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###
### Running command:
###
### rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FLAMES.buildbin-libdir FLAMES_1.0.2.tar.gz
###
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install for i386
* installing *source* package 'FLAMES' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
sh: C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin.R: No such file or directory
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c edit_dist.cpp -o edit_dist.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 '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/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 '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/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 '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: C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin.R: No such file or directory
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ssw.c -o ssw.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ssw_cpp.cpp -o ssw_cpp.o
C:/rtools40/mingw32/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 C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/FLAMES.buildbin-libdir/00LOCK-FLAMES/00new/FLAMES/libs/i386
** 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
install for x64
* installing *source* package 'FLAMES' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
sh: C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin.R: No such file or directory
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c edit_dist.cpp -o edit_dist.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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: C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin.R: No such file or directory
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ssw.c -o ssw.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/FLAMES.buildbin-libdir/FLAMES/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FLAMES' as FLAMES_1.0.2.zip
* DONE (FLAMES)
