Zheng Wei
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/Rbowtie2 |
| git_branch: RELEASE_3_13 |
| git_last_commit: f15bc6e |
| git_last_commit_date: 2021-05-19 12:29:56 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:49 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the Rbowtie2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie2.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1512/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbowtie2 1.14.0 (landing page) Zheng Wei
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Rbowtie2 |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Rbowtie2.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Rbowtie2_1.14.0.tar.gz |
| StartedAt: 2021-10-14 11:14:43 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 11:14:59 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 16.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rbowtie2.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Rbowtie2.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Rbowtie2_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Rbowtie2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Rbowtie2’ version ‘1.14.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Rbowtie2’ can be installed ... WARNING Found the following significant warnings: bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bt2_search.cpp:1458:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bt2_search.cpp:2840:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bt2_search.cpp:2841:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bt2_search.cpp:2867:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bt2_search.cpp:3964:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bt2_search.cpp:3965:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bt2_search.cpp:3977:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] bt2_search.cpp:4300:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair<DescentRedundancyKey, long int>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] See ‘/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 11.7Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * 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 vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2.Rcheck/00check.log’ for details.
Rbowtie2.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Rbowtie2
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘Rbowtie2’ ...
** using staged installation
** libs
** arch -
mkdir -p ../inst
(cd adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2/src/adapterremoval'
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c adapterset.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c alignment.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c argparse.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c debug.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c demultiplex.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_enc.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_io.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader_joined.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_id.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_rm.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_demultiplex.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c scheduler.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c strutils.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c threads.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c timer.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c trimmed_reads.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c userconfig.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main.cc
g++ -std=gnu++11 -O3 -pthread -DNDEBUG -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o
cp AdapterRemoval ../../inst/
make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2/src/adapterremoval'
(cd bowtie2 && (make CXX="g++" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2/src/bowtie2'
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_build.o bt2_build.cpp
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_build.cpp:27:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_build.cpp:27:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
827 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_build.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from bt2_build.cpp:27:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
831 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_build.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ccnt_lut.o ccnt_lut.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ref_read.o ref_read.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o alphabet.o alphabet.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o shmem.o shmem.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o edit.o edit.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_idx.o bt2_idx.cpp
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_idx.cpp:25:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_idx.cpp:25:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
827 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_idx.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from bt2_idx.cpp:25:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
831 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_idx.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_io.o bt2_io.cpp
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_io.cpp:25:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_io.cpp:25:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
827 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_io.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from bt2_io.cpp:25:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
831 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_io.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_util.o bt2_util.cpp
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_util.cpp:26:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_util.cpp:26:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
827 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_util.cpp:26:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from bt2_util.cpp:26:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
831 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_util.cpp:26:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o reference.o reference.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ds.o ds.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o multikey_qsort.o multikey_qsort.cpp
In file included from multikey_qsort.h:27,
from multikey_qsort.cpp:20:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o limit.o limit.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o random_source.o random_source.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o tinythread.o tinythread.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bowtie_build_main.o bowtie_build_main.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o diff_sample.o diff_sample.cpp
In file included from diff_sample.cpp:20:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -o bowtie2-build-s bt2_build.o ccnt_lut.o ref_read.o alphabet.o shmem.o edit.o bt2_idx.o bt2_io.o bt2_util.o reference.o ds.o multikey_qsort.o limit.o random_source.o tinythread.o bowtie_build_main.o diff_sample.o
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_search.o bt2_search.cpp
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_search.cpp:33:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_search.cpp:33:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
827 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from bt2_search.cpp:33:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
831 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
bt2_search.cpp: In function ‘void parseOptions(int, const char**)’:
bt2_search.cpp:1458:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1458 | auto_ptr<Presets> presets(new PresetsV0());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
bt2_search.cpp: In function ‘void multiseedSearchWorker(void*)’:
bt2_search.cpp:2840:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
2840 | auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, pp, tid));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
bt2_search.cpp:2841:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
2841 | auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
bt2_search.cpp:2867:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
2867 | auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
bt2_search.cpp: In function ‘void multiseedSearchWorker_2p5(void*)’:
bt2_search.cpp:3964:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3964 | auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, pp, tid));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
bt2_search.cpp:3965:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3965 | auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
bt2_search.cpp:3977:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3977 | auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
bt2_search.cpp: In function ‘void multiseedSearch(Scoring&, const PatternParams&, PatternComposer&, AlnSink&, Ebwt&, Ebwt&, OutFileBuf*)’:
bt2_search.cpp:4300:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
4300 | auto_ptr<BitPairReference> refs(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from bt2_search.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:31,
from blockwise_sa.h:34,
from bt2_idx.h:42,
from bt2_search.cpp:33:
ds.h: In instantiation of ‘EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]’:
ds.h:973:12: required from ‘void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:958:3: required from ‘void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:569:4: required from ‘void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
aligner_seed2.h:482:31: required from here
ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair<DescentRedundancyKey, long int>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:64,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/ostream:38,
from /usr/include/c++/9/iostream:39,
from bt2_search.cpp:21:
/usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair<DescentRedundancyKey, long int>’ declared here
208 | struct pair
| ^~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o qual.o qual.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o pat.o pat.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o sam.o sam.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o read_qseq.o read_qseq.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_seed_policy.o aligner_seed_policy.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_seed.o aligner_seed.cpp
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from aligner_seed.cpp:23:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from aligner_seed.cpp:23:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
827 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from aligner_seed.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_seed.cpp:23:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
831 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from aligner_seed.cpp:23:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_seed2.o aligner_seed2.cpp
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from aligner_seed2.h:103,
from aligner_seed2.cpp:22:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from aligner_seed2.h:103,
from aligner_seed2.cpp:22:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
827 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from aligner_seed2.h:103,
from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_seed2.h:103,
from aligner_seed2.cpp:22:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
831 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from aligner_seed2.h:103,
from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from random_util.h:25,
from aligner_seed2.h:101,
from aligner_seed2.cpp:22:
ds.h: In instantiation of ‘EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]’:
ds.h:973:12: required from ‘void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:958:3: required from ‘void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:569:4: required from ‘void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
aligner_seed2.h:482:31: required from here
ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair<DescentRedundancyKey, long int>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/utility:70,
from aligner_seed2.h:98,
from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair<DescentRedundancyKey, long int>’ declared here
208 | struct pair
| ^~~~
aligner_seed2.cpp: In member function ‘size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory<DescentPos>&, const EList<DescentRoot>&, const EList<DescentConfig>&, PerReadMetrics&)’:
aligner_seed2.cpp:585:14: warning: ‘edge.DescentEdge::nex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
585 | DescentEdge edge;
| ^~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_sw.o aligner_sw.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_sw_driver.o aligner_sw_driver.cpp
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from group_walk.h:86,
from aligner_sw_driver.h:84,
from aligner_sw_driver.cpp:47:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from group_walk.h:86,
from aligner_sw_driver.h:84,
from aligner_sw_driver.cpp:47:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
827 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from aligner_sw.h:78,
from aligner_sw_driver.h:81,
from aligner_sw_driver.cpp:47:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from group_walk.h:86,
from aligner_sw_driver.h:84,
from aligner_sw_driver.cpp:47:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
831 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from aligner_sw.h:78,
from aligner_sw_driver.h:81,
from aligner_sw_driver.cpp:47:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_cache.o aligner_cache.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_result.o aligner_result.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ref_coord.o ref_coord.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o mask.o mask.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o pe.o pe.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aln_sink.o aln_sink.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o dp_framer.o dp_framer.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o scoring.o scoring.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o presets.o presets.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o unique.o unique.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o simple_func.o simple_func.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o random_util.o random_util.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_bt.o aligner_bt.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o sse_util.o sse_util.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse.o aligner_swsse.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o outq.o outq.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_loc_i16.o aligner_swsse_loc_i16.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_ee_i16.o aligner_swsse_ee_i16.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_loc_u8.o aligner_swsse_loc_u8.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_ee_u8.o aligner_swsse_ee_u8.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_driver.o aligner_driver.cpp
In file included from blockwise_sa.h:34,
from bt2_idx.h:42,
from aligner_seed2.h:103,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from aligner_seed2.h:103,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
827 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from aligner_seed2.h:103,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_seed2.h:103,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
831 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from bt2_idx.h:28,
from aligner_seed2.h:103,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from random_util.h:25,
from aligner_seed2.h:101,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
ds.h: In instantiation of ‘EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]’:
ds.h:973:12: required from ‘void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:958:3: required from ‘void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
ds.h:569:4: required from ‘void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]’
aligner_seed2.h:482:31: required from here
ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair<DescentRedundancyKey, long int>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/utility:70,
from aligner_seed2.h:98,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair<DescentRedundancyKey, long int>’ declared here
208 | struct pair
| ^~~~
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bowtie_main.o bowtie_main.cpp
g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -o bowtie2-align-s bt2_search.o qual.o pat.o sam.o read_qseq.o aligner_seed_policy.o aligner_seed.o aligner_seed2.o aligner_sw.o aligner_sw_driver.o aligner_cache.o aligner_result.o ref_coord.o mask.o pe.o aln_sink.o dp_framer.o scoring.o presets.o unique.o simple_func.o random_util.o aligner_bt.o sse_util.o aligner_swsse.o outq.o aligner_swsse_loc_i16.o aligner_swsse_ee_i16.o aligner_swsse_loc_u8.o aligner_swsse_ee_u8.o aligner_driver.o ccnt_lut.o ref_read.o alphabet.o shmem.o edit.o bt2_idx.o bt2_io.o bt2_util.o reference.o ds.o multikey_qsort.o limit.o random_source.o tinythread.o bowtie_main.o
cp bowtie2-align-s ../../inst
cp bowtie2-build-s ../../inst
make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2/src/bowtie2'
g++ -shared -fPIC -o Rbowtie2.so version_info.cpp
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-Rbowtie2/00new/Rbowtie2/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 (Rbowtie2)
Rbowtie2.Rcheck/Rbowtie2-Ex.timings
| name | user | system | elapsed | |
| adapterremoval_usage | 0.004 | 0.014 | 0.019 | |
| adapterremoval_version | 0.002 | 0.003 | 0.006 | |
| bowtie2-build | 0.618 | 0.431 | 0.791 | |
| bowtie2 | 0.547 | 0.223 | 0.421 | |
| bowtie2_build_usage | 0.003 | 0.002 | 0.006 | |
| bowtie2_usage | 0.004 | 0.004 | 0.010 | |
| bowtie2_version | 0.003 | 0.001 | 0.005 | |
| identify_adapters | 0.011 | 0.016 | 0.024 | |
| remove_adapters | 0.030 | 0.013 | 0.040 | |