| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-10 10:04:33 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the IgGeneUsage package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IgGeneUsage.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 965/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IgGeneUsage 1.15.0 (landing page) Simo Kitanovski
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: IgGeneUsage |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IgGeneUsage.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings IgGeneUsage_1.15.0.tar.gz |
| StartedAt: 2023-05-09 18:54:59 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 19:18:06 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 1386.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IgGeneUsage.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IgGeneUsage.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings IgGeneUsage_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/IgGeneUsage.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘IgGeneUsage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IgGeneUsage’ version ‘1.15.0’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IgGeneUsage’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 40.3Mb
sub-directories of 1Mb or more:
libs 39.8Mb
* 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 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 ... OK
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
LOO 299.236 0.359 299.789
DGU 67.828 0.253 68.084
* 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 ...
‘User_Manual.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/IgGeneUsage.Rcheck/00check.log’
for details.
IgGeneUsage.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL IgGeneUsage
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘IgGeneUsage’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -c stanExports_zibb.cc -o stanExports_zibb.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_zibb.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_zibb.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_zibb.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_zibb.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_zibb.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_zibb.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_zibb.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_zibb.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/mat.hpp:142,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/gamma.hpp:2128:35: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false> >; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/scal/fun/gamma_p.hpp:76:30: required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
299 | result_type operator()()
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/scal/fun/owens_t.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/scal.hpp:133,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/arr.hpp:39,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/scal/fun/owens_t.hpp:57:72: required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
543 | std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol)
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/special_functions/gamma.hpp:18,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/prim/mat.hpp:142,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_zibb.h:20,
from stanExports_zibb.cc:5:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
217 | value_type v = g();
| ^
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/BH/include/boost/math/tools/fraction.hpp:217:20: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
217 | value_type v = g();
| ~^~
g++ -std=gnu++17 -shared -L/usr/local/lib -o IgGeneUsage.so RcppExports.o stanExports_zibb.o -L/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/lib/ -ltbb -ltbbmalloc
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-IgGeneUsage/00new/IgGeneUsage/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (IgGeneUsage)
IgGeneUsage.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(IgGeneUsage)
>
> test_check("IgGeneUsage")
Tests stan model
SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000127 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.27 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup)
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Chain 1: Iteration: 2500 / 2500 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 4.33579 seconds (Warm-up)
Chain 1: 20.1872 seconds (Sampling)
Chain 1: 24.523 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 9.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.91 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3).
Chain 3:
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 8e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 7.5e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.82 seconds.
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 7.6e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 7.1e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.84 seconds.
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 7.2e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 8.3e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.3e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 7.1e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 8.2e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.97 seconds.
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 7.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.73 seconds.
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 8e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.81 seconds.
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 7.2e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 7e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.3e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 6.8e-05 seconds
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SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 7.2e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.72 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
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Chain 3:
Chain 3: Elapsed Time: 7.51109 seconds (Warm-up)
Chain 3: 32.7211 seconds (Sampling)
Chain 3: 40.2322 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.79 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 5.66463 seconds (Warm-up)
Chain 1: 32.2776 seconds (Sampling)
Chain 1: 37.9422 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000105 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.05 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup)
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Chain 2: Iteration: 2250 / 2500 [ 90%] (Sampling)
Chain 2: Iteration: 2500 / 2500 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 5.20675 seconds (Warm-up)
Chain 2: 25.8588 seconds (Sampling)
Chain 2: 31.0655 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 8.8e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.88 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: Iteration: 1 / 2500 [ 0%] (Warmup)
Chain 3: Iteration: 250 / 2500 [ 10%] (Warmup)
Chain 3: Iteration: 500 / 2500 [ 20%] (Warmup)
Chain 3: Iteration: 501 / 2500 [ 20%] (Sampling)
Chain 3: Iteration: 750 / 2500 [ 30%] (Sampling)
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Chain 3: Iteration: 1250 / 2500 [ 50%] (Sampling)
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Chain 3: Iteration: 1750 / 2500 [ 70%] (Sampling)
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Chain 3: Iteration: 2500 / 2500 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 5.06325 seconds (Warm-up)
Chain 3: 16.8443 seconds (Sampling)
Chain 3: 21.9075 seconds (Total)
Chain 3:
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
>
> proc.time()
user system elapsed
684.093 2.211 686.870
IgGeneUsage.Rcheck/IgGeneUsage-Ex.timings
| name | user | system | elapsed | |
| DGU | 67.828 | 0.253 | 68.084 | |
| IGHV_Epitopes | 0.000 | 0.003 | 0.003 | |
| IGHV_HCV | 0.007 | 0.000 | 0.007 | |
| Ig | 0.004 | 0.000 | 0.004 | |
| Ig_SE | 0.041 | 0.000 | 0.041 | |
| LOO | 299.236 | 0.359 | 299.789 | |
| d_zibb | 0.001 | 0.003 | 0.004 | |