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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:metapod.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings metapod_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/metapod.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘metapod/DESCRIPTION’ ... OK
* this is package ‘metapod’ version ‘1.7.0’
* 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 ‘metapod’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘overview.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/metapod.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL metapod
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘metapod’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c combine_group.cpp -o combine_group.o
combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_simes; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
combine_group.cpp:81:64:   required from here
combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   41 |     for (size_t g = 0; g < runs.size(); ++g) {
      |                        ~~^~~~~~~~~~~~~
combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   68 |     if (counter != pvals.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~
combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_berger; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
combine_group.cpp:86:65:   required from here
combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   41 |     for (size_t g = 0; g < runs.size(); ++g) {
      |                        ~~^~~~~~~~~~~~~
combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   68 |     if (counter != pvals.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~
combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_wilkinson; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
combine_group.cpp:91:83:   required from here
combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   41 |     for (size_t g = 0; g < runs.size(); ++g) {
      |                        ~~^~~~~~~~~~~~~
combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   68 |     if (counter != pvals.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~
combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_holm_min; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
combine_group.cpp:96:82:   required from here
combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   41 |     for (size_t g = 0; g < runs.size(); ++g) {
      |                        ~~^~~~~~~~~~~~~
combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   68 |     if (counter != pvals.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~
combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_stouffer; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
combine_group.cpp:101:67:   required from here
combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   41 |     for (size_t g = 0; g < runs.size(); ++g) {
      |                        ~~^~~~~~~~~~~~~
combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   68 |     if (counter != pvals.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~
combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_fisher; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
combine_group.cpp:106:65:   required from here
combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   41 |     for (size_t g = 0; g < runs.size(); ++g) {
      |                        ~~^~~~~~~~~~~~~
combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   68 |     if (counter != pvals.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~
combine_group.cpp: In instantiation of ‘Rcpp::List compute_grouped(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::RObject, bool, const PREP&) [with PREP = p_pearson; Rcpp::List = Rcpp::Vector<19>; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
combine_group.cpp:111:66:   required from here
combine_group.cpp:41:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   41 |     for (size_t g = 0; g < runs.size(); ++g) {
      |                        ~~^~~~~~~~~~~~~
combine_group.cpp:68:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   68 |     if (counter != pvals.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c combine_parallel.cpp -o combine_parallel.o
combine_parallel.cpp: In constructor ‘parallel_weight_server::parallel_weight_server(size_t, size_t, Rcpp::RObject)’:
combine_parallel.cpp:28:36: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
   28 |                 if (wrepeat.size() != nvectors) {
      |                     ~~~~~~~~~~~~~~~^~~~~~~~~~~
In file included from p_berger.h:4,
                 from combine_parallel.cpp:1:
utils.h: In instantiation of ‘parallel_vectors<V>::parallel_vectors(Rcpp::List) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>]’:
combine_parallel.cpp:20:82:   required from here
utils.h:72:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   72 |                 if (nelements != vectors[p].size()) {
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c count_direction.cpp -o count_direction.o
count_direction.cpp: In function ‘Rcpp::List count_grouped_direction(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::NumericVector, int, double, double, bool)’:
count_direction.cpp:95:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   95 |     for (size_t g = 0; g < runs.size(); ++g) {
      |                        ~~^~~~~~~~~~~~~
count_direction.cpp:98:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   98 |             if (counter >= pvalues.size()) {
      |                 ~~~~~~~~^~~~~~~~~~~~~~~~~
count_direction.cpp:120:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  120 |     if (counter != pvalues.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from count_direction.cpp:2:
utils.h: In instantiation of ‘parallel_vectors<V>::parallel_vectors(Rcpp::List) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>]’:
count_direction.cpp:40:58:   required from here
utils.h:72:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   72 |                 if (nelements != vectors[p].size()) {
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c summarize_direction.cpp -o summarize_direction.o
summarize_direction.cpp: In function ‘Rcpp::IntegerVector summarize_grouped_direction(Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::LogicalVector, double)’:
summarize_direction.cpp:43:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   43 |     for (size_t g = 0; g < runs.size(); ++g) {
      |                        ~~^~~~~~~~~~~~~
summarize_direction.cpp:46:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   46 |             if (counter >= effects.size()) {
      |                 ~~~~~~~~^~~~~~~~~~~~~~~~~
summarize_direction.cpp:61:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   61 |     if (counter != effects.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from summarize_direction.cpp:2:
utils.h: In instantiation of ‘parallel_vectors<V>::parallel_vectors(Rcpp::List) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>]’:
summarize_direction.cpp:10:58:   required from here
utils.h:72:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   72 |                 if (nelements != vectors[p].size()) {
utils.h: In instantiation of ‘parallel_vectors<V>::parallel_vectors(Rcpp::List) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>]’:
summarize_direction.cpp:11:66:   required from here
utils.h:72:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o metapod.so RcppExports.o combine_group.o combine_parallel.o count_direction.o summarize_direction.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-metapod/00new/metapod/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metapod)

R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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Type 'contributors()' for more information and
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Type 'q()' to quit R.

> library(testthat)
> library(metapod)
> test_check("metapod")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 552 ]
> 
> proc.time()
   user  system elapsed 
  7.543   0.203   7.733