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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).

CHECK results for metapod on nebbiolo1

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? here 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 1091/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metapod 1.0.0  (landing page)
Aaron Lun
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/metapod
git_branch: RELEASE_3_13
git_last_commit: 704fa80
git_last_commit_date: 2021-05-19 12:58:08 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: metapod
Version: 1.0.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:metapod.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings metapod_1.0.0.tar.gz
StartedAt: 2021-10-14 10:31:13 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:31:37 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 24.2 seconds
RetCode: 0
Status:   OK  
CheckDir: metapod.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:metapod.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings metapod_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/metapod.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metapod/DESCRIPTION’ ... OK
* this is package ‘metapod’ version ‘1.0.0’
* 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
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/metapod.Rcheck/00check.log’
for details.



Installation output

metapod.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL metapod
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘metapod’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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)

Tests output

metapod.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

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 
  5.958   0.102   6.043 

Example timings

metapod.Rcheck/metapod-Ex.timings

nameusersystemelapsed
averageGroupedStats0.0020.0000.002
averageParallelStats0.0000.0010.001
combineGroupedPValues0.0250.0000.025
combineParallelPValues0.0130.0000.013
countGroupedDirection0.0010.0010.002
countParallelDirection0.0000.0020.002
groupedBerger0.0070.0030.010
groupedFisher0.0060.0000.007
groupedHolmMin0.010.000.01
groupedPearson0.0060.0040.010
groupedSimes0.010.000.01
groupedStouffer0.0100.0000.009
groupedWilkinson0.0030.0040.007
parallelBerger0.0080.0000.008
parallelFisher0.0030.0080.011
parallelHolmMin0.0120.0000.012
parallelPearson0.0000.0070.008
parallelSimes0.0110.0000.012
parallelStouffer0.0120.0040.017
parallelWilkinson0.0050.0040.008
summarizeGroupedDirection0.0010.0000.002
summarizeParallelDirection0.0000.0010.002