| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-10 10:04:37 -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 ppcseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ppcseq.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 1518/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ppcseq 1.9.0 (landing page) Stefano Mangiola
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ppcseq |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ppcseq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ppcseq_1.9.0.tar.gz |
| StartedAt: 2023-05-10 00:44:41 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 00:54:34 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 592.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ppcseq.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ppcseq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ppcseq_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ppcseq.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 ‘ppcseq/DESCRIPTION’ ... OK
* this is package ‘ppcseq’ version ‘1.9.0’
* 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 ‘ppcseq’ 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 46.2Mb
sub-directories of 1Mb or more:
data 1.6Mb
libs 44.2Mb
* 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 ... NOTE
.identify_abundant: no visible binding for global variable ‘.’
.identify_abundant: no visible binding for global variable ‘.abundant’
add_exposure_rate: no visible binding for global variable ‘.variable’
add_exposure_rate: no visible binding for global variable ‘S’
add_exposure_rate: no visible binding for global variable ‘exposure
rate’
add_partition: no visible binding for global variable ‘.’
add_scaled_counts_bulk.calcNormFactor: no visible binding for global
variable ‘transcript’
add_scaled_counts_bulk.get_low_expressed: no visible binding for global
variable ‘transcript’
check_if_within_posterior: no visible binding for global variable
‘.lower’
check_if_within_posterior: no visible binding for global variable
‘.upper’
check_if_within_posterior: no visible binding for global variable ‘ppc’
do_inference: no visible binding for global variable ‘idx_MPI’
do_inference: no visible binding for global variable ‘read count MPI
row’
do_inference: no visible binding for global variable ‘.’
do_inference: no visible binding for global variable ‘symbol MPI row’
draws_to_tibble_x: no visible binding for global variable ‘.’
draws_to_tibble_x: no visible binding for global variable ‘dummy’
draws_to_tibble_x: no visible binding for global variable ‘.variable’
draws_to_tibble_x: no visible binding for global variable ‘.chain’
draws_to_tibble_x: no visible binding for global variable ‘.iteration’
draws_to_tibble_x: no visible binding for global variable ‘.draw’
draws_to_tibble_x: no visible binding for global variable ‘.value’
draws_to_tibble_x_y: no visible binding for global variable ‘.’
draws_to_tibble_x_y: no visible binding for global variable ‘dummy’
draws_to_tibble_x_y: no visible binding for global variable ‘.variable’
draws_to_tibble_x_y: no visible binding for global variable ‘.chain’
draws_to_tibble_x_y: no visible binding for global variable
‘.iteration’
draws_to_tibble_x_y: no visible binding for global variable ‘.draw’
draws_to_tibble_x_y: no visible binding for global variable ‘.value’
find_optimal_number_of_chains: no visible binding for global variable
‘cc’
find_optimal_number_of_chains: no visible binding for global variable
‘tot’
find_optimal_number_of_chains: no visible binding for global variable
‘chains’
fit_to_counts_rng: no visible binding for global variable ‘.variable’
fit_to_counts_rng: no visible binding for global variable ‘S’
fit_to_counts_rng: no visible binding for global variable ‘G’
fit_to_counts_rng: no visible binding for global variable ‘.’
fit_to_counts_rng_approximated: no visible binding for global variable
‘.’
fit_to_counts_rng_approximated: no visible binding for global variable
‘S’
fit_to_counts_rng_approximated: no visible binding for global variable
‘G’
fit_to_counts_rng_approximated: no visible binding for global variable
‘CI’
format_for_MPI: no visible binding for global variable ‘.’
format_for_MPI: no visible binding for global variable ‘G’
format_for_MPI: no visible binding for global variable ‘idx_MPI’
format_input: no visible binding for global variable ‘.’
format_results: no visible binding for global variable ‘sample wise
data’
get_outlier_data_to_exlude: no visible binding for global variable
‘idx_MPI’
get_outlier_data_to_exlude: no visible binding for global variable ‘s’
get_outlier_data_to_exlude: no visible binding for global variable
‘read count MPI row’
get_outlier_data_to_exlude: no visible binding for global variable ‘.’
get_outlier_data_to_exlude: no visible binding for global variable
‘rowid’
get_scaled_counts_bulk: no visible binding for global variable ‘med’
get_scaled_counts_bulk: no visible binding for global variable
‘tot_filt’
get_scaled_counts_bulk: no visible binding for global variable ‘nf’
get_scaled_counts_bulk: no visible binding for global variable ‘.’
get_scaled_counts_bulk: no visible binding for global variable ‘tot’
identify_outliers: no visible binding for global variable ‘.’
identify_outliers: no visible binding for global variable ‘multiplier’
identify_outliers: no visible binding for global variable ‘TMM’
identify_outliers: no visible binding for global variable ‘l’
identify_outliers: no visible binding for global variable ‘l %>% sd’
identify_outliers: no visible binding for global variable ‘cc’
identify_outliers: no visible binding for global variable
‘write_on_disk’
identify_outliers: no visible binding for global variable ‘.variable’
identify_outliers: no visible binding for global variable ‘S’
identify_outliers: no visible binding for global variable ‘G’
identify_outliers: no visible binding for global variable ‘.lower’
identify_outliers: no visible binding for global variable ‘.upper’
identify_outliers_1_step: no visible binding for global variable ‘.’
identify_outliers_1_step: no visible global function definition for
‘scale_abundance’
identify_outliers_1_step: no visible binding for global variable ‘TMM’
identify_outliers_1_step: no visible binding for global variable
‘multiplier’
identify_outliers_1_step: no visible binding for global variable ‘l’
identify_outliers_1_step: no visible binding for global variable ‘l %>%
sd’
identify_outliers_1_step: no visible binding for global variable ‘cc’
identify_outliers_1_step: no visible binding for global variable
‘write_on_disk’
identify_outliers_1_step: no visible binding for global variable
‘.variable’
identify_outliers_1_step: no visible binding for global variable ‘S’
identify_outliers_1_step: no visible binding for global variable ‘G’
identify_outliers_1_step: no visible binding for global variable
‘.lower’
identify_outliers_1_step: no visible binding for global variable
‘.upper’
identify_outliers_1_step: no visible binding for global variable ‘ppc’
identify_outliers_1_step: no visible binding for global variable
‘exposure rate’
inits_fx: no visible binding for global variable ‘res_discovery’
inits_fx: no visible binding for global variable ‘.variable’
inits_fx: no visible binding for global variable ‘S’
inits_fx: no visible binding for global variable ‘G’
inits_fx: no visible binding for global variable ‘init’
merge_results: no visible binding for global variable ‘.variable’
merge_results: no visible binding for global variable ‘S’
merge_results: no visible binding for global variable ‘G’
merge_results: no visible binding for global variable ‘exposure rate’
merge_results: no visible binding for global variable ‘slope’
merge_results: no visible binding for global variable ‘.lower’
merge_results: no visible binding for global variable ‘.upper’
merge_results: no visible binding for global variable ‘ppc’
plot_credible_intervals: no visible binding for global variable ‘sample
wise data’
produce_plots: no visible binding for global variable ‘.upper_2’
select_to_check_and_house_keeping: no visible binding for global
variable ‘.’
summary_to_tibble: no visible binding for global variable ‘.’
Undefined global functions or variables:
. .abundant .chain .draw .iteration .lower .upper .upper_2 .value
.variable CI G S TMM cc chains dummy exposure rate idx_MPI init l l
%>% sd med multiplier nf ppc read count MPI row res_discovery rowid s
sample wise data scale_abundance slope symbol MPI row tot tot_filt
transcript write_on_disk
Consider adding
importFrom("base", "row", "sample")
importFrom("stats", "sd")
importFrom("utils", "data")
to your NAMESPACE file.
* 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 LazyData ... 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
identify_outliers 23.552 0.394 23.950
plot_credible_intervals 23.038 0.332 23.371
* 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 ...
‘introduction.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/ppcseq.Rcheck/00check.log’
for details.
ppcseq.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ppcseq
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘ppcseq’ ...
** 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/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/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_negBinomial_MPI.cc -o stanExports_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.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 ppcseq.so RcppExports.o stanExports_negBinomial_MPI.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-ppcseq/00new/ppcseq/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (ppcseq)
ppcseq.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(ppcseq)
>
> test_check("ppcseq")
No group or design set. Assuming all samples belong to one group.
executing do_inference
Storing counts in `nn`, as `n` already present in input
i Use `name = "new_name"` to pick a new name.
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Gradient evaluated at the initial value is not finite.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000695 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.95 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -12704.543 1.000 1.000
Chain 1: 200 -8674.572 0.732 1.000
Chain 1: 300 -7697.869 0.530 0.465
Chain 1: 400 -7535.077 0.403 0.465
Chain 1: 500 -7531.821 0.323 0.127
Chain 1: 600 -7531.815 0.269 0.127
Chain 1: 700 -7519.287 0.231 0.022
Chain 1: 800 -7534.495 0.202 0.022
Chain 1: 900 -7531.662 0.180 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
executing add_exposure_rate
executing check_if_within_posterior
executing save_generated_quantities_in_case
executing fit_to_counts_rng
executing do_inference
Storing counts in `nn`, as `n` already present in input
i Use `name = "new_name"` to pick a new name.
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 0.000838 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 8.38 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -12304.784 1.000 1.000
Chain 1: 200 -8491.867 0.725 1.000
Chain 1: 300 -7648.788 0.520 0.449
Chain 1: 400 -7505.870 0.395 0.449
Chain 1: 500 -7549.936 0.317 0.110
Chain 1: 600 -7495.810 0.265 0.110
Chain 1: 700 -7493.988 0.227 0.019
Chain 1: 800 -7500.775 0.199 0.019
Chain 1: 900 -7485.560 0.177 0.007
Chain 1: 1000 -7489.313 0.160 0.007
Chain 1: 1100 -7496.582 0.145 0.006
Chain 1: 1200 -7490.045 0.133 0.006
Chain 1: 1300 -7485.533 0.123 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
executing add_exposure_rate
executing check_if_within_posterior
executing save_generated_quantities_in_case
executing fit_to_counts_rng_approximated
No group or design set. Assuming all samples belong to one group.
executing do_inference
Storing counts in `nn`, as `n` already present in input
i Use `name = "new_name"` to pick a new name.
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 0.000788 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.88 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Iteration: 250 / 250 [100%] (Adaptation)
Chain 1: Success! Found best value [eta = 0.1].
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -307328.979 1.000 1.000
Chain 1: 200 -118412.330 1.298 1.595
Chain 1: 300 -51671.045 1.296 1.292
Chain 1: 400 -29429.364 1.161 1.292
Chain 1: 500 -19214.305 1.035 1.000
Chain 1: 600 -15131.258 0.907 1.000
Chain 1: 700 -13328.473 0.797 0.756
Chain 1: 800 -12355.015 0.707 0.756
Chain 1: 900 -11817.209 0.634 0.532
Chain 1: 1000 -11462.068 0.573 0.532
Chain 1: 1100 -11166.746 0.524 0.270 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1200 -10933.421 0.482 0.270
Chain 1: 1300 -10697.232 0.447 0.135
Chain 1: 1400 -10483.044 0.416 0.135
Chain 1: 1500 -10300.469 0.390 0.079
Chain 1: 1600 -10105.228 0.366 0.079
Chain 1: 1700 -9927.445 0.346 0.046
Chain 1: 1800 -9769.069 0.328 0.046
Chain 1: 1900 -9612.483 0.311 0.031
Chain 1: 2000 -9461.085 0.296 0.031
Chain 1: 2100 -9324.633 0.283 0.026
Chain 1: 2200 -9205.150 0.271 0.026
Chain 1: 2300 -9077.206 0.260 0.022
Chain 1: 2400 -8968.483 0.249 0.022
Chain 1: 2500 -8864.270 0.240 0.021
Chain 1: 2600 -8759.767 0.231 0.021
Chain 1: 2700 -8667.479 0.223 0.020
Chain 1: 2800 -8582.166 0.215 0.020
Chain 1: 2900 -8502.956 0.208 0.019
Chain 1: 3000 -8437.222 0.201 0.019
Chain 1: 3100 -8362.480 0.195 0.018
Chain 1: 3200 -8298.371 0.189 0.018
Chain 1: 3300 -8246.222 0.184 0.018
Chain 1: 3400 -8189.987 0.179 0.018
Chain 1: 3500 -8144.251 0.174 0.016
Chain 1: 3600 -8089.633 0.169 0.016
Chain 1: 3700 -8048.052 0.165 0.016
Chain 1: 3800 -8016.834 0.160 0.016
Chain 1: 3900 -7969.813 0.156 0.016
Chain 1: 4000 -7946.904 0.153 0.016
Chain 1: 4100 -7915.743 0.149 0.015
Chain 1: 4200 -7869.965 0.146 0.015
Chain 1: 4300 -7852.991 0.142 0.014
Chain 1: 4400 -7824.553 0.139 0.014
Chain 1: 4500 -7796.169 0.136 0.013
Chain 1: 4600 -7774.188 0.133 0.013
Chain 1: 4700 -7754.694 0.130 0.012
Chain 1: 4800 -7733.196 0.128 0.012
Chain 1: 4900 -7714.236 0.125 0.012
Chain 1: 5000 -7690.127 0.123 0.012
Chain 1: 5100 -7681.417 0.103 0.012
Chain 1: 5200 -7663.356 0.071 0.011
Chain 1: 5300 -7649.171 0.045 0.010
Chain 1: 5400 -7639.351 0.030 0.009
Chain 1: 5500 -7624.090 0.019 0.009
Chain 1: 5600 -7608.828 0.014 0.008
Chain 1: 5700 -7596.166 0.011 0.008
Chain 1: 5800 -7592.509 0.010 0.007
Chain 1: 5900 -7583.414 0.009 0.007
Chain 1: 6000 -7572.635 0.008 0.006
Chain 1: 6100 -7568.503 0.008 0.006
Chain 1: 6200 -7565.075 0.007 0.006
Chain 1: 6300 -7556.101 0.007 0.006
Chain 1: 6400 -7550.149 0.007 0.005
Chain 1: 6500 -7545.491 0.006 0.004 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
executing add_exposure_rate
executing check_if_within_posterior
executing save_generated_quantities_in_case
executing fit_to_counts_rng
executing do_inference
Storing counts in `nn`, as `n` already present in input
i Use `name = "new_name"` to pick a new name.
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 0.000795 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.95 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -12530.501 1.000 1.000
Chain 1: 200 -8525.310 0.735 1.000
Chain 1: 300 -7658.908 0.528 0.470
Chain 1: 400 -7514.685 0.401 0.470
Chain 1: 500 -7503.414 0.321 0.113
Chain 1: 600 -7508.541 0.267 0.113
Chain 1: 700 -7498.275 0.229 0.019
Chain 1: 800 -7503.680 0.201 0.019
Chain 1: 900 -7504.435 0.178 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 10500 from the approximate posterior...
Chain 1: COMPLETED.
executing add_exposure_rate
executing check_if_within_posterior
executing save_generated_quantities_in_case
executing fit_to_counts_rng
[ FAIL 0 | WARN 89 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 89 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
102.213 2.581 104.794
ppcseq.Rcheck/ppcseq-Ex.timings
| name | user | system | elapsed | |
| identify_outliers | 23.552 | 0.394 | 23.950 | |
| plot_credible_intervals | 23.038 | 0.332 | 23.371 | |