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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL CellaRepertorium
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘CellaRepertorium’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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;
      |                ^~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/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/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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
Warning in fun(libname, pkgname) :
  Package 'CellaRepertorium' is deprecated and will be removed from
  Bioconductor version 3.21
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'CellaRepertorium' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (CellaRepertorium)