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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CellaRepertorium_1.0.0.tar.gz && rm -rf CellaRepertorium.buildbin-libdir && mkdir CellaRepertorium.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellaRepertorium.buildbin-libdir CellaRepertorium_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CellaRepertorium_1.0.0.zip && rm CellaRepertorium_1.0.0.tar.gz CellaRepertorium_1.0.0.zip
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install for i386
* installing *source* package 'CellaRepertorium' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:2:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:160: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
cdhit-common.cpp:174: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
cdhit-common.cpp:2418: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
cdhit-common.cpp:2435: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
cdhit-common.cpp:2437: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush (stop)
cdhit-common.cpp:2458: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
cdhit-common.cpp:2467: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush (stop)
cdhit-common.cpp:2492: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
cdhit-common.cpp:3151: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
In file included from cdhit-common.cpp:37:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:545:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
int max_diag = 0;
^~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:669:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
int max_diag = 0;
^~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::SortDivide(Options&, bool)':
cdhit-common.cpp:1774:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if (len > max_len) max_len = len;
~~~~^~~~~~~~~
cdhit-common.cpp:1775:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
if (len < min_len) min_len = len;
~~~~^~~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::DoClustering(int, const Options&)':
cdhit-common.cpp:2379:9: warning: variable 'mem' set but not used [-Wunused-but-set-variable]
size_t mem, mega = 1000000;
^~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:32:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c progress.cpp -o progress.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CellaRepertorium.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CellaRepertorium.buildbin-libdir/00LOCK-CellaRepertorium/00new/CellaRepertorium/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CellaRepertorium'
finding HTML links ... done
ContigCellDB-fun html
canonicalize_cell html
canonicalize_cluster html
cash-ContigCellDB-method html
ccdb_ex html
ccdb_join html
cdhit html
cdhit_ccdb html
cluster_filterset html
cluster_germline html
cluster_logistic_test html
cluster_permute_test html
cluster_plot html
contigs_qc html
crosstab_by_celltype html
dot-cluster_permute_test html
entropy html
enumerate_pairing html
equalize_ccdb html
fancy_name_contigs html
fine_cluster_seqs html
fine_clustering html
generate_pseudobulk html
guess_celltype html
hushWarning html
left_join_warn html
map_axis_labels html
mutate_cdb html
pairing_tables html
purity html
rank_prevalence_ccdb html
rbind-ContigCellDB-method html
split_cdb html
sub-sub-ContigCellDB-character-missing-method
html
*** copying figures
** 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 'CellaRepertorium' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:2:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:160: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
cdhit-common.cpp:174: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
cdhit-common.cpp:2418: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
cdhit-common.cpp:2435: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
cdhit-common.cpp:2437: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush (stop)
cdhit-common.cpp:2458: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
cdhit-common.cpp:2467: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush (stop)
cdhit-common.cpp:2492: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
cdhit-common.cpp:3151: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
In file included from cdhit-common.cpp:37:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:545:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
int max_diag = 0;
^~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:669:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
int max_diag = 0;
^~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::SortDivide(Options&, bool)':
cdhit-common.cpp:1774:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if (len > max_len) max_len = len;
~~~~^~~~~~~~~
cdhit-common.cpp:1775:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if (len < min_len) min_len = len;
~~~~^~~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::DoClustering(int, const Options&)':
cdhit-common.cpp:2379:9: warning: variable 'mem' set but not used [-Wunused-but-set-variable]
size_t mem, mega = 1000000;
^~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:32:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c progress.cpp -o progress.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CellaRepertorium.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CellaRepertorium.buildbin-libdir/CellaRepertorium/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellaRepertorium' as CellaRepertorium_1.0.0.zip
* DONE (CellaRepertorium)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CellaRepertorium' successfully unpacked and MD5 sums checked
