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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CellaRepertorium
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘CellaRepertorium’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:160: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
160 | #pragma omp critical
|
cdhit-common.cpp:174: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
174 | #pragma omp critical
|
cdhit-common.cpp:2418: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2418 | #pragma omp parallel for schedule( dynamic, 1 )
|
cdhit-common.cpp:2435: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2435 | #pragma omp parallel for schedule( dynamic, 1 )
|
cdhit-common.cpp:2437: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas]
2437 | #pragma omp flush (stop)
|
cdhit-common.cpp:2458: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
2458 | #pragma omp critical
|
cdhit-common.cpp:2467: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas]
2467 | #pragma omp flush (stop)
|
cdhit-common.cpp:2492: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2492 | #pragma omp parallel for schedule( dynamic, 1 )
|
cdhit-common.cpp:3151: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
3151 | #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:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
494 | 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:545:13: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable]
545 | 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:669:13: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable]
669 | int max_diag = 0;
| ^~~~~~~~
cdhit-common.cpp: In member function ‘void SequenceDB::SortDivide(Options&, bool)’:
cdhit-common.cpp:1774:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1774 | if (len > max_len) max_len = len;
| ~~~~^~~~~~~~~
cdhit-common.cpp:1775:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1775 | if (len < min_len) min_len = len;
| ~~~~^~~~~~~~~
cdhit-common.cpp: In member function ‘void SequenceDB::DoClustering(int, const Options&)’:
cdhit-common.cpp:2379:16: warning: variable ‘mem’ set but not used [-Wunused-but-set-variable]
2379 | size_t mem, mega = 1000000;
| ^~~
In file included from cdhit-common.cpp:37:
In member function ‘void NVector<TYPE>::Resize(int, const TYPE&) [with TYPE = long int]’,
inlined from ‘NVector<TYPE>::NVector(int, const TYPE&) [with TYPE = long int]’ at cdhit-common.h:124:10,
inlined from ‘int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)’ at cdhit-common.cpp:802:36:
cdhit-common.h:149:55: warning: argument 1 range [18446744056529682448, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
149 | items = (TYPE*)realloc( items, capacity*sizeof(TYPE) );
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cdhit-common.h: In function ‘int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)’:
cdhit-common.h:149:55: note: in a call to built-in allocation function ‘void* __builtin_malloc(long unsigned int)’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c progress.cpp -o progress.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o CellaRepertorium.so RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-CellaRepertorium/00new/CellaRepertorium/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (CellaRepertorium)
