############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL FLAMES ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'FLAMES' ... ** using staged installation ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture using C compiler: 'gcc.exe (GCC) 12.2.0' using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++17 g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppFunctions.cpp -o RcppFunctions.o In file included from main-functions/../utility/fastq_utils.h:7, from main-functions/match_cell_barcode.h:13, from RcppFunctions.cpp:7: F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 185 | SCOPE int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:185:19: note: in definition of macro '__KSEQ_READ' 185 | SCOPE int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro 'KSEQ_INIT2' 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro 'KSEQ_INIT' 12 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: warning: 'void kseq_destroy(kseq_t*)' defined but not used [-Wunused-function] 171 | SCOPE void kseq_destroy(kseq_t *ks) \ | ^~~~~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:171:20: note: in definition of macro '__KSEQ_BASIC' 171 | SCOPE void kseq_destroy(kseq_t *ks) \ | ^~~~~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro 'KSEQ_INIT2' 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro 'KSEQ_INIT' 12 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: warning: 'kseq_t* kseq_init(bioc_gzFile)' defined but not used [-Wunused-function] 165 | SCOPE kseq_t *kseq_init(type_t fd) \ | ^~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:165:23: note: in definition of macro '__KSEQ_BASIC' 165 | SCOPE kseq_t *kseq_init(type_t fd) \ | ^~~~~~~~~ F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include/htslib/kseq.h:240:35: note: in expansion of macro 'KSEQ_INIT2' 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ main-functions/../utility/fastq_utils.h:12:1: note: in expansion of macro 'KSEQ_INIT' 12 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o main-functions/match_cell_barcode.cpp: In function 'std::pair get_bc_range(std::string, int, std::string, int)': main-functions/match_cell_barcode.cpp:304:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 304 | if (ix + 1 > vect.size()) { | ~~~~~~~^~~~~~~~~~~~~ main-functions/match_cell_barcode.cpp:313:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 313 | if (ix + 1 > vect_rev.size()) { | ~~~~~~~^~~~~~~~~~~~~~~~~ main-functions/match_cell_barcode.cpp: In function 'Rcpp::List match_cell_barcode(Rcpp::String, Rcpp::String, Rcpp::String, Rcpp::String, int, int, Rcpp::String, int, bool, bool)': main-functions/match_cell_barcode.cpp:601:24: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 601 | if (seq.size() > min_length) { | ~~~~~~~~~~~^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility/edit_dist.cpp -o utility/edit_dist.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility/fastq_utils.cpp -o utility/fastq_utils.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o /bin/sh: line 1: F:/biocbuild/bbs-3.17-bioc/R/bin.R: No such file or directory gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam.c -o bam.o bam.c: In function 'bam_remove_B': bam.c:164:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 164 | for (k = 0; k < b->core.n_cigar; ++k) | ^~~ bam.c:166:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 166 | if (k == b->core.n_cigar) return 0; // no 'B' | ^~ bam.c:227:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 227 | for (k = 1; k < l; ++k) | ^~~ bam.c:231:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 231 | for (k = i = 0; k < l; ++k) | ^~~ bam.c:231:25: warning: this 'for' clause does not guard... [-Wmisleading-indentation] bam.c:234:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 234 | l = i; | ^ /bin/sh: line 1: F:/biocbuild/bbs-3.17-bioc/R/bin.R: No such file or directory gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility/ssw/ssw.c -o utility/ssw/ssw.o g++ -shared -s -static-libgcc -o FLAMES.dll tmp.def RcppExports.o RcppFunctions.o main-functions/match_cell_barcode.o utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.o F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LF:/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-FLAMES/00new/FLAMES/libs/x64 ** 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 (FLAMES)