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This page was generated on 2024-07-09 17:43 -0400 (Tue, 09 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4709
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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Package 1690/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie 1.44.0  (landing page)
Michael Stadler
Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 2024)
git_url: https://git.bioconductor.org/packages/Rbowtie
git_branch: RELEASE_3_19
git_last_commit: ff58398
git_last_commit_date: 2024-04-30 10:30:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


INSTALL results for Rbowtie on kjohnson1

To the developers/maintainers of the Rbowtie package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Rbowtie
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbowtie
StartedAt: 2024-07-07 15:15:22 -0400 (Sun, 07 Jul 2024)
EndedAt: 2024-07-07 15:16:37 -0400 (Sun, 07 Jul 2024)
EllapsedTime: 75.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### 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="\"2024-07-07T15:15:23\"" -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="\"2024-07-07T15:15:36\"" -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)