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This page was generated on 2023-01-28 11:09:40 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4465
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4246
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4269
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Rhisat2 on merida1


To the developers/maintainers of the Rhisat2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhisat2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1660/2162HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhisat2 1.15.0  (landing page)
Charlotte Soneson
Snapshot Date: 2023-01-27 14:00:19 -0500 (Fri, 27 Jan 2023)
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)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    NA  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Rhisat2
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rhisat2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rhisat2_1.15.0.tar.gz
StartedAt: 2023-01-28 05:46:41 -0500 (Sat, 28 Jan 2023)
EndedAt: 2023-01-28 05:56:16 -0500 (Sat, 28 Jan 2023)
EllapsedTime: 575.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Rhisat2.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rhisat2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rhisat2_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Rhisat2.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rhisat2’ can be installed ... WARNING
Found the following significant warnings:
  ./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
  ./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
  hisat2.cpp:1823:2: warning: 'auto_ptr<Presets>' is deprecated [-Wdeprecated-declarations]
  hisat2.cpp:3167:2: warning: 'auto_ptr<PatternSourcePerThreadFactory>' is deprecated [-Wdeprecated-declarations]
  hisat2.cpp:3168:2: warning: 'auto_ptr<PatternSourcePerThread>' is deprecated [-Wdeprecated-declarations]
  hisat2.cpp:3189:2: warning: 'auto_ptr<Mapq>' is deprecated [-Wdeprecated-declarations]
  hisat2.cpp:4035:9: warning: 'auto_ptr<BitPairReference>' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.17-bioc/meat/Rhisat2.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
extract_splice_sites 5.229  0.178   6.698
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/Rhisat2.Rcheck/00check.log’
for details.



Installation output

Rhisat2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhisat2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘Rhisat2’ ...
** using staged installation
** libs
/usr/bin/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="\"merida1.bioconductor.org\"" -DBUILD_TIME="\"Fri Jan 27 15:34:42 EST 2023\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DUSESIMDE -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 \
	-lpthread 
In file included from hisat2_build.cpp:35:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from hisat2_build.cpp:35:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from gfm.cpp:21:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from gfm.cpp:21:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
/usr/bin/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="\"merida1.bioconductor.org\"" -DBUILD_TIME="\"Fri Jan 27 15:36:22 EST 2023\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DUSESIMDE  -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 \
	-lpthread  
In file included from hisat2.cpp:33:
In file included from ./hgfm.h:24:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from hisat2.cpp:33:
In file included from ./hgfm.h:24:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
hisat2.cpp:1823:2: warning: 'auto_ptr<Presets>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<Presets> presets(new PresetsV0());
        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<Presets>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
hisat2.cpp:3167:2: warning: 'auto_ptr<PatternSourcePerThreadFactory>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<PatternSourcePerThreadFactory>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
hisat2.cpp:3168:2: warning: 'auto_ptr<PatternSourcePerThread>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<PatternSourcePerThread>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
hisat2.cpp:3189:2: warning: 'auto_ptr<Mapq>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<Mapq>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
hisat2.cpp:4035:9: warning: 'auto_ptr<BitPairReference>' is deprecated [-Wdeprecated-declarations]
        auto_ptr<BitPairReference> refs(
        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<BitPairReference>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
7 warnings generated.
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from gfm.cpp:21:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from gfm.cpp:21:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_seed.cpp:21:
In file included from ./aligner_seed.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_seed.cpp:21:
In file included from ./aligner_seed.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_sw.cpp:25:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_sw.cpp:25:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_result.cpp:22:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_result.cpp:22:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aln_sink.cpp:22:
In file included from ./aln_sink.h:25:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aln_sink.cpp:22:
In file included from ./aln_sink.h:25:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from unique.cpp:20:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from unique.cpp:20:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_bt.cpp:20:
In file included from ./aligner_bt.h:25:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_bt.cpp:20:
In file included from ./aligner_bt.h:25:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_swsse.cpp:21:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_swsse.cpp:21:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_swsse_loc_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_swsse_loc_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_swsse_ee_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_swsse_ee_i16.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_swsse_loc_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_swsse_loc_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_swsse_ee_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_swsse_ee_u8.cpp:56:
In file included from ./aligner_sw.h:80:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from aligner_driver.cpp:20:
In file included from ./aligner_driver.h:78:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from aligner_driver.cpp:20:
In file included from ./aligner_driver.h:78:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:30:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
In file included from splice_site.cpp:20:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1185:3: warning: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' is deprecated [-Wdeprecated-declarations]
                auto_ptr<stringstream> ss(new stringstream());
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from splice_site.cpp:20:
In file included from ./edit.h:30:
In file included from ./splice_site.h:34:
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
                auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
                ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
mkdir -p ../inst
cp hisat2-align-s ../inst/hisat2
cp hisat2-build-s ../inst/hisat2-build
/usr/bin/g++ -shared -fPIC -o Rhisat2.so get_info.cpp
installing to /Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-Rhisat2/00new/Rhisat2/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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] "  --mm               use memory-mapped I/O for index; many 'hisat2's can share"                                                                                                                    
[123] ""                                                                                                                                                                                                  
[124] " Other:"                                                                                                                                                                                           
[125] "  --qc-filter        filter out reads that are bad according to QSEQ filter"                                                                                                                       
[126] "  --seed <int>       seed for random number generator (0)"                                                                                                                                         
[127] "  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes"                                                                                                                
[128] "  --remove-chrname   remove 'chr' from reference names in alignment"                                                                                                                               
[129] "  --add-chrname      add 'chr' to reference names in alignment "                                                                                                                                   
[130] "  --version          print version information and quit"                                                                                                                                           
[131] "  -h/--help          print this usage message"                                                                                                                                                     
[1] "/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhisat2/hisat2 version 2.2.1"
[2] "64-bit"                                                                                     
[3] "Built on merida1.bioconductor.org"                                                          
[4] "Fri Jan 27 15:36:22 EST 2023"                                                               
[5] "Compiler: InstalledDir: /Library/Developer/CommandLineTools/usr/bin"                        
[6] "Options: -O3 -m64 -msse2 -funroll-loops -g3 -std=c++11"                                     
[7] "Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}"                    
Settings:
  Output files: "/tmp/RtmpFtiD9i/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:8, size_t:8
Input files DNA, FASTA:
  /Library/Frameworks/R.framework/Versions/4.3/Resources/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: /tmp/RtmpFtiD9i/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: /tmp/RtmpFtiD9i/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: /tmp/RtmpFtiD9i/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: /tmp/RtmpFtiD9i/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: "/tmp/RtmpFtiD9i/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:8, size_t:8
Input files DNA, FASTA:
  /Library/Frameworks/R.framework/Versions/4.3/Resources/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: /tmp/RtmpFtiD9i/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: /tmp/RtmpFtiD9i/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: /tmp/RtmpFtiD9i/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: /tmp/RtmpFtiD9i/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 
 36.898   1.311  46.998 

Example timings

Rhisat2.Rcheck/Rhisat2-Ex.timings

nameusersystemelapsed
extract_splice_sites5.2290.1786.698
hisat20.3110.0540.389
hisat2_build0.2910.0350.343
hisat2_build_usage0.0050.0040.015
hisat2_usage0.0090.0060.020
hisat2_version0.0060.0050.014