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This page was generated on 2023-01-02 09:00:47 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for Rhisat2 on palomino5


To the developers/maintainers of the Rhisat2 package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1657/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhisat2 1.15.0  (landing page)
Charlotte Soneson
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/Rhisat2
git_branch: master
git_last_commit: c237dc8
git_last_commit_date: 2022-11-01 11:19:06 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: Rhisat2
Version: 1.15.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhisat2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Rhisat2_1.15.0.tar.gz
StartedAt: 2022-12-29 02:52:28 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 02:55:44 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 195.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Rhisat2.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rhisat2.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Rhisat2_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Rhisat2.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.15.0'
* 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]
  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-3.17-bioc-rtools43/meat/Rhisat2.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 60.5Mb
* 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 R 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 ... NOTE
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 in 'inst/doc' ... 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, 3 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Rhisat2.Rcheck/00check.log'
for details.

Installation output

Rhisat2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Rhisat2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'Rhisat2' ...
** 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="\"palomino5\"" -DBUILD_TIME="\"Wed Dec 28 15:52:32 EST 2022\"" -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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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]'
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]'
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>]'
hisat2_build.cpp:786:39:   required from here
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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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="\"palomino5\"" -DBUILD_TIME="\"Wed Dec 28 15:53:40 EST 2022\"" -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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from spliced_aligner.h:23,
                 from hisat2.cpp:46:
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]'
hisat2.cpp:3537:48:   required from here
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>]'
hisat2.cpp:4351:26:   required from here
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]'
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]'
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]'
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]'
hisat2.cpp:3537:48:   required from here
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>]'
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]'
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]'
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]'
hisat2.cpp:3537:48:   required from here
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>]'
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]'
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]'
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]'
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]'
hisat2.cpp:3537:48:   required from here
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>]'
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>]'
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]'
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]'
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]'
hisat2.cpp:3537:48:   required from here
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
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]'
spliced_aligner.h:331:9:   required from here
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) {
      |                        ~~~~~~~~^~~~~~
In file included from gfm.h:59:
In member function 'bool RepeatCoord<index_t>::operator<(const RepeatCoord<index_t>&) const [with index_t = unsigned int]',
    inlined from 'bool RepeatCoord<index_t>::operator<(const RepeatCoord<index_t>&) const [with index_t = unsigned int]' at repeat.h:38:10,
    inlined from 'size_t EList<T, S>::bsearchLoBound(const T&) const [with T = RepeatCoord<unsigned int>; int S = 128]' at ds.h:919:18,
    inlined from 'bool RepeatDB<index_t>::findCoords(index_t, index_t, index_t, index_t, index_t, const EList<T>&, const ALTDB<index_t>&, EList<std::pair<RepeatCoord<index_t>, RepeatCoord<index_t> > >&, index_t, index_t) const [with index_t = unsigned int]' at repeat.h:466:45,
    inlined 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]' at hi_aligner.h:4391:44:
repeat.h:41:20: warning: 'cmp.RepeatCoord<unsigned int>::fw' may be used uninitialized [-Wmaybe-uninitialized]
   41 |         if(fw != o.fw)
      |                  ~~^~
repeat.h: In member function '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]':
repeat.h:464:30: note: 'cmp' declared here
  464 |         RepeatCoord<index_t> cmp;
      |                              ^~~
In member function 'bool RepeatCoord<index_t>::operator<(const RepeatCoord<index_t>&) const [with index_t = unsigned int]',
    inlined from 'bool RepeatCoord<index_t>::operator<(const RepeatCoord<index_t>&) const [with index_t = unsigned int]' at repeat.h:38:10,
    inlined from 'size_t EList<T, S>::bsearchLoBound(const T&) const [with T = RepeatCoord<unsigned int>; int S = 128]' at ds.h:919:18,
    inlined from 'bool RepeatDB<index_t>::findCoords(index_t, index_t, index_t, index_t, index_t, const EList<T>&, const ALTDB<index_t>&, EList<std::pair<RepeatCoord<index_t>, RepeatCoord<index_t> > >&, index_t, index_t) const [with index_t = unsigned int]' at repeat.h:466:45,
    inlined 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]' at hi_aligner.h:4391:44:
repeat.h:43:26: warning: 'cmp.RepeatCoord<unsigned int>::alleleID' may be used uninitialized [-Wmaybe-uninitialized]
   43 |         if(alleleID != o.alleleID)
      |                        ~~^~~~~~~~
repeat.h: In member function '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]':
repeat.h:464:30: note: 'cmp' declared here
  464 |         RepeatCoord<index_t> cmp;
      |                              ^~~
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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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_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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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_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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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_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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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_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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from gfm.h:28:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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
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)

Tests output

Rhisat2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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-3.17-bioc\\R\\library\\Rhisat2\\hisat2.exe version 2.2.1"
[2] "64-bit"                                                                     
[3] "Built on palomino5"                                                         
[4] "Wed Dec 28 15:53:40 EST 2022"                                               
[5] "Compiler: gcc version 12.2.0 (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-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/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-3.17-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-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/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-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/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: 00:00:01
Settings:
  Output files: "F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/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-3.17-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-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/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-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpyuuylZ/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 0 | SKIP 0 | PASS 59 ]
> 
> proc.time()
   user  system elapsed 
  13.95    0.85   16.39

Example timings

Rhisat2.Rcheck/Rhisat2-Ex.timings

nameusersystemelapsed
extract_splice_sites2.170.052.22
hisat20.000.000.52
hisat2_build0.010.020.26
hisat2_build_usage0.000.000.25
hisat2_usage0.000.030.27
hisat2_version0.000.000.23