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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL FLAMES
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* installing to library 'D:/biocbuild/bbs-3.15-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

"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
sh: D:/biocbuild/bbs-3.15-bioc/R/bin.R: No such file or directory
"C:/rtools40/mingw64/bin/"gcc   -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
  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'
   if (k == b->core.n_cigar) return 0; // no 'B'
   ^~
bam.c:226:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   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'
    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'
     l = i;
     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c edit_dist.cpp -o edit_dist.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fastq_utils.cpp -o fastq_utils.o
In file included from fastq_utils.h:4,
                 from fastq_utils.cpp:1:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
fastq_utils.h: At global scope:
kseq.h:171:13: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
  static int kseq_read(kseq_t *seq)         \
             ^~~~~~~~~
kseq.h:171:13: note: in definition of macro '__KSEQ_READ'
  static int kseq_read(kseq_t *seq)         \
             ^~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c match_cell_barcode.cpp -o match_cell_barcode.o
In file included from fastq_utils.h:4,
                 from match_cell_barcode.cpp:13:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c merge_bulk.cpp -o merge_bulk.o
In file included from fastq_utils.h:4,
                 from merge_bulk.cpp:1:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
sh: D:/biocbuild/bbs-3.15-bioc/R/bin.R: No such file or directory
"C:/rtools40/mingw64/bin/"gcc   -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ssw.c -o ssw.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ssw_cpp.cpp -o ssw_cpp.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o FLAMES.dll tmp.def RcppExports.o bam.o edit_dist.o fastq_utils.o match_cell_barcode.o merge_bulk.o ssw.o ssw_cpp.o D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LD:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-FLAMES/00new/FLAMES/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FLAMES'
    finding HTML links ... done
    bulk_long_pipeline                      html  
    finding level-2 HTML links ... done

    bulk_windows_pipeline_setup             html  
    callBasilisk                            html  
    create_config                           html  
    generate_umap                           html  
    generic_long_pipeline                   html  
    get_default_config_file                 html  
    gff3_to_bed12                           html  
    match_cell_barcode                      html  
    merge_bulk_fastq                        html  
    merge_bulk_fastq_cpp                    html  
    merge_bulk_fastq_python                 html  
    minimap2_align                          html  
    minimap2_check_callable                 html  
    parse_gff_tree                          html  
    parse_json_config                       html  
    print_config                            html  
    samtools_as_bam                         html  
    samtools_sort_index                     html  
    sc_DTU_analysis                         html  
    sc_long_pipeline                        html  
    sc_mutations                            html  
    sc_windows_pipeline_setup               html  
    windows_pipeline_isoforms               html  
    windows_pipeline_quantification         html  
    write_config                            html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MWASTools' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'OncoSimulR' is missing or broken
 done