Package: Rhisat2

Version: 1.0.3

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rhisat2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rhisat2_1.0.3.tar.gz

StartedAt: 2019-10-16 04:31:49 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:35:32 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 223.5 seconds

RetCode: 0

Status:  OK

CheckDir: Rhisat2.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rhisat2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rhisat2_1.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Rhisat2.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhisat2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhisat2’ version ‘1.0.3’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 16.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/Rhisat2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rhisat2
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Rhisat2’ ...
** using staged installation
** libs
** arch - 
/usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \
 -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:35:0:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from hisat2_build.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from hisat2_build.cpp:35:0:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from hisat2_build.cpp:30:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’:
ref_read.cpp:327:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(i + 1 >= recs.size() || recs[i+1].first) {
                ~~~~~~^~~~~~~~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from gfm.cpp:21:0:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from gfm.cpp:21:0:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
   uint64_t origBufOff = bufOff;
            ^~~~~~~~~~
reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  bool binarySearched = false;
       ^~~~~~~~~~~~~~
/usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM   -DBOWTIE2 -DNDEBUG -Wall \
 -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 hgfm.h:24:0,
                 from hisat2.cpp:33:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from hgfm.h:24:0,
                 from hisat2.cpp:33:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
hisat2.cpp: In function ‘void parseOptions(int, const char**)’:
hisat2.cpp:1753:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  auto_ptr presets(new PresetsV0());
  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’:
hisat2.cpp:3068:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid));
  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
hisat2.cpp:3069:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  auto_ptr ps(patsrcFact->create());
  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
hisat2.cpp:3085:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc));
  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’:
hisat2.cpp:3826:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         auto_ptr refs(
         ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from hgfm.h:24:0,
                 from hisat2.cpp:33:
gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’:
hisat2.cpp:3686:17:   required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::__cxx11::string = std::__cxx11::basic_string]’
hisat2.cpp:4115:51:   required from here
gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
         int lastorig = -1;
             ^~~~~~~~
In file included from aligner_seed2.h:109:0,
                 from aligner_driver.h:78,
                 from hi_aligner.h:41,
                 from spliced_aligner.h:23,
                 from hisat2.cpp:45:
group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’:
group_walk.h:1542:4:   required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’
hi_aligner.h:5003:9:   required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:4773:38:   required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:48:   required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151:   required from here
group_walk.h:1172:60: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                             if(new_node_bot - new_node_top < gws.map.size()) {
group_walk.h:1183:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                                 for(index_t j = 0; j + 1 < gws.map.size(); j++) {
group_walk.h:1238:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                             if(node_range.second - node_range.first < st.back().map_.size()) {
group_walk.h:1249:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                                 for(index_t j = 0; j + 1 < st.back().map_.size(); j++) {
In file included from spliced_aligner.h:23:0,
                 from hisat2.cpp:45:
hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’:
hi_aligner.h:706:28:   required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:2194:47:   required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’
hi_aligner.h:4796:54:   required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:48:   required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151:   required from here
hi_aligner.h:2625:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(rfoff >= contig_len) return 0;
        ~~~~~~^~~~~~~~~~~~~
hi_aligner.h:2703:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(alt_range.first >= alts.size()) {
hi_aligner.h:2868:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                         for(int i = 0; i < alt.len; i++) {
                                        ~~^~~~~~~~~
hi_aligner.h:2909:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) {
                    ~~~~~^~~~~~~~
hi_aligner.h:2985:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if(alignedLen == next_rdlen) return rdlen;
                    ~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3021:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if(mm_max_rd_i + rdoff > best_rdoff) {
            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
hi_aligner.h:3026:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         } else if(mm_max_rd_i + rdoff == best_rdoff) {
                   ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3278:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if(best_rdoff < rdoff + rd_i) {
                        ~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from aligner_seed2.h:109:0,
                 from aligner_driver.h:78,
                 from hi_aligner.h:41,
                 from spliced_aligner.h:23,
                 from hisat2.cpp:45:
group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’:
group_walk.h:492:14:   required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’
group_walk.h:1478:3:   required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’
hi_aligner.h:4998:5:   required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:4773:38:   required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:48:   required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151:   required from here
group_walk.h:794:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 while(new_top - top < tmp_gbwt_to_node.size()) {
group_walk.h:801:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if(new_top - top == tmp_gbwt_to_node.size()) {
group_walk.h:817:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if(i + 1 < tmp_zOffs.size()) {
group_walk.h:823:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 while(new_bot2 - top < tmp_gbwt_to_node.size()) {
group_walk.h:830:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if(new_bot2 - top < tmp_gbwt_to_node.size()) {
In file included from spliced_aligner.h:23:0,
                 from hisat2.cpp:45:
hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’:
hi_aligner.h:2739:39:   required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:706:28:   required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:2194:47:   required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’
hi_aligner.h:4796:54:   required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:48:   required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151:   required from here
hi_aligner.h:2484:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ht_range.first >= haplotypes.size())
hi_aligner.h:2499:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if(ht_list[h].first == ht_range.first) {
                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2537:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if(ht_list[h].first == ht_range.first) {
                        ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2561:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(; ht_range.second < haplotypes.size(); ht_range.second++) {
hi_aligner.h:2568:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if(ht_list[h].first == ht_range.second) {
                        ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from hisat2.cpp:45:0:
spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’:
hisat2.cpp:4134:1:   required from here
spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable]
             bool another_spliced = false;
                  ^~~~~~~~~~~~~~~
In file included from spliced_aligner.h:23:0,
                 from hisat2.cpp:45:
hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long int]’:
spliced_aligner.h:365:30:   required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’
hisat2.cpp:4134:1:   required from here
hi_aligner.h:1790:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if(alt.seq == rdc) {
                        ~~~~~~~~^~~~~~
ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’:
ref_read.cpp:327:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if(i + 1 >= recs.size() || recs[i+1].first) {
                ~~~~~~^~~~~~~~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from gfm.cpp:21:0:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from gfm.cpp:21:0:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
   uint64_t origBufOff = bufOff;
            ^~~~~~~~~~
reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  bool binarySearched = false;
       ^~~~~~~~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_seed2.cpp:22:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_seed2.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_seed2.cpp:22:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_seed2.cpp:22:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_sw.cpp:25:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_sw.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_sw.cpp:25:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_sw.cpp:25:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_result.cpp:22:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from aligner_result.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_result.cpp:22:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from aligner_result.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from aln_sink.h:25,
                 from aln_sink.cpp:22:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from aln_sink.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from aln_sink.h:25,
                 from aln_sink.cpp:22:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from aln_sink.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from unique.cpp:20:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from unique.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from unique.cpp:20:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from unique.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_loc_i16.cpp:56:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_loc_i16.cpp:56:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_loc_i16.cpp:56:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_loc_i16.cpp:56:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_ee_i16.cpp:56:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_ee_i16.cpp:56:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_ee_i16.cpp:56:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_ee_i16.cpp:56:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_loc_u8.cpp:56:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_loc_u8.cpp:56:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_loc_u8.cpp:56:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_loc_u8.cpp:56:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_ee_u8.cpp:56:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_ee_u8.cpp:56:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_ee_u8.cpp:56:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:74,
                 from aligner_swsse_ee_u8.cpp:56:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from splice_site.cpp:20:
gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr ss(new stringstream());
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from splice_site.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
In file included from splice_site.h:34:0,
                 from edit.h:30,
                 from splice_site.cpp:20:
gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
                 from /usr/include/c++/7/locale:43,
                 from /usr/include/c++/7/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from splice_site.cpp:20:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template class auto_ptr;
                            ^~~~~~~~
splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’:
splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context]
             exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC);
                                                 ~~~~~~~~~~^~~~~~~~~~~~~~~~~
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 /home/biocbuild/bbs-3.9-bioc/R/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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Rhisat2)
> 
> test_check("Rhisat2")

*** Warning ***
'hisat2-build-s' was run directly.  It is recommended that you run the wrapper script 'hisat2-build' instead.

 [1] "HISAT2 version 2.1.0 by Daehwan Kim ([email protected], http://www.ccb.jhu.edu/people/infphilo)"
 [2] "Usage: hisat2-build [options]*  "                                  
 [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] "                            )"                                                     
 [8] "    -a/--noauto             disable automatic -p/--bmax/--dcv memory-fitting"                    
 [9] "    -p                      number of threads"                                                   
[10] "    --bmax             max bucket sz for blockwise suffix-array builder"                    
[11] "    --bmaxdivn         max bucket sz as divisor of ref len (default: 4)"                    
[12] "    --dcv              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       SA is sampled every 2^offRate BWT chars (default: 5)"                
[17] "    -t/--ftabchars     # of chars consumed in initial lookup (default: 10)"                 
[18] "    --localoffrate     SA (local) is sampled every 2^offRate BWT chars (default: 3)"        
[19] "    --localftabchars   # of chars consumed in initial lookup in a local index (default: 6)" 
[20] "    --snp             SNP file name"                                                       
[21] "    --haplotype       haplotype file name"                                                 
[22] "    --ss              Splice site file name"                                               
[23] "    --exon            Exon file name"                                                      
[24] "    --seed             seed for random number generator"                                    
[25] "    -q/--quiet              verbose output (for debugging)"                                      
[26] "    -h/--help               print detailed description of tool and its options"                  
[27] "    --usage                 print this usage message"                                            
[28] "    --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 2.1.0 by Daehwan Kim ([email protected], www.ccb.jhu.edu/people/infphilo)"                  
  [2] "Usage: "                                                                                                    
  [3] "  hisat2-align [options]* -x  {-1  -2  | -U } [-S ]"                               
  [4] ""                                                                                                           
  [5] "    Index filename prefix (minus trailing .X.ht2)."                                                
  [6] "         Files with #1 mates, paired with files in ."                                               
  [7] "         Files with #2 mates, paired with files in ."                                               
  [8] "          Files with unpaired reads."                                                                    
  [9] "        File for SAM output (default: stdout)"                                                         
 [10] ""                                                                                                           
 [11] "  , ,  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                 , ,  are sequences themselves, not files"                                   
 [22] "  -s/--skip     skip the first  reads/pairs in the input (none)"                                  
 [23] "  -u/--upto     stop after first  reads/pairs (no limit)"                                         
 [24] "  -5/--trim5    trim  bases from 5'/left end of reads (0)"                                        
 [25] "  -3/--trim3    trim  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] " Alignment:"                                                                                                
 [31] "  --n-ceil     func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)"                               
 [32] "  --ignore-quals     treat all quality values as 30 on Phred scale (off)"                                   
 [33] "  --nofw             do not align forward (original) version of read (off)"                                 
 [34] "  --norc             do not align reverse-complement version of read (off)"                                 
 [35] ""                                                                                                           
 [36] " Spliced Alignment:"                                                                                        
 [37] "  --pen-cansplice               penalty for a canonical splice site (0)"                               
 [38] "  --pen-noncansplice            penalty for a non-canonical splice site (12)"                          
 [39] "  --pen-canintronlen           penalty for long introns (G,-8,1) with canonical splice sites"         
 [40] "  --pen-noncanintronlen        penalty for long introns (G,-8,1) with noncanonical splice sites"      
 [41] "  --min-intronlen               minimum intron length (20)"                                            
 [42] "  --max-intronlen               maximum intron length (500000)"                                        
 [43] "  --known-splicesite-infile    provide a list of known splice sites"                                  
 [44] "  --novel-splicesite-outfile   report a list of splice sites"                                         
 [45] "  --novel-splicesite-infile    provide a list of novel splice sites"                                  
 [46] "  --no-temp-splicesite               disable the use of splice sites found"                                 
 [47] "  --no-spliced-alignment             disable spliced alignment"                                             
 [48] "  --rna-strandness           specify strand-specific information (unstranded)"                      
 [49] "  --tmo                              reports only those alignments within known transcriptome"              
 [50] "  --dta                              reports alignments tailored for transcript assemblers"                 
 [51] "  --dta-cufflinks                    reports alignments tailored specifically for cufflinks"                
 [52] "  --avoid-pseudogene                 tries to avoid aligning reads to pseudogenes (experimental option)\023"
 [53] "  --no-templatelen-adjustment        disables template length adjustment for RNA-seq reads"                 
 [54] ""                                                                                                           
 [55] " Scoring:"                                                                                                  
 [56] "  --mp ,   max and min penalties for mismatch; lower qual = lower penalty <6,2>"                  
 [57] "  --sp ,   max and min penalties for soft-clipping; lower qual = lower penalty <2,1>"             
 [58] "  --no-softclip      no soft-clipping"                                                                      
 [59] "  --np          penalty for non-A/C/G/Ts in read/ref (1)"                                              
 [60] "  --rdg ,  read gap open, extend penalties (5,3)"                                                 
 [61] "  --rfg ,  reference gap open, extend penalties (5,3)"                                            
 [62] "  --score-min  min acceptable alignment score w/r/t read length"                                      
 [63] "                     (L,0.0,-0.2)"                                                                          
 [64] ""                                                                                                           
 [65] " Reporting:"                                                                                                
 [66] "  -k  (default: 5) report up to  alns per read"                                                   
 [67] ""                                                                                                           
 [68] " Paired-end:"                                                                                               
 [69] "  -I/--minins   minimum fragment length (0), only valid with --no-spliced-alignment"                   
 [70] "  -X/--maxins   maximum fragment length (500), only valid with --no-spliced-alignment"                 
 [71] "  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)"                                       
 [72] "  --no-mixed         suppress unpaired alignments for paired reads"                                         
 [73] "  --no-discordant    suppress discordant alignments for paired reads"                                       
 [74] ""                                                                                                           
 [75] " Output:"                                                                                                   
 [76] "  -t/--time          print wall-clock time taken by search phases"                                          
 [77] "  --summary-file     print alignment summary to this file."                                                 
 [78] "  --new-summary      print alignment summary in a new style, which is more machine-friendly."               
 [79] "  --quiet            print nothing to stderr except serious errors"                                         
 [80] "  --met-file   send metrics to file at  (off)"                                                  
 [81] "  --met-stderr       send metrics to stderr (off)"                                                          
 [82] "  --met         report internal counters & metrics every  secs (1)"                               
 [83] "  --no-head          supppress header lines, i.e. lines starting with @"                                    
 [84] "  --no-sq            supppress @SQ header lines"                                                            
 [85] "  --rg-id      set read group id, reflected in @RG line and RG:Z: opt field"                          
 [86] "  --rg         add  (\"lab:value\") to @RG line of SAM header."                                 
 [87] "                     Note: @RG line only printed when --rg-id is set."                                      
 [88] "  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments."                              
 [89] ""                                                                                                           
 [90] " Performance:"                                                                                              
 [91] "  -o/--offrate  override offrate of index; must be >= index's offrate"                                 
 [92] "  -p/--threads  number of alignment threads to launch (1)"                                             
 [93] "  --reorder          force SAM output order to match order of input reads"                                  
 [94] "  --mm               use memory-mapped I/O for index; many 'hisat2's can share"                             
 [95] ""                                                                                                           
 [96] " Other:"                                                                                                    
 [97] "  --qc-filter        filter out reads that are bad according to QSEQ filter"                                
 [98] "  --seed        seed for random number generator (0)"                                                  
 [99] "  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes"                         
[100] "  --remove-chrname   remove 'chr' from reference names in alignment"                                        
[101] "  --add-chrname      add 'chr' to reference names in alignment "                                            
[102] "  --version          print version information and quit"                                                    
[103] "  -h/--help          print this usage message"                                                              
[1] "/home/biocbuild/bbs-3.9-bioc/R/library/Rhisat2/hisat2 version 2.1.0"    
[2] "64-bit"                                                                 
[3] "Built on malbec2"                                                       
[4] "Tue Oct 15 19:12:17 EDT 2019"                                           
[5] "Compiler: gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1) "           
[6] "Options: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY"        
[7] "Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}"
Settings:
  Output files: "/tmp/RtmpdDgdNa/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:
  /home/biocbuild/bbs-3.9-bioc/R/library/Rhisat2/extdata/refs/chr1.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 18650 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 18650 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 26955
fchr[G]: 49554
fchr[T]: 72459
fchr[$]: 99465
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4227718 bytes to primary GFM file: /tmp/RtmpdDgdNa/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: /tmp/RtmpdDgdNa/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/RtmpdDgdNa/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: /tmp/RtmpdDgdNa/hisat2indexdir/index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HierEbwt constructor
Headers:
    len: 99465
    gbwtLen: 99466
    nodes: 99466
    sz: 24867
    gbwtSz: 24867
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 6217
    offsSz: 24868
    lineSz: 64
    sideSz: 64
    sideGbwtSz: 48
    sideGbwtLen: 192
    numSides: 519
    numLines: 519
    gbwtTotLen: 33216
    gbwtTotSz: 33216
    reverse: 0
    linearFM: Yes
Total time for call to driver() for forward index: 00:00:01
Settings:
  Output files: "/tmp/RtmpdDgdNa/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:
  /home/biocbuild/bbs-3.9-bioc/R/library/Rhisat2/extdata/refs/chr1.fa
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 18650 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 18650 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 26955
fchr[G]: 49554
fchr[T]: 72459
fchr[$]: 99465
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 4227718 bytes to primary GFM file: /tmp/RtmpdDgdNa/hisat2indexdir/index.1.ht2
Wrote 24872 bytes to secondary GFM file: /tmp/RtmpdDgdNa/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/RtmpdDgdNa/hisat2indexdir/index.5.ht2
Wrote 25130 bytes to secondary GFM file: /tmp/RtmpdDgdNa/hisat2indexdir/index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HierEbwt 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 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
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 32 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 14.550   0.896  16.875 

name	user	system	elapsed
extract_splice_sites	2.226	0.049	3.877
hisat2	0.276	0.187	4.232
hisat2_build	0.242	0.126	0.817
hisat2_build_usage	0.007	0.051	0.059
hisat2_usage	0.006	0.048	0.052
hisat2_version	0.003	0.044	0.048