Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 |
Package 1212/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metapod 1.14.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the metapod package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: metapod |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metapod.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metapod_1.14.0.tar.gz |
StartedAt: 2024-12-20 02:23:53 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:28:02 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 249.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metapod.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:metapod.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings metapod_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/metapod.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘metapod/DESCRIPTION’ ... OK * this is package ‘metapod’ version ‘1.14.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 code 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/metapod.Rcheck/00check.log’ for details.
metapod.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL metapod ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘metapod’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-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:81:27: 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:86:27: 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:91:27: 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:96:27: 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:101:27: 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:106:27: 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:111:27: 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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-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-3.20-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-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-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)
metapod.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 6.313 0.162 6.464
metapod.Rcheck/metapod-Ex.timings
name | user | system | elapsed | |
averageGroupedStats | 0.001 | 0.000 | 0.001 | |
averageParallelStats | 0.000 | 0.000 | 0.001 | |
combineGroupedPValues | 0.020 | 0.000 | 0.021 | |
combineParallelPValues | 0.015 | 0.000 | 0.015 | |
countGroupedDirection | 0.001 | 0.000 | 0.000 | |
countParallelDirection | 0.001 | 0.000 | 0.000 | |
groupedBerger | 0.008 | 0.000 | 0.007 | |
groupedFisher | 0.008 | 0.000 | 0.008 | |
groupedHolmMin | 0.008 | 0.000 | 0.008 | |
groupedPearson | 0.005 | 0.000 | 0.005 | |
groupedSimes | 0.008 | 0.000 | 0.008 | |
groupedStouffer | 0.007 | 0.001 | 0.008 | |
groupedWilkinson | 0.007 | 0.000 | 0.008 | |
parallelBerger | 0.005 | 0.000 | 0.006 | |
parallelFisher | 0.006 | 0.000 | 0.006 | |
parallelHolmMin | 0.009 | 0.000 | 0.009 | |
parallelPearson | 0.007 | 0.000 | 0.006 | |
parallelSimes | 0.011 | 0.000 | 0.011 | |
parallelStouffer | 0.009 | 0.000 | 0.009 | |
parallelWilkinson | 0.006 | 0.001 | 0.006 | |
summarizeGroupedDirection | 0.000 | 0.000 | 0.001 | |
summarizeParallelDirection | 0.000 | 0.000 | 0.001 | |