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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rhisat2
###
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* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
* installing *source* package 'Rhisat2' ...
** using staged installation
** libs
running 'src/Makefile.win' ...
C:/Rtools/mingw_64/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="\"`C:/Rtools/mingw_64/bin//g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -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 \
In file included from gfm.h:64:0,
from hisat2_build.cpp:35:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from hisat2_build.cpp:35:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from hisat2_build.cpp:35:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
ref_read.cpp: In function 'std::pair<long long unsigned int, long long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, 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 gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from gfm.cpp:21:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from gfm.cpp:21:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from gfm.cpp:21:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
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;
^
C:/Rtools/mingw_64/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="\"`C:/Rtools/mingw_64/bin//g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -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 \
In file included from gfm.h:64:0,
from hgfm.h:24,
from hisat2.cpp:33:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from hgfm.h:24,
from hisat2.cpp:33:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from hgfm.h:24,
from hisat2.cpp:33:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from hgfm.h:24:0,
from hisat2.cpp:33:
gfm.h: In instantiation of 'void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = unsigned int]':
hisat2.cpp:3686:27: required from 'void driver(const char*, const string&, const string&) [with TStr = SString<char>; std::string = std::basic_string<char>]'
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<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]':
group_walk.h:1542:4: required from 'bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]'
hi_aligner.h:5003:9: required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]'
hi_aligner.h:4791:48: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]'
hi_aligner.h:3945:70: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [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<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]':
hi_aligner.h:734:41: required from 'static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]'
hi_aligner.h:2214:64: required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]'
hi_aligner.h:4806:59: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]'
hi_aligner.h:3945:70: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [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<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]':
group_walk.h:492:66: required from 'std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]'
group_walk.h:1478:3: required from 'void GroupWalk2S<index_t, T, S>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]'
hi_aligner.h:4998:5: required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]'
hi_aligner.h:4791:48: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]'
hi_aligner.h:3945:70: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [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<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, Haplotype<index_t>&, EList<std::pair<_FIter, _FIter> >&, index_t, bool, bool) [with index_t = unsigned int]':
hi_aligner.h:2744:45: required from 'static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]'
hi_aligner.h:734:41: required from 'static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]'
hi_aligner.h:2214:64: required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]'
hi_aligner.h:4806:59: required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]'
hi_aligner.h:3945:70: required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [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<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long 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<index_t>::combineWith(const GenomeHit<index_t>&, const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, 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 long int]':
spliced_aligner.h:384:88: required from 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long 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<long long unsigned int, long long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, 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 gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from gfm.cpp:21:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from gfm.cpp:21:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from gfm.cpp:21:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
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 gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
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:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
gbwt_graph.h: In constructor 'RefGraph<index_t>::RefGraph(const SString<char>&, const EList<RefRecord>&, const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const string&, int, bool)':
gbwt_graph.h:749:30: warning: name lookup of 's' changed
int nt = s[j];
^
gbwt_graph.h:363:50: warning: matches this 's' under ISO standard rules
RefGraph<index_t>::RefGraph(const SString<char>& s,
^
gbwt_graph.h:639:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
gbwt_graph.h: In static member function 'static void RefGraph<index_t>::buildGraph_worker(void*)':
gbwt_graph.h:1072:30: warning: name lookup of 's' changed
int nt = s[j];
^
In file included from gfm.h:64:0,
from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
gbwt_graph.h:870:26: warning: matches this 's' under ISO standard rules
const SString<char>& s = *(threadParam->s);
^
gbwt_graph.h:955:25: warning: matches this 's' under old rules
for(index_t s = 0; s < snpIDs.size(); s++) {
^
echo "@echo off" > hisat2.bat
echo "perl %~dp0/hisat2 %*" >> hisat2.bat
echo "@echo off" > hisat2-build.bat
echo "python %~dp0/hisat2-build %*" >> hisat2-build.bat
echo "@echo off" > hisat2-inspect.bat
echo "python %~dp0/hisat2-inspect %*" >> hisat2-inspect.bat
mkdir -p ../inst
cp hisat2-align-s ../inst/hisat2
cp hisat2-build-s ../inst/hisat2-build
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rhisat2'
finding HTML links ... done
Rhisat2-package html
dot-createFlags html
dot-hisat2Bin html
extract_splice_sites html
hisat2 html
hisat2_build html
hisat2_build_usage html
hisat2_usage html
hisat2_version html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rhisat2)
Making 'packages.html' ... done
