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This page was generated on 2022-10-19 13:21:48 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for metapod on palomino3


To the developers/maintainers of the metapod package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metapod.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.

raw results

Package 1133/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metapod 1.4.0  (landing page)
Aaron Lun
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/metapod
git_branch: RELEASE_3_15
git_last_commit: e71c207
git_last_commit_date: 2022-04-26 12:11:10 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: metapod
Version: 1.4.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metapod.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings metapod_1.4.0.tar.gz
StartedAt: 2022-10-19 01:42:24 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 01:43:21 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 57.5 seconds
RetCode: 0
Status:   OK  
CheckDir: metapod.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metapod.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings metapod_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/metapod.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'metapod/DESCRIPTION' ... OK
* this is package 'metapod' version '1.4.0'
* 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 whether package 'metapod' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/metapod/libs/x64/metapod.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/metapod.Rcheck/00check.log'
for details.



Installation output

metapod.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL metapod
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'metapod' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   68 |     if (counter != pvals.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long int'} and 'const size_t' {aka 'const long 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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   72 |                 if (nelements != vectors[p].size()) {
      |                     ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   72 |                 if (nelements != vectors[p].size()) {
      |                     ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long 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 long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
g++ -shared -s -static-libgcc -o metapod.dll tmp.def RcppExports.o combine_group.o combine_parallel.o count_direction.o summarize_direction.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-metapod/00new/metapod/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metapod)

Tests output

metapod.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(metapod)
> test_check("metapod")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 552 ]
> 
> proc.time()
   user  system elapsed 
   7.95    0.18    8.18 

Example timings

metapod.Rcheck/metapod-Ex.timings

nameusersystemelapsed
averageGroupedStats000
averageParallelStats000
combineGroupedPValues0.010.000.02
combineParallelPValues0.020.020.03
countGroupedDirection000
countParallelDirection000
groupedBerger0.010.000.02
groupedFisher000
groupedHolmMin0.020.000.01
groupedPearson0.000.010.02
groupedSimes000
groupedStouffer0.010.000.01
groupedWilkinson000
parallelBerger0.020.000.02
parallelFisher0.020.000.01
parallelHolmMin000
parallelPearson0.010.000.02
parallelSimes0.020.000.02
parallelStouffer000
parallelWilkinson0.010.000.01
summarizeGroupedDirection000
summarizeParallelDirection000