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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL FLAMES
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘FLAMES’ ...
** using staged installation
** libs
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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:7,
                 from main-functions/match_cell_barcode.h:13,
                 from RcppFunctions.cpp:7:
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:185:12: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function]
  185 |  SCOPE int kseq_read(kseq_t *seq) \
      |            ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:185:12: note: in definition of macro ‘__KSEQ_READ’
  185 |  SCOPE int kseq_read(kseq_t *seq) \
      |            ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-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)
      | ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:171:13: warning: ‘void kseq_destroy(kseq_t*)’ defined but not used [-Wunused-function]
  171 |  SCOPE void kseq_destroy(kseq_t *ks)         \
      |             ^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:171:13: note: in definition of macro ‘__KSEQ_BASIC’
  171 |  SCOPE void kseq_destroy(kseq_t *ks)         \
      |             ^~~~~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-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)
      | ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:165:16: warning: ‘kseq_t* kseq_init(gzFile)’ defined but not used [-Wunused-function]
  165 |  SCOPE kseq_t *kseq_init(type_t fd)         \
      |                ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include/htslib/kseq.h:165:16: note: in definition of macro ‘__KSEQ_BASIC’
  165 |  SCOPE kseq_t *kseq_init(type_t fd)         \
      |                ^~~~~~~~~
/home/biocbuild/bbs-3.16-bioc/R/site-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"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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:164:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  164 |  for (k = 0; k < b->core.n_cigar; ++k)
      |  ^~~
bam.c:166:3: 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:227:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  227 |   for (k = 1; k < l; ++k)
      |   ^~~
bam.c:231:4: 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:231:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
bam.c:234:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  234 |     l = i;
      |     ^
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/lib -L/usr/local/lib -o FLAMES.so RcppFunctions.o RcppExports.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 /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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)