##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rbowtie.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rbowtie_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rbowtie.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbowtie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbowtie’ version ‘1.46.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
Found the following non-portable file paths:
  Rbowtie/src/SpliceMap/getSpliceMapUnmapped.dSYM/Contents/Resources/Relocations/aarch64/getSpliceMapUnmapped.yml
  Rbowtie/src/SpliceMap/runSpliceMap_QuasR.dSYM/Contents/Resources/Relocations/aarch64/runSpliceMap_QuasR.yml

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rbowtie’ can be installed ... WARNING
Found the following significant warnings:
  ./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]
  ./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
  amalgamateSAM.cpp:29:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rbowtie.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) SpliceMap.Rd:21: Lost braces
    21 |     (see sQuote{Details} or SpliceMap documentation).}
       |                ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rbowtie.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbowtie
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘Rbowtie’ ...
** using staged installation
** 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="\"2024-11-08T15:14:10\"" -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]
                        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]
        size_t amapEnts = 1;
               ^
./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        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]
                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]
typedef union {
             ^
              PartialAlignment
./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration
        bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) {
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration
} 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]
                                int loHalfMms = 0, hiHalfMms = 0;
                                                   ^
./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable]
                uint32_t cumSz = 0;
                         ^
./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable]
                uint32_t eligiblesVisited = 0;
                         ^
./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable]
                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]
        TIndexOffU restOff = 0;
                   ^
./ebwt.h:3889:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
                TIndexOffU patoff = 0;
                           ^
./ebwt.h:3881:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable]
        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]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                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]
                        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]
                        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="\"2024-11-08T15:14:14\"" -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]
                        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]
        size_t amapEnts = 1;
               ^
./diff_sample.h:669:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        TIndexOffU added = 0;
                   ^
./diff_sample.h:738:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
        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]
                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]
typedef union {
             ^
              PartialAlignment
./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration
        bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) {
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration
} 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]
                                int loHalfMms = 0, hiHalfMms = 0;
                                                   ^
./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable]
                uint32_t cumSz = 0;
                         ^
./ebwt_search_backtrack.h:1675:12: warning: variable 'eligiblesVisited' set but not used [-Wunused-but-set-variable]
                uint32_t eligiblesVisited = 0;
                         ^
./ebwt_search_backtrack.h:2726:12: warning: variable 'sLeft' set but not used [-Wunused-but-set-variable]
                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]
        TIndexOffU restOff = 0;
                   ^
./ebwt.h:3889:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
                TIndexOffU patoff = 0;
                           ^
./ebwt.h:3881:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable]
        TIndexOffU seqsRead = 0;
                   ^
ebwt_search.cpp:1426:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
                        int orig_threads = nthreads, steal_ctr = 1;
                                                     ^
ebwt_search.cpp:1807:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
                        int orig_threads = nthreads, steal_ctr = 1;
                                                     ^
ebwt_search.cpp:2303:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
                        int orig_threads = nthreads, steal_ctr = 1;
                                                     ^
ebwt_search.cpp:2849:33: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
                        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]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
18 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]
                        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]
                        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]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
In file included from pat.cpp: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]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
pat.cpp:382:3: note: in instantiation of function template specialization 'itoa10<unsigned long long>' requested here
                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]
                        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]
                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]
typedef union {
             ^
              PartialAlignment
./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration
        bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) {
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration
} 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]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
4 warnings generated.
In file included from hit_set.cpp:11:
./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
                        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]
                        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]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
In file included from 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]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./sstring.h:2154:2: note: in instantiation of function template specialization 'itoa10<unsigned int>' requested here
        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
                        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]
                        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]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
                                itoa10(ops[i].n, buf); o.append(buf);
                                ^
In file included from 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]
                if (value <= 0 && value != 0) *out++ = '-';
                    ~~~~~~~~~~~^~~~~~~~~~~~~
./sstring.h:2154:2: note: in instantiation of function template specialization 'itoa10<unsigned int>' requested here
        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
                                        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]
                        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]
        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]
            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]
    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]
    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]
    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]
    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]
    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]
    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]
                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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> library(testthat)
> library(Rbowtie)
> 
> test_check("Rbowtie")

*** Warning ***
'bowtie2-build-s' was run directly.  It is recommended that you run the wrapper script 'bowtie-build' instead.

 [1] "Usage: bowtie2-build-s [options]* <reference_in> <ebwt_outfile_base>"            
 [2] "    reference_in            comma-separated list of files with ref sequences"    
 [3] "    ebwt_outfile_base       write Ebwt data to files with this dir/basename"     
 [4] "Options:"                                                                        
 [5] "    -f                      reference files are Fasta (default)"                 
 [6] "    -c                      reference sequences given on cmd line (as <seq_in>)" 
 [7] "    -a/--noauto             disable automatic -p/--bmax/--dcv memory-fitting"    
 [8] "    -p/--packed             use packed strings internally; slower, uses less mem"
 [9] "    --bmax <int>            max bucket sz for blockwise suffix-array builder"    
[10] "    --bmaxdivn <int>        max bucket sz as divisor of ref len (default: 4)"    
[11] "    --dcv <int>             diff-cover period for blockwise (default: 1024)"     
[12] "    --nodc                  disable diff-cover (algorithm becomes quadratic)"    
[13] "    -r/--noref              don't build .3/.4.ebwt (packed reference) portion"   
[14] "    -3/--justref            just build .3/.4.ebwt (packed reference) portion"    
[15] "    -o/--offrate <int>      SA is sampled every 2^offRate BWT chars (default: 5)"
[16] "    -t/--ftabchars <int>    # of chars consumed in initial lookup (default: 10)" 
[17] "    --threads <int>         # of threads"                                        
[18] "    --ntoa                  convert Ns in reference to As"                       
[19] "    --seed <int>            seed for random number generator"                    
[20] "    -q/--quiet              verbose output (for debugging)"                      
[21] "    -h/--help               print detailed description of tool and its options"  
[22] "    --usage                 print this usage message"                            
[23] "    --version               print version information and quit"                  

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

 [1] "Usage: "                                                                                           
 [2] "bowtie-align-s [options]* -x <ebwt> {-1 <m1> -2 <m2> | --12 <r> | --interleaved <i> | <s>} [<hit>]"
 [3] ""                                                                                                  
 [4] "  <ebwt>  Index filename prefix (minus trailing .X.ebwt)."                                         
 [5] "  <m1>    Comma-separated list of files containing upstream mates (or the"                         
 [6] "          sequences themselves, if -c is set) paired with mates in <m2>"                           
 [7] "  <m2>    Comma-separated list of files containing downstream mates (or the"                       
 [8] "          sequences themselves if -c is set) paired with mates in <m1>"                            
 [9] "  <r>     Comma-separated list of files containing Crossbow-style reads.  Can be"                  
[10] "          a mixture of paired and unpaired.  Specify \"-\" for stdin."                             
[11] "  <i>     Files with interleaved paired-end FASTQ reads."                                          
[12] "  <s>     Comma-separated list of files containing unpaired reads, or the"                         
[13] "          sequences themselves, if -c is set.  Specify \"-\" for stdin."                           
[14] "  <hit>   File to write hits to (default: stdout)"                                                 
[15] "Input:"                                                                                            
[16] "  -q                 query input files are FASTQ .fq/.fastq (default)"                             
[17] "  -f                 query input files are (multi-)FASTA .fa/.mfa"                                 
[18] "  -F k:<int>,i:<int> query input files are continuous FASTA where reads"                           
[19] "                     are substrings (k-mers) extracted from a FASTA file <s>"                      
[20] "                     and aligned at offsets 1, 1+i, 1+2i ... end of reference"                     
[21] "  -r                 query input files are raw one-sequence-per-line"                              
[22] "  -c                 query sequences given on cmd line (as <mates>, <singles>)"                    
[23] "  -Q/--quals <file>  QV file(s) corresponding to CSFASTA inputs; use with -f -C"                   
[24] "  --Q1/--Q2 <file>   same as -Q, but for mate files 1 and 2 respectively"                          
[25] "  -s/--skip <int>    skip the first <int> reads/pairs in the input"                                
[26] "  -u/--qupto <int>   stop after first <int> reads/pairs (excl. skipped reads)"                     
[27] "  -5/--trim5 <int>   trim <int> bases from 5' (left) end of reads"                                 
[28] "  -3/--trim3 <int>   trim <int> bases from 3' (right) end of reads"                                
[29] "  --phred33-quals    input quals are Phred+33 (default)"                                           
[30] "  --phred64-quals    input quals are Phred+64 (same as --solexa1.3-quals)"                         
[31] "  --solexa-quals     input quals are from GA Pipeline ver. < 1.3"                                  
[32] "  --solexa1.3-quals  input quals are from GA Pipeline ver. >= 1.3"                                 
[33] "  --integer-quals    qualities are given as space-separated integers (not ASCII)"                  
[34] "Alignment:"                                                                                        
[35] "  -v <int>           report end-to-end hits w/ <=v mismatches; ignore qualities"                   
[36] "    or"                                                                                            
[37] "  -n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2)"                           
[38] "  -e/--maqerr <int>  max sum of mismatch quals across alignment for -n (def: 70)"                  
[39] "  -l/--seedlen <int> seed length for -n (default: 28)"                                             
[40] "  --nomaqround       disable Maq-like quality rounding for -n (nearest 10 <= 30)"                  
[41] "  -I/--minins <int>  minimum insert size for paired-end alignment (default: 0)"                    
[42] "  -X/--maxins <int>  maximum insert size for paired-end alignment (default: 250)"                  
[43] "  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)"                     
[44] "  --nofw/--norc      do not align to forward/reverse-complement reference strand"                  
[45] "  --maxbts <int>     max # backtracks for -n 2/3 (default: 125, 800 for --best)"                   
[46] "  --pairtries <int>  max # attempts to find mate for anchor hit (default: 100)"                    
[47] "  -y/--tryhard       try hard to find valid alignments, at the expense of speed"                   
[48] "  --chunkmbs <int>   max megabytes of RAM for best-first search frames (def: 64)"                  
[49] " --reads-per-batch   # of reads to read from input file at once (default: 16)"                     
[50] "Reporting:"                                                                                        
[51] "  -k <int>           report up to <int> good alignments per read (default: 1)"                     
[52] "  -a/--all           report all alignments per read (much slower than low -k)"                     
[53] "  -m <int>           suppress all alignments if > <int> exist (def: no limit)"                     
[54] "  -M <int>           like -m, but reports 1 random hit (MAPQ=0); requires --best"                  
[55] "  --best             hits guaranteed best stratum; ties broken by quality"                         
[56] "  --strata           hits in sub-optimal strata aren't reported (requires --best)"                 
[57] "Output:"                                                                                           
[58] "  -t/--time          print wall-clock time taken by search phases"                                 
[59] "  -B/--offbase <int> leftmost ref offset = <int> in bowtie output (default: 0)"                    
[60] "  --quiet            print nothing but the alignments"                                             
[61] "  --refidx           refer to ref. seqs by 0-based index rather than name"                         
[62] "  --al <fname>       write aligned reads/pairs to file(s) <fname>"                                 
[63] "  --un <fname>       write unaligned reads/pairs to file(s) <fname>"                               
[64] "  --no-unal          suppress SAM records for unaligned reads"                                     
[65] "  --max <fname>      write reads/pairs over -m limit to file(s) <fname>"                           
[66] "  --suppress <cols>  suppresses given columns (comma-delim'ed) in default output"                  
[67] "  --fullref          write entire ref name (default: only up to 1st space)"                        
[68] "SAM:"                                                                                              
[69] "  -S/--sam           write hits in SAM format"                                                     
[70] "  --mapq <int>       default mapping quality (MAPQ) to print for SAM alignments"                   
[71] "  --sam-nohead       supppress header lines (starting with @) for SAM output"                      
[72] "  --sam-nosq         supppress @SQ header lines for SAM output"                                    
[73] "  --sam-RG <text>    add <text> (usually \"lab=value\") to @RG line of SAM header"                 
[74] "Performance:"                                                                                      
[75] "  -o/--offrate <int> override offrate of index; must be >= index's offrate"                        
[76] "  -p/--threads <int> number of alignment threads to launch (default: 1)"                           
[77] "  --mm               use memory-mapped I/O for index; many 'bowtie's can share"                    
[78] "  --shmem            use shared mem for index; many 'bowtie's can share"                           
[79] "Other:"                                                                                            
[80] "  --seed <int>       seed for random number generator"                                             
[81] "  --verbose          verbose output (for debugging)"                                               
[82] "  --version          print version information and quit"                                           
[83] "  -h/--help          print this usage message"                                                     
[1] "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rbowtie/bowtie version 1.3.0"   
[2] "64-bit"                                                                                              
[3] "Built on kjohnson3"                                                                                  
[4] "2024-11-08T15:14:14"                                                                                 
[5] "Compiler: InstalledDir: /Library/Developer/CommandLineTools/usr/bin"                                 
[6] "Options: -O3  -stdlib=libc++ -falign-functions=64 -Wall -g -O2   -falign-functions=64 -Wall -g -O2  "
[7] "Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}"                             
# reads processed: 3
# reads with at least one alignment: 2 (66.67%)
# reads that failed to align: 1 (33.33%)
Reported 2 alignments
# reads processed: 3
# reads with at least one alignment: 2 (66.67%)
# reads that failed to align: 1 (33.33%)
Reported 2 alignments
# reads processed: 3
# reads with at least one alignment: 0 (0.00%)
# reads that failed to align: 3 (100.00%)
No alignments
# reads processed: 3
# reads with at least one alignment: 2 (66.67%)
# reads that failed to align: 1 (33.33%)
Reported 2 alignments
# reads processed: 3
# reads with at least one alignment: 0 (0.00%)
# reads that failed to align: 3 (100.00%)
No alignments
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 68 ]
> 
> proc.time()
   user  system elapsed 
  0.476   0.182   1.079