,
| ~~~~~~~~~
549 | svfile,
| ~~~~~~~
550 | repeatfile,
| ~~~~~~~~~~~
551 | outfile, // basename for .?.ht2 files
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | reverse == 0, // fw
| ~~~~~~~~~~~~~~~~~~~
553 | !entireSA, // useBlockwise
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | bmax, // block size for blockwise SA builder
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | bmaxMultSqrt, // block size as multiplier of sqrt(len)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
556 | bmaxDivN, // block size as divisor of len
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
557 | noDc? 0 : dcv,// difference-cover period
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
558 | is, // list of input streams
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
559 | szs, // list of reference sizes
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
561 | refparams, // reference read-in parameters
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
562 | localindex, // create local indexes?
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
563 | parent_szs, // parent szs
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
564 | parent_refnames, // parent refence names
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
565 | seed, // pseudo-random number generator seed
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
566 | -1, // override offRate
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
567 | verbose, // be talkative
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | sanityCheck); // verify results and internal consistency
| ~~~~~~~~~~~~
hisat2_build.cpp:786:39: required from here
786 | driver<SString<char> >(infile,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
787 | infiles,
| ~~~~~~~~
788 | snp_fname,
| ~~~~~~~~~~
789 | ht_fname,
| ~~~~~~~~~
790 | ss_fname,
| ~~~~~~~~~
791 | exon_fname,
| ~~~~~~~~~~~
792 | sv_fname,
| ~~~~~~~~~
793 | dummy_fname,
| ~~~~~~~~~~~~
794 | outfile,
| ~~~~~~~~
795 | false,
| ~~~~~~
796 | REF_READ_FORWARD,
| ~~~~~~~~~~~~~~~~~
797 | true, // create local indexes
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
798 | NULL, // no parent szs
| ~~~~~~~~~~~~~~~~~~~~~~
799 | NULL, // no parent refnames
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
800 | &parent_szs, // get parent szs
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
801 | &parent_refnames); // get parent refnames
| ~~~~~~~~~~~~~~~~~
gfm.h:2167:33: warning: variable 'template_len' set but not used [-Wunused-but-set-variable]
2167 | index_t template_len = 0;
| ^~~~~~~~~~~~
In file included from sequence_io.h:30,
from hisat2_build.cpp:28:
In member function 'void SString<T>::resize(size_t) [with T = char]',
inlined from 'void SString<T>::install(const T*, size_t) [with T = char]' at sstring.h:687:9,
inlined from 'void SString<T>::install(const T*, size_t) [with T = char]' at sstring.h:685:15,
inlined from 'HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; local_index_t = short unsigned int]' at hgfm.h:2259:41:
sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
602 | delete cs_;
| ^~~~~~~~~~
In member function 'void SString<T>::resize(size_t) [with T = char]',
inlined from 'HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; local_index_t = short unsigned int]' at hgfm.h:2255:36:
sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)'
610 | cs_ = new T[sz+1];
| ^~~~~~~~~~~
In member function 'void SString<T>::resize(size_t) [with T = char]',
inlined from 'void SString<T>::install(const T*, size_t) [with T = char]' at sstring.h:687:9,
inlined from 'void SString<T>::install(const T*, size_t) [with T = char]' at sstring.h:685:15,
inlined from 'HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; local_index_t = short unsigned int]' at hgfm.h:2257:41:
sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
602 | delete cs_;
| ^~~~~~~~~~
In member function 'void SString<T>::resize(size_t) [with T = char]',
inlined from 'HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; local_index_t = short unsigned int]' at hgfm.h:2255:36:
sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)'
610 | cs_ = new T[sz+1];
| ^~~~~~~~~~~
In member function 'void SString<T>::resize(size_t) [with T = char]',
inlined from 'void SString<T>::install(const T*, size_t) [with T = char]' at sstring.h:687:9,
inlined from 'void SString<T>::install(const T*, size_t) [with T = char]' at sstring.h:685:15,
inlined from 'RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int]' at rfm.h:768:29,
inlined from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>]' at hisat2_build.cpp:571:15:
sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
602 | delete cs_;
| ^~~~~~~~~~
In member function 'void SString<T>::resize(size_t) [with T = char]',
inlined from 'RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int]' at rfm.h:764:24,
inlined from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>]' at hisat2_build.cpp:571:15:
sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)'
610 | cs_ = new T[sz+1];
| ^~~~~~~~~~~
In member function 'void SString<T>::resize(size_t) [with T = char]',
inlined from 'void SString<T>::install(const T*, size_t) [with T = char]' at sstring.h:687:9,
inlined from 'void SString<T>::install(const T*, size_t) [with T = char]' at sstring.h:685:15,
inlined from 'RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int]' at rfm.h:766:29,
inlined from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>]' at hisat2_build.cpp:571:15:
sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
602 | delete cs_;
| ^~~~~~~~~~
In member function 'void SString<T>::resize(size_t) [with T = char]',
inlined from 'RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int]' at rfm.h:764:24,
inlined from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>]' at hisat2_build.cpp:571:15:
sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)'
610 | cs_ = new T[sz+1];
| ^~~~~~~~~~~
ref_read.cpp: In function 'std::pair<long long unsigned int, long long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)':
ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
367 | if(i + 1 >= recs.size() || recs[i+1].first) {
| ~~~~~~^~~~~~~~~~~~~~
ref_read.cpp: In function 'std::pair<long long unsigned int, long long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)':
ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
440 | if(i + 1 >= recs.size() || recs[i+1].first) {
| ~~~~~~^~~~~~~~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.cpp:522:26: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
522 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:516:14: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
516 | bool binarySearched = false;
| ^~~~~~~~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"2.2.1\"" -DBUILD_HOST="\"palomino8\"" -DBUILD_TIME="\"Thu Aug 14 16:44:18 EDT 2025\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE2 -DNDEBUG -Wall \
-I. -I third_party \
-o hisat2-align-s hisat2.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \
In file included from hgfm.h:24,
from hisat2.cpp:33:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_sw.h:81,
from aligner_sw_driver.h:86,
from hi_aligner.h:42,
from spliced_aligner.h:23,
from hisat2.cpp:46:
aligner_sw_nuc.h: At global scope:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
hisat2.cpp: In function 'void parseOptions(int, const char**)':
hisat2.cpp:1823:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1823 | auto_ptr<Presets> presets(new PresetsV0());
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp: In function 'void multiseedSearchWorker_hisat2(void*)':
hisat2.cpp:3167:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
3167 | auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp:3168:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
3168 | auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp:3189:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
3189 | auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp: In function 'void driver(const char*, const std::string&, const std::string&)':
hisat2.cpp:4035:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
4035 | auto_ptr<BitPairReference> refs(
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
hi_aligner.h: In instantiation of 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]':
hi_aligner.h:4107:39: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]'
4107 | mate_found |= alignMate(
| ^~~~~~~~~
hisat2.cpp:3537:48: required from here
3537 | int ret = splicedAligner.go(
| ~~~~~~~~~~~~~~~~~^
3538 | sc,
| ~~~
3539 | pepol,
| ~~~~~~
3540 | *multiseed_tpol,
| ~~~~~~~~~~~~~~~~
3541 | *gpol,
| ~~~~~~
3542 | gfm,
| ~~~~
3543 | rgfm,
| ~~~~~
3544 | *altdb,
| ~~~~~~~
3545 | *repeatdb,
| ~~~~~~~~~~
3546 | *raltdb,
| ~~~~~~~~
3547 | ref,
| ~~~~
3548 | rref,
| ~~~~~
3549 | sw,
| ~~~
3550 | *ssdb,
| ~~~~~~
3551 | wlm,
| ~~~~
3552 | prm,
| ~~~~
3553 | swmSeed,
| ~~~~~~~~
3554 | him,
| ~~~~
3555 | rnd,
| ~~~~
3556 | msinkwrap);
| ~~~~~~~~~~
hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'TRefOff' {aka 'long long int'} [-Wsign-compare]
5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off())
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
gfm.h: In instantiation of 'void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = unsigned int]':
hisat2.cpp:3815:17: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
3815 | gfm.checkOrigs(os, false);
| ~~~~~~~~~~~~~~^~~~~~~~~~~
hisat2.cpp:4351:26: required from here
4351 | driver<SString<char> >("DNA", bt2index, outfile);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
6935 | int lastorig = -1;
| ^~~~~~~~
In file included from aligner_seed2.h:109,
from aligner_driver.h:78,
from hi_aligner.h:41:
group_walk.h: In instantiation of 'std::pair<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]':
group_walk.h:1517:14: required from 'bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]'
1517 | st.advance(
| ~~~~~~~~~~^
1518 | gfmFw,
| ~~~~~~
1519 | ref,
| ~~~~
1520 | sa,
| ~~~
1521 | hit_,
| ~~~~~
1522 | (index_t)range,
| ~~~~~~~~~~~~~~~
1523 | false,
| ~~~~~~
1524 | NULL,
| ~~~~~
1525 | st_,
| ~~~~
1526 | gws,
| ~~~~
1527 | met,
| ~~~~
1528 | prm);
| ~~~~
hi_aligner.h:5901:34: required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]'
5901 | _gws_local.advanceElement(
| ~~~~~~~~~~~~~~~~~~~~~~~~~^
5902 | off,
| ~~~~
5903 | gfm, // forward Bowtie index for walking left
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5904 | ref, // bitpair-encoded reference
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5905 | _sas_local, // SA range with offsets
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5906 | _gwstate_local, // GroupWalk state; scratch space
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5907 | wr, // put the result here
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5908 | met, // metrics
| ~~~~~~~~~~~~~~~~~~~~~~~~
5909 | prm); // per-read metrics
| ~~~~
hi_aligner.h:5664:17: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]'
5664 | getGenomeCoords_local(
| ^~~~~~~~~~~~~~~~~~~~~
hi_aligner.h:4107:39: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]'
4107 | mate_found |= alignMate(
| ^~~~~~~~~
hisat2.cpp:3537:48: required from here
3537 | int ret = splicedAligner.go(
| ~~~~~~~~~~~~~~~~~^
3538 | sc,
| ~~~
3539 | pepol,
| ~~~~~~
3540 | *multiseed_tpol,
| ~~~~~~~~~~~~~~~~
3541 | *gpol,
| ~~~~~~
3542 | gfm,
| ~~~~
3543 | rgfm,
| ~~~~~
3544 | *altdb,
| ~~~~~~~
3545 | *repeatdb,
| ~~~~~~~~~~
3546 | *raltdb,
| ~~~~~~~~
3547 | ref,
| ~~~~
3548 | rref,
| ~~~~~
3549 | sw,
| ~~~
3550 | *ssdb,
| ~~~~~~
3551 | wlm,
| ~~~~
3552 | prm,
| ~~~~
3553 | swmSeed,
| ~~~~~~~~
3554 | him,
| ~~~~
3555 | rnd,
| ~~~~
3556 | msinkwrap);
| ~~~~~~~~~~
group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
1147 | if(new_node_bot - new_node_top < gws.map.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) {
| ~~~~~~^~~~~~~~~~~~~~~~
group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
1213 | if(node_range.second - node_range.first < st.back().map_.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
hi_aligner.h: In instantiation of 'static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]':
hi_aligner.h:717:28: required from 'static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]'
717 | alignWithALTs_recur(
| ~~~~~~~~~~~~~~~~~~~^
718 | alts,
| ~~~~~
719 | haplotypes,
| ~~~~~~~~~~~
720 | haplotype_maxrights,
| ~~~~~~~~~~~~~~~~~~~~
721 | joinedOff,
| ~~~~~~~~~~
722 | rdseq,
| ~~~~~~
723 | rdoff - base_rdoff,
| ~~~~~~~~~~~~~~~~~~~
724 | rdoff,
| ~~~~~~
725 | rdlen,
| ~~~~~~
726 | ref,
| ~~~~
727 | sharedVar.raw_refbufs,
| ~~~~~~~~~~~~~~~~~~~~~~
728 | ASSERT_ONLY(sharedVar.destU32,)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | alt_edits,
| ~~~~~~~~~~
730 | best_rdoff,
| ~~~~~~~~~~~
731 | NULL, /* rfseq */
| ~~~~~~~~~~~~~~~~~
732 | tidx,
| ~~~~~
733 | rfoff,
| ~~~~~~
734 | rflen,
| ~~~~~~
735 | left,
| ~~~~~
736 | edits,
| ~~~~~~
737 | mm,
| ~~~
738 | ht_llist,
| ~~~~~~~~~
739 | cmp_ht,
| ~~~~~~~
740 | candidate_edits,
| ~~~~~~~~~~~~~~~~
741 | 0, /* tmp_numNs */
| ~~~~~~~~~~~~~~~~~~
742 | numNs,
| ~~~~~~
743 | 0, /* dep */
| ~~~~~~~~~~~~~~~
744 | gpol,
| ~~~~~
745 | numALTsTried);
| ~~~~~~~~~~~~~
hi_aligner.h:2337:47: required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]'
2337 | index_t alignedLen = alignWithALTs(
| ~~~~~~~~~~~~~^
2338 | alts,
| ~~~~~
2339 | altdb.haplotypes(),
| ~~~~~~~~~~~~~~~~~~~
2340 | altdb.haplotype_maxrights(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2341 | genomeHit._joinedOff,
| ~~~~~~~~~~~~~~~~~~~~~
2342 | seq,
| ~~~~
2343 | genomeHit._rdoff,
| ~~~~~~~~~~~~~~~~~
2344 | genomeHit._rdoff,
| ~~~~~~~~~~~~~~~~~
2345 | genomeHit._len,
| ~~~~~~~~~~~~~~~
2346 | ref,
| ~~~~
2347 | sharedVars,
| ~~~~~~~~~~~
2348 | genomeHit._tidx,
| ~~~~~~~~~~~~~~~~
2349 | (int)genomeHit._toff,
| ~~~~~~~~~~~~~~~~~~~~~
2350 | reflen,
| ~~~~~~~
2351 | false, /* left? */
| ~~~~~~~~~~~~~~~~~~
2352 | gpol,
| ~~~~~
2353 | *genomeHit._edits,
| ~~~~~~~~~~~~~~~~~~
2354 | sharedVars.ht_llist,
| ~~~~~~~~~~~~~~~~~~~~
2355 | *genomeHit._ht_list,
| ~~~~~~~~~~~~~~~~~~~~
2356 | sharedVars.cmp_ht,
| ~~~~~~~~~~~~~~~~~~
2357 | &candidate_edits);
| ~~~~~~~~~~~~~~~~~
hi_aligner.h:5692:54: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]'
5692 | GenomeHit<index_t>::adjustWithALT(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
5693 | hitoff - hitlen + 1,
| ~~~~~~~~~~~~~~~~~~~~
5694 | hitlen,
| ~~~~~~~
5695 | coord,
| ~~~~~~
5696 | _sharedVars,
| ~~~~~~~~~~~~
5697 | _genomeHits,
| ~~~~~~~~~~~~
5698 | *this->_rds[ordi],
| ~~~~~~~~~~~~~~~~~~
5699 | gfm,
| ~~~~
5700 | altdb,
| ~~~~~~
5701 | ref,
| ~~~~
5702 | gpol);
| ~~~~~
hi_aligner.h:4107:39: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]'
4107 | mate_found |= alignMate(
| ^~~~~~~~~
hisat2.cpp:3537:48: required from here
3537 | int ret = splicedAligner.go(
| ~~~~~~~~~~~~~~~~~^
3538 | sc,
| ~~~
3539 | pepol,
| ~~~~~~
3540 | *multiseed_tpol,
| ~~~~~~~~~~~~~~~~
3541 | *gpol,
| ~~~~~~
3542 | gfm,
| ~~~~
3543 | rgfm,
| ~~~~~
3544 | *altdb,
| ~~~~~~~
3545 | *repeatdb,
| ~~~~~~~~~~
3546 | *raltdb,
| ~~~~~~~~
3547 | ref,
| ~~~~
3548 | rref,
| ~~~~~
3549 | sw,
| ~~~
3550 | *ssdb,
| ~~~~~~
3551 | wlm,
| ~~~~
3552 | prm,
| ~~~~
3553 | swmSeed,
| ~~~~~~~~
3554 | him,
| ~~~~
3555 | rnd,
| ~~~~
3556 | msinkwrap);
| ~~~~~~~~~~
hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
2801 | if(rfoff >= contig_len) return 0;
| ~~~~~~^~~~~~~~~~~~~
hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
2879 | if(alt_range.first >= alts.size()) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
3044 | for(int i = 0; i < alt.len; i++) {
| ~~^~~~~~~~~
hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) {
| ~~~~~^~~~~~~~
hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
3161 | if(alignedLen == next_rdlen) return rdlen;
| ~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
3197 | if(mm_max_rd_i + rdoff > best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
3454 | if(best_rdoff < rdoff + rd_i) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~
group_walk.h: In instantiation of 'std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]':
group_walk.h:494:14: required from 'std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]'
494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met);
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
group_walk.h:1453:18: required from 'void GroupWalk2S<index_t, T, S>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]'
1453 | st_.back().init(
| ~~~~~~~~~~~~~~~^
1454 | gfmFw, // Bowtie index
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1455 | ref, // bitpair-encoded reference
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1456 | sa, // SA range with offsets
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1457 | st_, // EList<GWState>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1458 | hit_, // GWHit
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1459 | 0, // range 0
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1460 | false, // put resolved elements into res_?
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1461 | NULL, // put resolved elements here
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1462 | top, // GBW row at top
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1463 | bot, // GBW row at bot
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1464 | node_top, // node at top
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1465 | node_bot, // node at bot
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1466 | sa.node_iedge_count,
| ~~~~~~~~~~~~~~~~~~~~
1467 | 0, // # steps taken
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1468 | met); // update metrics here
| ~~~~
hi_aligner.h:5896:20: required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]'
5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hi_aligner.h:5664:17: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]'
5664 | getGenomeCoords_local(
| ^~~~~~~~~~~~~~~~~~~~~
hi_aligner.h:4107:39: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]'
4107 | mate_found |= alignMate(
| ^~~~~~~~~
hisat2.cpp:3537:48: required from here
3537 | int ret = splicedAligner.go(
| ~~~~~~~~~~~~~~~~~^
3538 | sc,
| ~~~
3539 | pepol,
| ~~~~~~
3540 | *multiseed_tpol,
| ~~~~~~~~~~~~~~~~
3541 | *gpol,
| ~~~~~~
3542 | gfm,
| ~~~~
3543 | rgfm,
| ~~~~~
3544 | *altdb,
| ~~~~~~~
3545 | *repeatdb,
| ~~~~~~~~~~
3546 | *raltdb,
| ~~~~~~~~
3547 | ref,
| ~~~~
3548 | rref,
| ~~~~~
3549 | sw,
| ~~~
3550 | *ssdb,
| ~~~~~~
3551 | wlm,
| ~~~~
3552 | prm,
| ~~~~
3553 | swmSeed,
| ~~~~~~~~
3554 | him,
| ~~~~
3555 | rnd,
| ~~~~
3556 | msinkwrap);
| ~~~~~~~~~~
group_walk.h:785:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) {
| ~~~~~~^~~~~~~~~~~~~~~~~~
group_walk.h:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
789 | if(new_top - top == tmp_gbwt_to_node.size()) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
group_walk.h:795:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
795 | if(i + 1 < tmp_zOffs.size()) {
| ~~~~~~^~~~~~~~~~~~~~~~~~
group_walk.h:801:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
801 | if(new_bot - top < tmp_gbwt_to_node.size()) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
hi_aligner.h: In instantiation of 'void add_haplotypes(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, Haplotype<index_t>&, EList<std::pair<_FIter, _FIter> >&, index_t, bool, bool) [with index_t = unsigned int]':
hi_aligner.h:2915:39: required from 'static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]'
2915 | add_haplotypes(alts,
| ~~~~~~~~~~~~~~^~~~~~
2916 | haplotypes,
| ~~~~~~~~~~~
2917 | haplotype_maxrights,
| ~~~~~~~~~~~~~~~~~~~~
2918 | cmp_ht,
| ~~~~~~~
2919 | ht_list,
| ~~~~~~~~
2920 | rdlen);
| ~~~~~~
hi_aligner.h:717:28: required from 'static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]'
717 | alignWithALTs_recur(
| ~~~~~~~~~~~~~~~~~~~^
718 | alts,
| ~~~~~
719 | haplotypes,
| ~~~~~~~~~~~
720 | haplotype_maxrights,
| ~~~~~~~~~~~~~~~~~~~~
721 | joinedOff,
| ~~~~~~~~~~
722 | rdseq,
| ~~~~~~
723 | rdoff - base_rdoff,
| ~~~~~~~~~~~~~~~~~~~
724 | rdoff,
| ~~~~~~
725 | rdlen,
| ~~~~~~
726 | ref,
| ~~~~
727 | sharedVar.raw_refbufs,
| ~~~~~~~~~~~~~~~~~~~~~~
728 | ASSERT_ONLY(sharedVar.destU32,)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | alt_edits,
| ~~~~~~~~~~
730 | best_rdoff,
| ~~~~~~~~~~~
731 | NULL, /* rfseq */
| ~~~~~~~~~~~~~~~~~
732 | tidx,
| ~~~~~
733 | rfoff,
| ~~~~~~
734 | rflen,
| ~~~~~~
735 | left,
| ~~~~~
736 | edits,
| ~~~~~~
737 | mm,
| ~~~
738 | ht_llist,
| ~~~~~~~~~
739 | cmp_ht,
| ~~~~~~~
740 | candidate_edits,
| ~~~~~~~~~~~~~~~~
741 | 0, /* tmp_numNs */
| ~~~~~~~~~~~~~~~~~~
742 | numNs,
| ~~~~~~
743 | 0, /* dep */
| ~~~~~~~~~~~~~~~
744 | gpol,
| ~~~~~
745 | numALTsTried);
| ~~~~~~~~~~~~~
hi_aligner.h:2337:47: required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]'
2337 | index_t alignedLen = alignWithALTs(
| ~~~~~~~~~~~~~^
2338 | alts,
| ~~~~~
2339 | altdb.haplotypes(),
| ~~~~~~~~~~~~~~~~~~~
2340 | altdb.haplotype_maxrights(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2341 | genomeHit._joinedOff,
| ~~~~~~~~~~~~~~~~~~~~~
2342 | seq,
| ~~~~
2343 | genomeHit._rdoff,
| ~~~~~~~~~~~~~~~~~
2344 | genomeHit._rdoff,
| ~~~~~~~~~~~~~~~~~
2345 | genomeHit._len,
| ~~~~~~~~~~~~~~~
2346 | ref,
| ~~~~
2347 | sharedVars,
| ~~~~~~~~~~~
2348 | genomeHit._tidx,
| ~~~~~~~~~~~~~~~~
2349 | (int)genomeHit._toff,
| ~~~~~~~~~~~~~~~~~~~~~
2350 | reflen,
| ~~~~~~~
2351 | false, /* left? */
| ~~~~~~~~~~~~~~~~~~
2352 | gpol,
| ~~~~~
2353 | *genomeHit._edits,
| ~~~~~~~~~~~~~~~~~~
2354 | sharedVars.ht_llist,
| ~~~~~~~~~~~~~~~~~~~~
2355 | *genomeHit._ht_list,
| ~~~~~~~~~~~~~~~~~~~~
2356 | sharedVars.cmp_ht,
| ~~~~~~~~~~~~~~~~~~
2357 | &candidate_edits);
| ~~~~~~~~~~~~~~~~~
hi_aligner.h:5692:54: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]'
5692 | GenomeHit<index_t>::adjustWithALT(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
5693 | hitoff - hitlen + 1,
| ~~~~~~~~~~~~~~~~~~~~
5694 | hitlen,
| ~~~~~~~
5695 | coord,
| ~~~~~~
5696 | _sharedVars,
| ~~~~~~~~~~~~
5697 | _genomeHits,
| ~~~~~~~~~~~~
5698 | *this->_rds[ordi],
| ~~~~~~~~~~~~~~~~~~
5699 | gfm,
| ~~~~
5700 | altdb,
| ~~~~~~
5701 | ref,
| ~~~~
5702 | gpol);
| ~~~~~
hi_aligner.h:4107:39: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]'
4107 | mate_found |= alignMate(
| ^~~~~~~~~
hisat2.cpp:3537:48: required from here
3537 | int ret = splicedAligner.go(
| ~~~~~~~~~~~~~~~~~^
3538 | sc,
| ~~~
3539 | pepol,
| ~~~~~~
3540 | *multiseed_tpol,
| ~~~~~~~~~~~~~~~~
3541 | *gpol,
| ~~~~~~
3542 | gfm,
| ~~~~
3543 | rgfm,
| ~~~~~
3544 | *altdb,
| ~~~~~~~
3545 | *repeatdb,
| ~~~~~~~~~~
3546 | *raltdb,
| ~~~~~~~~
3547 | ref,
| ~~~~
3548 | rref,
| ~~~~~
3549 | sw,
| ~~~
3550 | *ssdb,
| ~~~~~~
3551 | wlm,
| ~~~~
3552 | prm,
| ~~~~
3553 | swmSeed,
| ~~~~~~~~
3554 | him,
| ~~~~
3555 | rnd,
| ~~~~
3556 | msinkwrap);
| ~~~~~~~~~~
hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
2660 | if(ht_range.first >= haplotypes.size())
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
2675 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
2713 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
2744 | if(ht_list[h].first == ht_range.second) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
spliced_aligner.h: In instantiation of 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]':
spliced_aligner.h:331:9: required from here
331 | int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spliced_aligner.h:408:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable]
408 | bool another_spliced = false;
| ^~~~~~~~~~~~~~~
hi_aligner.h: In instantiation of 'bool GenomeHit<index_t>::combineWith(const GenomeHit<index_t>&, const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long long int]':
spliced_aligner.h:494:60: required from 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]'
494 | bool combined = tempHit.combineWith(
| ~~~~~~~~~~~~~~~~~~~^
495 | hit,
| ~~~~
496 | rd,
| ~~~
497 | gfm,
| ~~~~
498 | ref,
| ~~~~
499 | altdb,
| ~~~~~~
500 | repeatdb,
| ~~~~~~~~~
501 | ssdb,
| ~~~~~
502 | swa,
| ~~~~
503 | swm,
| ~~~~
504 | sc,
| ~~~
505 | minsc,
| ~~~~~~
506 | rnd,
| ~~~~
507 | (index_t)this->_minK_local,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
508 | (index_t)tpol.minIntronLen(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
509 | (index_t)tpol.maxIntronLen(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
510 | 1,
| ~~
511 | 1,
| ~~
512 | gpol.maxAltsTried(),
| ~~~~~~~~~~~~~~~~~~~~
513 | &ss,
| ~~~~
514 | tpol.no_spliced_alignment());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spliced_aligner.h:331:9: required from here
331 | int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: 'const uint64_t' {aka 'const long long unsigned int'} and 'char' [-Wsign-compare]
1926 | if(alt.seq == rdc) {
| ~~~~~~~~^~~~~~
ref_read.cpp: In function 'std::pair<long long unsigned int, long long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)':
ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
367 | if(i + 1 >= recs.size() || recs[i+1].first) {
| ~~~~~~^~~~~~~~~~~~~~
ref_read.cpp: In function 'std::pair<long long unsigned int, long long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)':
ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long long int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
440 | if(i + 1 >= recs.size() || recs[i+1].first) {
| ~~~~~~^~~~~~~~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.cpp:522:26: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
522 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:516:14: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
516 | bool binarySearched = false;
| ^~~~~~~~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
from aligner_sw.cpp:25:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_sw.h:81:
aligner_sw_nuc.h: At global scope:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
from aligner_swsse_loc_i16.cpp:56:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_sw.h:81:
aligner_sw_nuc.h: At global scope:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
from aligner_swsse_ee_i16.cpp:56:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_sw.h:81:
aligner_sw_nuc.h: At global scope:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
from aligner_swsse_loc_u8.cpp:56:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_sw.h:81:
aligner_sw_nuc.h: At global scope:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
from aligner_swsse_ee_u8.cpp:56:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_sw.h:81:
aligner_sw_nuc.h: At global scope:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
191 | NBest<T>() { nelt_ = nbest_ = n_ = 0; }
| ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)':
gfm.h:1185:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1185 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/memory:78,
from gfm.h:28:
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
1189 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
C:/rtools45/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/14.2.0/include/c++/bits/unique_ptr.h:59:28: note: declared here
59 | template<typename> class auto_ptr;
| ^~~~~~~~
splice_site.cpp: In member function 'void SpliceSiteDB::read(const GFM<unsigned int>&, const EList<ALT<unsigned int> >&)':
splice_site.cpp:717:59: warning: '?:' using integer constants in boolean context, the expression will always evaluate to 'true' [-Wint-in-bool-context]
717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from edit.h:29:
ds.h: In instantiation of 'void EList<T, S>::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long long unsigned int]':
splice_site.cpp:722:31: required from here
722 | _exons.push_back_array(exons.begin(), exons.size());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ds.h:663:28: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class Exon'; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
663 | std::memcpy(list_ + cur_, l, bytes);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
splice_site.h:377:7: note: 'class Exon' declared here
377 | class Exon {
| ^~~~
echo "@echo off" > hisat2.bat
echo "perl %~dp0/hisat2 %*" >> hisat2.bat
echo "@echo off" > hisat2-build.bat
echo "python %~dp0/hisat2-build %*" >> hisat2-build.bat
echo "@echo off" > hisat2-inspect.bat
echo "python %~dp0/hisat2-inspect %*" >> hisat2-inspect.bat
mkdir -p ../inst
cp hisat2-align-s ../inst/hisat2
cp hisat2-build-s ../inst/hisat2-build
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rhisat2)
Rhisat2.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Rhisat2)
>
> test_check("Rhisat2")
*** Warning ***
'hisat2-build-s' was run directly. It is recommended that you run the wrapper script 'hisat2-build' instead.
[1] "HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)"
[2] "Usage: hisat2-build [options]* <reference_in> <ht2_index_base>"
[3] " reference_in comma-separated list of files with ref sequences"
[4] " hisat2_index_base write ht2 data to files with this dir/basename"
[5] "Options:"
[6] " -c reference sequences given on cmd line (as"
[7] " <reference_in>)"
[8] " -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting"
[9] " -p <int> number of threads"
[10] " --bmax <int> max bucket sz for blockwise suffix-array builder"
[11] " --bmaxdivn <int> max bucket sz as divisor of ref len (default: 4)"
[12] " --dcv <int> diff-cover period for blockwise (default: 1024)"
[13] " --nodc disable diff-cover (algorithm becomes quadratic)"
[14] " -r/--noref don't build .3/.4.ht2 (packed reference) portion"
[15] " -3/--justref just build .3/.4.ht2 (packed reference) portion"
[16] " -o/--offrate <int> SA is sampled every 2^offRate BWT chars (default: 5)"
[17] " -t/--ftabchars <int> # of chars consumed in initial lookup (default: 10)"
[18] " --localoffrate <int> SA (local) is sampled every 2^offRate BWT chars (default: 3)"
[19] " --localftabchars <int> # of chars consumed in initial lookup in a local index (default: 6)"
[20] " --snp <path> SNP file name"
[21] " --haplotype <path> haplotype file name"
[22] " --ss <path> Splice site file name"
[23] " --exon <path> Exon file name"
[24] " --repeat-ref <path> Repeat reference file name"
[25] " --repeat-info <path> Repeat information file name"
[26] " --repeat-snp <path> Repeat snp file name"
[27] " --repeat-haplotype <path> Repeat haplotype file name"
[28] " --seed <int> seed for random number generator"
[29] " -q/--quiet disable verbose output (for debugging)"
[30] " -h/--help print detailed description of tool and its options"
[31] " --usage print this usage message"
[32] " --version print version information and quit"
*** Warning ***
'hisat2-align' was run directly. It is recommended that you run the wrapper script 'hisat2' instead.
[1] "HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)"
[2] "Usage: "
[3] " hisat2-align [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]"
[4] ""
[5] " <ht2-idx> Index filename prefix (minus trailing .X.ht2)."
[6] " <m1> Files with #1 mates, paired with files in <m2>."
[7] " <m2> Files with #2 mates, paired with files in <m1>."
[8] " <r> Files with unpaired reads."
[9] " <sam> File for SAM output (default: stdout)"
[10] ""
[11] " <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be"
[12] " specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'."
[13] ""
[14] "Options (defaults in parentheses):"
[15] ""
[16] " Input:"
[17] " -q query input files are FASTQ .fq/.fastq (default)"
[18] " --qseq query input files are in Illumina's qseq format"
[19] " -f query input files are (multi-)FASTA .fa/.mfa"
[20] " -r query input files are raw one-sequence-per-line"
[21] " -c <m1>, <m2>, <r> are sequences themselves, not files"
[22] " -s/--skip <int> skip the first <int> reads/pairs in the input (none)"
[23] " -u/--upto <int> stop after first <int> reads/pairs (no limit)"
[24] " -5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)"
[25] " -3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)"
[26] " --phred33 qualities are Phred+33 (default)"
[27] " --phred64 qualities are Phred+64"
[28] " --int-quals qualities encoded as space-delimited integers"
[29] ""
[30] " Presets: Same as:"
[31] " --fast --no-repeat-index"
[32] " --sensitive --bowtie2-dp 1 -k 30 --score-min L,0,-0.5"
[33] " --very-sensitive --bowtie2-dp 2 -k 50 --score-min L,0,-1"
[34] ""
[35] " Alignment:"
[36] " --bowtie2-dp <int> use Bowtie2's dynamic programming alignment algorithm (0) - 0: no dynamic programming, 1: conditional dynamic programming, and 2: unconditional dynamic programming (slowest)"
[37] " --n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)"
[38] " --ignore-quals treat all quality values as 30 on Phred scale (off)"
[39] " --nofw do not align forward (original) version of read (off)"
[40] " --norc do not align reverse-complement version of read (off)"
[41] " --no-repeat-index do not use repeat index"
[42] ""
[43] " Spliced Alignment:"
[44] " --pen-cansplice <int> penalty for a canonical splice site (0)"
[45] " --pen-noncansplice <int> penalty for a non-canonical splice site (12)"
[46] " --pen-canintronlen <func> penalty for long introns (G,-8,1) with canonical splice sites"
[47] " --pen-noncanintronlen <func> penalty for long introns (G,-8,1) with noncanonical splice sites"
[48] " --min-intronlen <int> minimum intron length (20)"
[49] " --max-intronlen <int> maximum intron length (500000)"
[50] " --known-splicesite-infile <path> provide a list of known splice sites"
[51] " --novel-splicesite-outfile <path> report a list of splice sites"
[52] " --novel-splicesite-infile <path> provide a list of novel splice sites"
[53] " --no-temp-splicesite disable the use of splice sites found"
[54] " --no-spliced-alignment disable spliced alignment"
[55] " --rna-strandness <string> specify strand-specific information (unstranded)"
[56] " --tmo reports only those alignments within known transcriptome"
[57] " --dta reports alignments tailored for transcript assemblers"
[58] " --dta-cufflinks reports alignments tailored specifically for cufflinks"
[59] " --avoid-pseudogene tries to avoid aligning reads to pseudogenes (experimental option)"
[60] " --no-templatelen-adjustment disables template length adjustment for RNA-seq reads"
[61] ""
[62] " Scoring:"
[63] " --mp <int>,<int> max and min penalties for mismatch; lower qual = lower penalty <6,2>"
[64] " --sp <int>,<int> max and min penalties for soft-clipping; lower qual = lower penalty <2,1>"
[65] " --no-softclip no soft-clipping"
[66] " --np <int> penalty for non-A/C/G/Ts in read/ref (1)"
[67] " --rdg <int>,<int> read gap open, extend penalties (5,3)"
[68] " --rfg <int>,<int> reference gap open, extend penalties (5,3)"
[69] " --score-min <func> min acceptable alignment score w/r/t read length"
[70] " (L,0.0,-0.2)"
[71] ""
[72] " Reporting:"
[73] " -k <int> It searches for at most <int> distinct, primary alignments for each read. Primary alignments mean "
[74] " alignments whose alignment score is equal to or higher than any other alignments. The search terminates "
[75] " when it cannot find more distinct valid alignments, or when it finds <int>, whichever happens first. "
[76] " The alignment score for a paired-end alignment equals the sum of the alignment scores of "
[77] " the individual mates. Each reported read or pair alignment beyond the first has the SAM ‘secondary’ bit "
[78] " (which equals 256) set in its FLAGS field. For reads that have more than <int> distinct, "
[79] " valid alignments, hisat2 does not guarantee that the <int> alignments reported are the best possible "
[80] " in terms of alignment score. Default: 5 (linear index) or 10 (graph index)."
[81] " Note: HISAT2 is not designed with large values for -k in mind, and when aligning reads to long, "
[82] " repetitive genomes, large -k could make alignment much slower."
[83] " --max-seeds <int> HISAT2, like other aligners, uses seed-and-extend approaches. HISAT2 tries to extend seeds to "
[84] " full-length alignments. In HISAT2, --max-seeds is used to control the maximum number of seeds that "
[85] " will be extended. For DNA-read alignment (--no-spliced-alignment), HISAT2 extends up to these many seeds"
[86] " and skips the rest of the seeds. For RNA-read alignment, HISAT2 skips extending seeds and reports "
[87] " no alignments if the number of seeds is larger than the number specified with the option, "
[88] " to be compatible with previous versions of HISAT2. Large values for --max-seeds may improve alignment "
[89] " sensitivity, but HISAT2 is not designed with large values for --max-seeds in mind, and when aligning "
[90] " reads to long, repetitive genomes, large --max-seeds could make alignment much slower. "
[91] " The default value is the maximum of 5 and the value that comes with -k times 2."
[92] " -a/--all HISAT2 reports all alignments it can find. Using the option is equivalent to using both --max-seeds "
[93] " and -k with the maximum value that a 64-bit signed integer can represent (9,223,372,036,854,775,807)."
[94] " --repeat report alignments to repeat sequences directly"
[95] ""
[96] " Paired-end:"
[97] " -I/--minins <int> minimum fragment length (0), only valid with --no-spliced-alignment"
[98] " -X/--maxins <int> maximum fragment length (500), only valid with --no-spliced-alignment"
[99] " --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)"
[100] " --no-mixed suppress unpaired alignments for paired reads"
[101] " --no-discordant suppress discordant alignments for paired reads"
[102] ""
[103] " Output:"
[104] " -t/--time print wall-clock time taken by search phases"
[105] " --summary-file <path> print alignment summary to this file."
[106] " --new-summary print alignment summary in a new style, which is more machine-friendly."
[107] " --quiet print nothing to stderr except serious errors"
[108] " --met-file <path> send metrics to file at <path> (off)"
[109] " --met-stderr send metrics to stderr (off)"
[110] " --met <int> report internal counters & metrics every <int> secs (1)"
[111] " --no-head suppress header lines, i.e. lines starting with @"
[112] " --no-sq suppress @SQ header lines"
[113] " --rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field"
[114] " --rg <text> add <text> (\"lab:value\") to @RG line of SAM header."
[115] " Note: @RG line only printed when --rg-id is set."
[116] " --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments."
[117] ""
[118] " Performance:"
[119] " -o/--offrate <int> override offrate of index; must be >= index's offrate"
[120] " -p/--threads <int> number of alignment threads to launch (1)"
[121] " --reorder force SAM output order to match order of input reads"
[122] ""
[123] " Other:"
[124] " --qc-filter filter out reads that are bad according to QSEQ filter"
[125] " --seed <int> seed for random number generator (0)"
[126] " --non-deterministic seed rand. gen. arbitrarily instead of using read attributes"
[127] " --remove-chrname remove 'chr' from reference names in alignment"
[128] " --add-chrname add 'chr' to reference names in alignment "
[129] " --version print version information and quit"
[130] " -h/--help print this usage message"
[1] "F:\\biocbuild\\bbs-3.22-bioc\\R\\library\\Rhisat2\\hisat2.exe version 2.2.1"
[2] "64-bit"
[3] "Built on palomino8"
[4] "Thu Aug 14 16:44:18 EDT 2025"
[5] "Compiler: gcc version 14.2.0 (GCC) "
[6] "Options: -O3 -m64 -msse2 -funroll-loops -g3 -std=c++11"
[7] "Sizeof {int, long, long long, void*, size_t, off_t}: {4, 4, 8, 8, 8, 8}"
Settings:
Output files: "F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.*.ht2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:4, size_t:8
Input files DNA, FASTA:
F:/biocbuild/bbs-3.22-bioc/R/library/Rhisat2/extdata/refs/chr1.fa
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 18650 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 18650 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 26955
fchr[G]: 49554
fchr[T]: 72459
fchr[$]: 99465
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4227718 bytes to primary GFM file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 45363 bytes to primary GFM file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
len: 99465
gbwtLen: 99466
nodes: 99466
sz: 24867
gbwtSz: 24867
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 0
eftabSz: 0
ftabLen: 1048577
ftabSz: 4194308
offsLen: 6217
offsSz: 24868
lineSz: 64
sideSz: 64
sideGbwtSz: 48
sideGbwtLen: 192
numSides: 519
numLines: 519
gbwtTotLen: 33216
gbwtTotSz: 33216
reverse: 0
linearFM: Yes
Total time for call to driver() for forward index: 00:00:00
Settings:
Output files: "F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.*.ht2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:4, size_t:8
Input files DNA, FASTA:
F:/biocbuild/bbs-3.22-bioc/R/library/Rhisat2/extdata/refs/chr1.fa
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 18650 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 18650 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 26955
fchr[G]: 49554
fchr[T]: 72459
fchr[$]: 99465
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4227718 bytes to primary GFM file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 45363 bytes to primary GFM file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: F:\biocbuild\bbs-3.22-bioc\tmpdir\Rtmp0KJtS6/hisat2indexdir/index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
len: 99465
gbwtLen: 99466
nodes: 99466
sz: 24867
gbwtSz: 24867
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 0
eftabSz: 0
ftabLen: 1048577
ftabSz: 4194308
offsLen: 6217
offsSz: 24868
lineSz: 64
sideSz: 64
sideGbwtSz: 48
sideGbwtLen: 192
numSides: 519
numLines: 519
gbwtTotLen: 33216
gbwtTotSz: 33216
reverse: 0
linearFM: Yes
Total time for call to driver() for forward index: 00:00:00
4 reads; of these:
4 (100.00%) were paired; of these:
4 (100.00%) aligned concordantly 0 times
0 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
4 pairs aligned concordantly 0 times; of these:
2 (50.00%) aligned discordantly 1 time
----
2 pairs aligned 0 times concordantly or discordantly; of these:
4 mates make up the pairs; of these:
4 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
50.00% overall alignment rate
4 reads; of these:
4 (100.00%) were unpaired; of these:
2 (50.00%) aligned 0 times
2 (50.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
50.00% overall alignment rate
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 59 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 59 ]
>
> proc.time()
user system elapsed
23.25 1.43 26.42
Rhisat2.Rcheck/Rhisat2-Ex.timings
| name | user | system | elapsed | |
| extract_splice_sites | 3.70 | 0.14 | 3.84 | |
| hisat2 | 0.00 | 0.03 | 0.63 | |
| hisat2_build | 0.00 | 0.03 | 0.47 | |
| hisat2_build_usage | 0.00 | 0.00 | 0.25 | |
| hisat2_usage | 0.00 | 0.03 | 0.28 | |
| hisat2_version | 0.00 | 0.00 | 0.25 | |