Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1747/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rhisat2 1.22.0 (landing page) Charlotte Soneson
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 1.22.0 |
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_1.22.0.tar.gz |
StartedAt: 2024-12-20 08:32:17 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 08:41:41 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 564.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Rhisat2.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rhisat2.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * 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 ‘1.22.0’ * 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-3.20-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 ... 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 5.6 0.372 6.02 * 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rhisat2.Rcheck/00check.log’ for details.
Rhisat2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhisat2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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\"" -DBUILD_TIME="\"Thu Dec 19 15:38:10 EST 2024\"" -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="\"merida1\"" -DBUILD_TIME="\"Thu Dec 19 15:39:17 EST 2024\"" -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/4.4-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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/4.4-x86_64/Resources/library/Rhisat2/hisat2 version 2.2.1" [2] "64-bit" [3] "Built on merida1" [4] "Thu Dec 19 15:39:17 EST 2024" [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/RtmpC6lhGU/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/4.4-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/RtmpC6lhGU/hisat2indexdir/index.1.ht2 Wrote 24872 bytes to secondary GFM file: /tmp/RtmpC6lhGU/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/RtmpC6lhGU/hisat2indexdir/index.5.ht2 Wrote 25130 bytes to secondary GFM file: /tmp/RtmpC6lhGU/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/RtmpC6lhGU/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/4.4-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/RtmpC6lhGU/hisat2indexdir/index.1.ht2 Wrote 24872 bytes to secondary GFM file: /tmp/RtmpC6lhGU/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/RtmpC6lhGU/hisat2indexdir/index.5.ht2 Wrote 25130 bytes to secondary GFM file: /tmp/RtmpC6lhGU/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 41.528 1.908 44.222
Rhisat2.Rcheck/Rhisat2-Ex.timings
name | user | system | elapsed | |
extract_splice_sites | 5.600 | 0.372 | 6.020 | |
hisat2 | 0.309 | 0.102 | 0.427 | |
hisat2_build | 0.290 | 0.079 | 0.383 | |
hisat2_build_usage | 0.009 | 0.010 | 0.022 | |
hisat2_usage | 0.012 | 0.014 | 0.029 | |
hisat2_version | 0.008 | 0.008 | 0.020 | |