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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings CellaRepertorium_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CellaRepertorium.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CellaRepertorium/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellaRepertorium’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CellaRepertorium’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cross_tab_tbl: no visible binding for global variable ‘.’
cross_tab_tbl: no visible binding for global variable ‘x_key__’
fancy_name_contigs: no visible binding for global variable ‘.’
pairing_tables: no visible binding for global variable ‘.’
plot_cluster_factors: no visible binding for global variable ‘chain’
Undefined global functions or variables:
  . chain x_key__
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/CellaRepertorium/libs/CellaRepertorium.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘cdr3_clustering.Rmd’ using ‘UTF-8’... OK
  ‘cr-overview.Rmd’ using ‘UTF-8’... OK
  ‘mouse_tcell_qc.Rmd’ using ‘UTF-8’... OK
  ‘repertoire_and_expression.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/CellaRepertorium.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL CellaRepertorium
###
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* installing to library ‘/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-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-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-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-3.18-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-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-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)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CellaRepertorium)
> 
> test_check("CellaRepertorium")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 81 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 81 ]
> 
> proc.time()
   user  system elapsed 
 20.558   0.925  21.473