| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:20 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1499/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ppcseq 1.7.0 (landing page) Stefano Mangiola
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ppcseq |
| Version: 1.7.0 |
| 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/library --timings ppcseq_1.7.0.tar.gz |
| StartedAt: 2023-02-07 11:38:25 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 11:54:48 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 983.6 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/library --timings ppcseq_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ppcseq.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ppcseq/DESCRIPTION’ ... OK
* this is package ‘ppcseq’ version ‘1.7.0’
* 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 installed package size ... NOTE
installed size is 46.0Mb
sub-directories of 1Mb or more:
data 1.6Mb
libs 44.0Mb
* 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 25.306 0.226 25.571
plot_credible_intervals 24.447 0.215 24.710
* 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
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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++14
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_negBinomial_MPI.cc -o stanExports_negBinomial_MPI.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/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/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/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/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/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/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/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/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/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/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/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/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/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/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/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/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/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/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/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/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/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/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/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/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/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/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/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/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/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/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/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/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/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/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/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/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_args.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:20,
from /home/biocbuild/bbs-3.17-bioc/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/library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:278,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/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/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpmf(const T_prob&, const T_prior_size&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_prob, T_prior_size>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
60 | using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
| ^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:328,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/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/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T4>::value, Eigen::Array<typename stan::partials_return_type<T_alpha>::type, -1, 1>, typename stan::partials_return_type<T_alpha>::type>’ locally defined but not used [-Wunused-local-typedefs]
52 | using T_alpha_val = typename std::conditional_t<
| ^~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/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/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/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/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/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/library/StanHeaders/include/stan/math/rev/mat.hpp:51,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/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/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vv_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<stan::math::var, R2, C2, (Eigen::AutoAlign | (((R2 == 1) && (C2 != 1)) ? Eigen::RowMajor : (((C2 == 1) && (R2 != 1)) ? Eigen::ColMajor : Eigen::ColMajor))), R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<stan::math::var, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
27 | using idx_t = typename index_type<matrix_v>::type;
| ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vd_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<double, R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<double, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
64 | using idx_t = typename index_type<matrix_d>::type;
| ^~~~~
In file included from stanExports_negBinomial_MPI.cc:5:
stanExports_negBinomial_MPI.h: In member function ‘virtual void model_negBinomial_MPI_namespace::model_negBinomial_MPI::transform_inits(const stan::io::var_context&, std::vector<int>&, std::vector<double>&, std::ostream*) const’:
stanExports_negBinomial_MPI.h:764:24: warning: typedef ‘local_scalar_t__’ locally defined but not used [-Wunused-local-typedefs]
764 | typedef double local_scalar_t__;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/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/library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
74 | for (int i = 0; i < dims.size(); i++) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/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/library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_negBinomial_MPI_namespace::model_negBinomial_MPI; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’:
stanExports_negBinomial_MPI.cc:30:89: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1238:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
1238 | int ret = stan::services::error_codes::CONFIG;
| ^~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/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/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_negBinomial_MPI_namespace::model_negBinomial_MPI; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_negBinomial_MPI_namespace::model_negBinomial_MPI; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_negBinomial_MPI.cc:30:89: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:91:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
91 | if (p_names.size() != draws.cols()) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:109:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
109 | for (size_t i = 0; i < draws.rows(); ++i) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/err/check_cholesky_factor.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:9,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/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/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp: In instantiation of ‘static void stan::math::internal::less_or_equal<T_y, T_high, is_vec>::check(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int; bool is_vec = false]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:64:74: required from ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:19:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘long int’ [-Wsign-compare]
19 | if (!(y <= high_vec[n])) {
| ~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/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/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘void stan::services::get_model_parameters(const Model&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::vector<long unsigned int> >&) [with Model = model_negBinomial_MPI_namespace::model_negBinomial_MPI]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:105:23: required from ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_negBinomial_MPI_namespace::model_negBinomial_MPI; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_negBinomial_MPI_namespace::model_negBinomial_MPI; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_negBinomial_MPI.cc:30:89: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:41:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
41 | for (int j = 0; j < dimss[i].size(); ++j)
| ~~^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:46,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/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/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
14 | static void set_zero_all_adjoints() {
| ^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Core:503,
from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stanExports_negBinomial_MPI.h:20,
from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function ‘static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, false>; Lhs = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, 1> >, const Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>, -1, 1, false> >]’:
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:227:7: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
225 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
226 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
227 | (
| ^
228 | lhs.rows(), // size
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
229 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
230 | actualRhsPtr, // rhs info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
231 | actualDestPtr, // result info
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
232 | actualAlpha // scale factor
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
233 | );
| ~
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:39:24: note: by argument 4 of type ‘const double*’ to ‘static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]’ declared here
39 | EIGEN_DONT_INLINE void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o ppcseq.so RcppExports.o stanExports_negBinomial_MPI.o -L/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "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:
Chain 1: Gradient evaluation took 0.000748 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.48 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 -12604.314 1.000 1.000
Chain 1: 200 -8487.256 0.743 1.000
Chain 1: 300 -7642.400 0.532 0.485
Chain 1: 400 -7543.865 0.402 0.485
Chain 1: 500 -7531.826 0.322 0.111
Chain 1: 600 -7533.844 0.268 0.111
Chain 1: 700 -7521.979 0.230 0.013
Chain 1: 800 -7524.587 0.202 0.013
Chain 1: 900 -7518.693 0.179 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 0.000777 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.77 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 -12261.043 1.000 1.000
Chain 1: 200 -8491.215 0.722 1.000
Chain 1: 300 -7601.884 0.520 0.444
Chain 1: 400 -7529.367 0.393 0.444
Chain 1: 500 -7523.123 0.314 0.117
Chain 1: 600 -7511.846 0.262 0.117
Chain 1: 700 -7504.601 0.225 0.010
Chain 1: 800 -7510.263 0.197 0.010
Chain 1: 900 -7504.849 0.175 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 0.000821 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 8.21 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 -12737.498 1.000 1.000
Chain 1: 200 -8641.491 0.737 1.000
Chain 1: 300 -7624.115 0.536 0.474
Chain 1: 400 -7530.887 0.405 0.474
Chain 1: 500 -7526.744 0.324 0.133
Chain 1: 600 -7538.364 0.270 0.133
Chain 1: 700 -7522.167 0.232 0.012
Chain 1: 800 -7523.188 0.203 0.012
Chain 1: 900 -7530.113 0.181 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: 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:
Chain 1: Gradient evaluation took 0.000668 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.68 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 -541778.926 1.000 1.000
Chain 1: 200 -193059.514 1.403 1.806
Chain 1: 300 -134758.881 1.080 1.000
Chain 1: 400 -27323.561 1.793 1.806
Chain 1: 500 -17851.300 1.540 1.000
Chain 1: 600 -13679.799 1.334 1.000
Chain 1: 700 -10747.206 1.183 0.531
Chain 1: 800 -8793.049 1.063 0.531
Chain 1: 900 -7917.084 0.957 0.433
Chain 1: 1000 -7606.871 0.865 0.433
Chain 1: 1100 -7513.594 0.788 0.305 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1200 -7503.265 0.722 0.305 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1300 -7507.155 0.667 0.273 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1400 -7498.275 0.619 0.273 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1500 -7493.815 0.578 0.222 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1600 -7489.159 0.542 0.222 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1700 -7491.067 0.510 0.111 MAY BE DIVERGING... INSPECT ELBO
Chain 1: 1800 -7485.753 0.482 0.111
Chain 1: 1900 -7486.930 0.456 0.041
Chain 1: 2000 -7503.969 0.434 0.041
Chain 1: 2100 -7489.090 0.413 0.012
Chain 1: 2200 -7504.398 0.394 0.012
Chain 1: 2300 -7483.510 0.377 0.003 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 91 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 91 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
97.645 4.155 119.696
ppcseq.Rcheck/ppcseq-Ex.timings
| name | user | system | elapsed | |
| identify_outliers | 25.306 | 0.226 | 25.571 | |
| plot_credible_intervals | 24.447 | 0.215 | 24.710 | |