############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL FLAMES ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘FLAMES’ ... ** using staged installation ** libs g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppFunctions.cpp -o RcppFunctions.o In file included from main-functions/../utility/fastq_utils.h:9, from main-functions/match_cell_barcode.h:16, from RcppFunctions.cpp:7: /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:190:12: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function] 190 | SCOPE int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:190:12: note: in definition of macro ‘__KSEQ_READ’ 190 | SCOPE int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ 244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ main-functions/../utility/fastq_utils.h:15:1: note: in expansion of macro ‘KSEQ_INIT’ 15 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: warning: ‘void kseq_destroy(kseq_t*)’ defined but not used [-Wunused-function] 176 | SCOPE void kseq_destroy(kseq_t *ks) \ | ^~~~~~~~~~~~ /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:176:13: note: in definition of macro ‘__KSEQ_BASIC’ 176 | SCOPE void kseq_destroy(kseq_t *ks) \ | ^~~~~~~~~~~~ /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ 244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ main-functions/../utility/fastq_utils.h:15:1: note: in expansion of macro ‘KSEQ_INIT’ 15 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: warning: ‘kseq_t* kseq_init(gzFile)’ defined but not used [-Wunused-function] 170 | SCOPE kseq_t *kseq_init(type_t fd) \ | ^~~~~~~~~ /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:170:16: note: in definition of macro ‘__KSEQ_BASIC’ 170 | SCOPE kseq_t *kseq_init(type_t fd) \ | ^~~~~~~~~ /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ 244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ main-functions/../utility/fastq_utils.h:15:1: note: in expansion of macro ‘KSEQ_INIT’ 15 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c main-functions/merge_bulk.cpp -o main-functions/merge_bulk.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/edit_dist.cpp -o utility/edit_dist.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/fastq_utils.cpp -o utility/fastq_utils.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c bam.c -o bam.o bam.c: In function ‘bam_remove_B’: bam.c:163:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 163 | for (k = 0; k < b->core.n_cigar; ++k) | ^~~ bam.c:165:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 165 | if (k == b->core.n_cigar) return 0; // no 'B' | ^~ bam.c:226:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 226 | for (k = 1; k < l; ++k) | ^~~ bam.c:230:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 230 | for (k = i = 0; k < l; ++k) | ^~~ bam.c:230:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] bam.c:233:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 233 | l = i; | ^ gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c utility/ssw/ssw.c -o utility/ssw/ssw.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o FLAMES.so RcppFunctions.o RcppExports.o main-functions/match_cell_barcode.o main-functions/merge_bulk.o utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.o /home/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-FLAMES/00new/FLAMES/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (FLAMES)