##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbowtie_1.51.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rbowtie.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rbowtie.buildbin-libdir Rbowtie_1.51.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rbowtie’ ...
** this is package ‘Rbowtie’ version ‘1.51.0’
** using staged installation
rm -f bowtie-build-s bowtie-align-s \
bowtie_prof \
bowtie-build-s.exe bowtie-align-s.exe bowtie_prof.exe \
bowtie-src.zip bowtie-bin.zip
rm -f *.core
rm -f bowtie-align-s-master* bowtie-align-s-no-io*
rm -rf .lib .include
rm -f SpliceMap/*.o SpliceMap/SpliceMap SpliceMap/amalgamateSAM SpliceMap/getSpliceMapUnmapped SpliceMap/fuseReorder SpliceMap/runSpliceMap_QuasR SpliceMap/sortsam
rm -f ../inst/bowtie ../inst/bowtie-build ../inst/SpliceMap ../inst/amalgamateSAM ../inst/getSpliceMapUnmapped ../inst/fuseReorder ../inst/runSpliceMap_QuasR ../inst/sortsam
** libs
clang++ -O3 -DCOMPILER_OPTIONS="\"-O3 -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \"" -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2026-03-17T21:16:49\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \
-I third_party \
-o bowtie-build-s ebwt_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp bowtie_build_main.cpp \
-L/opt/R/arm64/lib -lz -lpthread
In file included from ebwt_build.cpp:8:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
In file included from ebwt_build.cpp:10:
In file included from ./ebwt.h:25:
In file included from ./blockwise_sa.h:17:
./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
464 | size_t amapEnts = 1;
| ^
./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
669 | TIndexOffU added = 0;
| ^
./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
738 | TIndexOffU added = 0;
| ^
In file included from ebwt_build.cpp:10:
In file included from ./ebwt.h:1524:
In file included from ./ebwt_search_backtrack.h:8:
./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable]
70 | uint32_t qual = 0;
| ^
./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
37 | typedef union {
| ^
| PartialAlignment
./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration
69 | bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | uint32_t qual = 0;
| ~~~~~~~~~~~~~~~~~~
71 | assert_leq(slen, quals.length());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | if(entry.pos0 != 0xffff) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | assert_lt(entry.pos0, slen);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
74 | qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos0]));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
75 | }
| ~
76 | if(entry.pos1 != 0xffff) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
77 | assert_lt(entry.pos1, slen);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
78 | qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos1]));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
79 | }
| ~
80 | if(entry.pos2 != 0xffff) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
81 | assert_lt(entry.pos2, slen);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
82 | qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos2]));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
83 | }
| ~
84 | assert_leq(qual, qualMax);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration
88 | } PartialAlignment;
| ^
In file included from ebwt_build.cpp:10:
In file included from ./ebwt.h:1524:
./ebwt_search_backtrack.h:1245:24: warning: variable 'hiHalfMms' set but not used [-Wunused-but-set-variable]
1245 | int loHalfMms = 0, hiHalfMms = 0;
| ^
./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable]
1674 | uint32_t cumSz = 0;
| ^
./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable]
1675 | uint32_t eligiblesVisited = 0;
| ^
./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable]
2726 | uint32_t sLeft = s >> 1;
| ^
In file included from ebwt_build.cpp:10:
./ebwt.h:2790:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable]
2790 | TIndexOffU restOff = 0;
| ^
./ebwt.h:3889:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
3889 | TIndexOffU patoff = 0;
| ^
./ebwt.h:3881:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable]
3881 | TIndexOffU seqsRead = 0;
| ^
In file included from ebwt_build.cpp:10:
In file included from ./ebwt.h:25:
In file included from ./blockwise_sa.h:16:
In file included from ./binary_sa_search.h:12:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
50 | if (value <= 0 && value != 0) *out++ = '-';
| ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
331 | itoa10(ops[i].n, buf); o.append(buf);
| ^
14 warnings generated.
In file included from ref_read.cpp:2:
In file included from ./ref_read.h:13:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
1 warning generated.
In file included from bowtie_build_main.cpp:13:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
1 warning generated.
clang++ -O3 -DCOMPILER_OPTIONS="\"-O3 -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \"" -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2026-03-17T21:16:54\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \
-I third_party \
-o bowtie-align-s ebwt_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \
-L/opt/R/arm64/lib -lz -lpthread
In file included from ebwt_search.cpp:17:
In file included from ./aligner.h:17:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
In file included from ebwt_search.cpp:17:
In file included from ./aligner.h:18:
In file included from ./ebwt.h:25:
In file included from ./blockwise_sa.h:17:
./diff_sample.h:464:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
464 | size_t amapEnts = 1;
| ^
./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
669 | TIndexOffU added = 0;
| ^
./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
738 | TIndexOffU added = 0;
| ^
In file included from ebwt_search.cpp:17:
In file included from ./aligner.h:18:
In file included from ./ebwt.h:1524:
In file included from ./ebwt_search_backtrack.h:8:
./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable]
70 | uint32_t qual = 0;
| ^
./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
37 | typedef union {
| ^
| PartialAlignment
./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration
69 | bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | uint32_t qual = 0;
| ~~~~~~~~~~~~~~~~~~
71 | assert_leq(slen, quals.length());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | if(entry.pos0 != 0xffff) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | assert_lt(entry.pos0, slen);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
74 | qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos0]));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
75 | }
| ~
76 | if(entry.pos1 != 0xffff) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
77 | assert_lt(entry.pos1, slen);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
78 | qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos1]));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
79 | }
| ~
80 | if(entry.pos2 != 0xffff) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
81 | assert_lt(entry.pos2, slen);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
82 | qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos2]));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
83 | }
| ~
84 | assert_leq(qual, qualMax);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration
88 | } PartialAlignment;
| ^
In file included from ebwt_search.cpp:17:
In file included from ./aligner.h:18:
In file included from ./ebwt.h:1524:
./ebwt_search_backtrack.h:1245:24: warning: variable 'hiHalfMms' set but not used [-Wunused-but-set-variable]
1245 | int loHalfMms = 0, hiHalfMms = 0;
| ^
./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable]
1674 | uint32_t cumSz = 0;
| ^
./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable]
1675 | uint32_t eligiblesVisited = 0;
| ^
./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable]
2726 | uint32_t sLeft = s >> 1;
| ^
In file included from ebwt_search.cpp:17:
In file included from ./aligner.h:18:
./ebwt.h:2790:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable]
2790 | TIndexOffU restOff = 0;
| ^
./ebwt.h:3889:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
3889 | TIndexOffU patoff = 0;
| ^
./ebwt.h:3881:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable]
3881 | TIndexOffU seqsRead = 0;
| ^
ebwt_search.cpp:1045:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
1045 | sprintf(fname,"%s/%d",dirname,pid);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
ebwt_search.cpp:1061:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
1061 | sprintf(fname,"%s/%d",dirname,pid);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
ebwt_search.cpp:1078:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
1078 | sprintf(fname,"/proc/%s", ent->d_name);
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
180 | __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
218 | #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
| ^
ebwt_search.cpp:1426:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
1426 | int orig_threads = nthreads, steal_ctr = 1;
| ^
ebwt_search.cpp:1807:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
1807 | int orig_threads = nthreads, steal_ctr = 1;
| ^
ebwt_search.cpp:2303:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
2303 | int orig_threads = nthreads, steal_ctr = 1;
| ^
ebwt_search.cpp:2849:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
2849 | int orig_threads = nthreads, steal_ctr = 1;
| ^
In file included from ebwt_search.cpp:17:
In file included from ./aligner.h:15:
In file included from ./aligner_metrics.h:11:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
50 | if (value <= 0 && value != 0) *out++ = '-';
| ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
331 | itoa10(ops[i].n, buf); o.append(buf);
| ^
21 warnings generated.
In file included from ref_read.cpp:2:
In file included from ./ref_read.h:13:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
1 warning generated.
In file included from pat.cpp:10:
In file included from ./pat.h:17:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
In file included from pat.cpp:10:
In file included from ./pat.h:22:
In file included from ./read.h:29:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
50 | if (value <= 0 && value != 0) *out++ = '-';
| ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
331 | itoa10(ops[i].n, buf); o.append(buf);
| ^
In file included from pat.cpp:10:
In file included from ./pat.h:22:
In file included from ./read.h:29:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
50 | if (value <= 0 && value != 0) *out++ = '-';
| ~~~~~~~~~~~^~~~~~~~~~~~~
pat.cpp:382:3: note: in instantiation of function template specialization 'itoa10<unsigned long long>' requested here
382 | itoa10<TReadId>(static_cast<TReadId>(i), nametmp_);
| ^
3 warnings generated.
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:8:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
In file included from ebwt_search_util.cpp:1:
./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable]
70 | uint32_t qual = 0;
| ^
./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
37 | typedef union {
| ^
| PartialAlignment
./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration
69 | bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | uint32_t qual = 0;
| ~~~~~~~~~~~~~~~~~~
71 | assert_leq(slen, quals.length());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 | if(entry.pos0 != 0xffff) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
73 | assert_lt(entry.pos0, slen);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
74 | qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos0]));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
75 | }
| ~
76 | if(entry.pos1 != 0xffff) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
77 | assert_lt(entry.pos1, slen);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
78 | qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos1]));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
79 | }
| ~
80 | if(entry.pos2 != 0xffff) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
81 | assert_lt(entry.pos2, slen);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
82 | qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos2]));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
83 | }
| ~
84 | assert_leq(qual, qualMax);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration
88 | } PartialAlignment;
| ^
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
50 | if (value <= 0 && value != 0) *out++ = '-';
| ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
331 | itoa10(ops[i].n, buf); o.append(buf);
| ^
4 warnings generated.
In file included from hit_set.cpp:11:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
1 warning generated.
In file included from sam.cpp:8:
In file included from ./hit.h:16:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
In file included from sam.cpp:8:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
50 | if (value <= 0 && value != 0) *out++ = '-';
| ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
331 | itoa10(ops[i].n, buf); o.append(buf);
| ^
In file included from sam.cpp:8:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
50 | if (value <= 0 && value != 0) *out++ = '-';
| ~~~~~~~~~~~^~~~~~~~~~~~~
./sstring.h:2154:2: note: in instantiation of function template specialization 'itoa10<unsigned int>' requested here
2154 | itoa10<A>(static_cast<A>(i), buf);
| ^
sam.cpp:42:17: note: in instantiation of function template specialization 'operator<<<char, 25, 2, 0, unsigned int>' requested here
42 | o << "\tLN:" << (plen[i]) << '\n';
| ^
3 warnings generated.
In file included from hit.cpp:1:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
In file included from hit.cpp:2:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
50 | if (value <= 0 && value != 0) *out++ = '-';
| ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
331 | itoa10(ops[i].n, buf); o.append(buf);
| ^
In file included from hit.cpp:2:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
50 | if (value <= 0 && value != 0) *out++ = '-';
| ~~~~~~~~~~~^~~~~~~~~~~~~
./sstring.h:2154:2: note: in instantiation of function template specialization 'itoa10<unsigned int>' requested here
2154 | itoa10<A>(static_cast<A>(i), buf);
| ^
hit.cpp:109:8: note: in instantiation of function template specialization 'operator<<<char, 25, 2, 0, unsigned int>' requested here
109 | o << h.h.first;
| ^
3 warnings generated.
In file included from bowtie_main.cpp:13:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4077 | int thru = 0;
| ^
1 warning generated.
mkdir -p ../inst
cp bowtie-align-s ../inst/bowtie
cp bowtie-build-s ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile; \
echo "MAKE of SpliceMap DONE"
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
SpliceMap_utils_QuasR.cpp:299:6: warning: variable 'number' set but not used [-Wunused-but-set-variable]
299 | int number = 1;
| ^
1 warning generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
runSpliceMap_QuasR.cpp:108:31: warning: unused variable 'chr_file_list_it' [-Wunused-variable]
108 | vector<string>::iterator chr_file_list_it = chr_file_list.begin();
| ^~~~~~~~~~~~~~~~
runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable]
1327 | int min_mismatch;
| ^
2 warnings generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
29 | while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| &&
amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning
amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
29 | while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| &&
amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning
amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
29 | while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| &&
amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning
amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
29 | while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| &&
amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning
amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
29 | while(fhS1.good() & fhS2.good() & fhI1.good() & fhI2.good() & fhQ1.good() & fhQ2.good()) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~
| &&
amalgamateSAM.cpp:29:11: note: cast one or both operands to int to silence this warning
amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable]
695 | uint_fast32_t front_clip = 0;
| ^
6 warnings generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rbowtie)
