Charlotte Soneson
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/Rhisat2 |
| git_branch: RELEASE_3_21 |
| git_last_commit: bc31541 |
| git_last_commit_date: 2025-04-15 11:40:26 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1779/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rhisat2 1.24.0 (landing page) Charlotte Soneson
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the Rhisat2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhisat2.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: Rhisat2 |
| Version: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2025-04-21 23:03:20 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 23:08:23 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 302.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rhisat2.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### 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_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Rhisat2.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhisat2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhisat2’ version ‘1.24.0’
* 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
./gfm.h:1189:3: warning: 'auto_ptr<FileBuf>' is deprecated [-Wdeprecated-declarations]
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
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-3.21-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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/Rhisat2.Rcheck/00check.log’
for details.
Rhisat2.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhisat2
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Rhisat2’ ...
** this is package ‘Rhisat2’ version ‘1.24.0’
** 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="\"lconway\"" -DBUILD_TIME="\"Mon Apr 21 15:36:22 EDT 2025\"" -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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
In file included from hisat2_build.cpp:35:
./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
3 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:31:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 warnings generated.
In file included from gfm.cpp:21:
./gfm.h:1185:3: warning: 'auto_ptr<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
In file included from gfm.cpp:21:
./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
3 warnings generated.
reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
uint64_t origBufOff = bufOff;
^
reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
bool binarySearched = false;
^
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="\"lconway\"" -DBUILD_TIME="\"Mon Apr 21 15:37:01 EDT 2025\"" -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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from hisat2.cpp:46:
In file included from ./spliced_aligner.h:23:
In file included from ./hi_aligner.h:42:
./aligner_sw_driver.h:1597:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable]
int64_t pastedRefoff = (int64_t)wr.toff - rdoff;
^
./aligner_sw_driver.h:2295:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable]
int64_t pastedRefoff = (int64_t)wr.toff - rdoff;
^
In file included from hisat2.cpp:46:
./spliced_aligner.h:408:18: warning: variable 'another_spliced' set but not used [-Wunused-but-set-variable]
bool another_spliced = false;
^
hisat2.cpp:1823:2: warning: 'auto_ptr<Presets>' is deprecated [-Wdeprecated-declarations]
auto_ptr<Presets> presets(new PresetsV0());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<Presets>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<PatternSourcePerThreadFactory>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<PatternSourcePerThread>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<Mapq>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<BitPairReference>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
In file included from hisat2.cpp:38:
In file included from ./aln_sink.h:24:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
In file included from hisat2.cpp:38:
In file included from ./aln_sink.h:24:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./pat.h:1298:6: note: in instantiation of function template specialization 'itoa10<unsigned long long>' requested here
itoa10<TReadId>(readCnt_ - subReadCnt_, cbuf);
^
In file included from hisat2.cpp:38:
In file included from ./aln_sink.h:24:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./sam.h:705:9: note: in instantiation of function template specialization 'itoa10<unsigned int>' requested here
itoa10<uint32_t>(rd.seed, buf);
^
./aln_sink.h:3225:9: note: in instantiation of member function 'SamConfig<unsigned int>::printAlignedOptFlags' requested here
samc_.printAlignedOptFlags(
^
./aln_sink.h:1569:4: note: in instantiation of member function 'AlnSinkSam<unsigned int>::appendMate' requested here
appendMate(o, staln, *rd1, rd2, rdid, rs1, rs2, summ, ssm1, ssm2,
^
./aln_sink.h:1521:2: note: in instantiation of member function 'AlnSinkSam<unsigned int>::append' requested here
AlnSinkSam(
^
hisat2.cpp:4116:18: note: in instantiation of member function 'AlnSinkSam<unsigned int>::AlnSinkSam' requested here
mssink = new AlnSinkSam<index_t>(
^
hisat2.cpp:4351:4: note: in instantiation of function template specialization 'driver<SString<char>>' requested here
driver<SString<char> >("DNA", bt2index, outfile);
^
14 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from edit.cpp:21:
In file included from ./edit.h:30:
In file included from ./splice_site.h:31:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 warnings generated.
In file included from gfm.cpp:21:
./gfm.h:1185:3: warning: 'auto_ptr<std::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
In file included from gfm.cpp:21:
./gfm.h:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
3 warnings generated.
reference.cpp:522:12: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
uint64_t origBufOff = bufOff;
^
reference.cpp:516:7: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
bool binarySearched = false;
^
2 warnings generated.
In file included from pat.cpp:26:
In file included from ./pat.h:41:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
In file included from pat.cpp:26:
In file included from ./pat.h:41:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./pat.h:1298:6: note: in instantiation of function template specialization 'itoa10<unsigned long long>' requested here
itoa10<TReadId>(readCnt_ - subReadCnt_, cbuf);
^
2 warnings generated.
In file included from read_qseq.cpp:20:
In file included from ./pat.h:41:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
In file included from read_qseq.cpp:20:
In file included from ./pat.h:41:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./pat.h:1298:6: note: in instantiation of function template specialization 'itoa10<unsigned long long>' requested here
itoa10<TReadId>(readCnt_ - subReadCnt_, cbuf);
^
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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from aligner_seed.cpp:20:
In file included from ./aligner_cache.h:60:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from aligner_seed2.cpp:22:
In file included from ./aligner_seed2.h:102:
In file included from ./aligner_result.h:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
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:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 warnings generated.
In file included from aligner_cache.cpp:20:
In file included from ./aligner_cache.h:60:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
1 warning 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from aligner_result.cpp:22:
In file included from ./aligner_result.h:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from aln_sink.cpp:22:
In file included from ./aln_sink.h:24:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from unique.cpp:20:
In file included from ./unique.h:38:
In file included from ./aligner_result.h:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
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:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from aligner_swsse.cpp:21:
In file included from ./aligner_sw_common.h:23:
In file included from ./aligner_result.h:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 warnings generated.
In file included from outq.cpp:20:
In file included from ./outq.h:26:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
1 warning 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
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:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
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:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
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:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
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:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
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:27:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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::basic_stringstream<char>>' is deprecated [-Wdeprecated-declarations]
auto_ptr<stringstream> ss(new stringstream());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<std::basic_stringstream<char>>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1851:28: note: 'auto_ptr<FileBuf>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1046:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: 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:6935:13: warning: variable 'lastorig' set but not used [-Wunused-but-set-variable]
int lastorig = -1;
^
In file included from splice_site.cpp:20:
In file included from ./edit.h:30:
In file included from ./splice_site.h:31:
In file included from ./read.h:28:
./util.h:46:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:418:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
4 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/4.5-x86_64/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)
Rhisat2.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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/4.5-x86_64/Resources/library/Rhisat2/hisat2 version 2.2.1"
[2] "64-bit"
[3] "Built on lconway"
[4] "Mon Apr 21 15:37:01 EDT 2025"
[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/RtmpiMJS2D/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/4.5-x86_64/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/RtmpiMJS2D/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: /tmp/RtmpiMJS2D/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/RtmpiMJS2D/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: /tmp/RtmpiMJS2D/hisat2indexdir/index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
len: 99465
gbwtLen: 99466
nodes: 99466
sz: 24867
gbwtSz: 24867
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 0
eftabSz: 0
ftabLen: 1048577
ftabSz: 4194308
offsLen: 6217
offsSz: 24868
lineSz: 64
sideSz: 64
sideGbwtSz: 48
sideGbwtLen: 192
numSides: 519
numLines: 519
gbwtTotLen: 33216
gbwtTotSz: 33216
reverse: 0
linearFM: Yes
Total time for call to driver() for forward index: 00:00:00
Settings:
Output files: "/tmp/RtmpiMJS2D/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/4.5-x86_64/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/RtmpiMJS2D/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: /tmp/RtmpiMJS2D/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/RtmpiMJS2D/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: /tmp/RtmpiMJS2D/hisat2indexdir/index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
len: 99465
gbwtLen: 99466
nodes: 99466
sz: 24867
gbwtSz: 24867
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 0
eftabSz: 0
ftabLen: 1048577
ftabSz: 4194308
offsLen: 6217
offsSz: 24868
lineSz: 64
sideSz: 64
sideGbwtSz: 48
sideGbwtLen: 192
numSides: 519
numLines: 519
gbwtTotLen: 33216
gbwtTotSz: 33216
reverse: 0
linearFM: Yes
Total time for call to driver() for forward index: 00:00:00
4 reads; of these:
4 (100.00%) were paired; of these:
4 (100.00%) aligned concordantly 0 times
0 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
4 pairs aligned concordantly 0 times; of these:
2 (50.00%) aligned discordantly 1 time
----
2 pairs aligned 0 times concordantly or discordantly; of these:
4 mates make up the pairs; of these:
4 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
50.00% overall alignment rate
4 reads; of these:
4 (100.00%) were unpaired; of these:
2 (50.00%) aligned 0 times
2 (50.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
50.00% overall alignment rate
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 59 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 59 ]
>
> proc.time()
user system elapsed
21.425 1.044 22.705
Rhisat2.Rcheck/Rhisat2-Ex.timings
| name | user | system | elapsed | |
| extract_splice_sites | 3.002 | 0.144 | 3.165 | |
| hisat2 | 0.220 | 0.065 | 0.326 | |
| hisat2_build | 0.202 | 0.048 | 0.271 | |
| hisat2_build_usage | 0.004 | 0.007 | 0.024 | |
| hisat2_usage | 0.007 | 0.011 | 0.030 | |
| hisat2_version | 0.006 | 0.007 | 0.033 | |