Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-02 12:05 -0400 (Sat, 02 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4535 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 1668/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ramr 1.17.1 (landing page) Oleksii Nikolaienko
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the ramr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ramr.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: ramr |
Version: 1.17.1 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ramr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ramr_1.17.1.tar.gz |
StartedAt: 2025-08-02 01:49:48 -0400 (Sat, 02 Aug 2025) |
EndedAt: 2025-08-02 01:54:29 -0400 (Sat, 02 Aug 2025) |
EllapsedTime: 280.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ramr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ramr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ramr_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ramr.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘ramr/DESCRIPTION’ ... OK * this is package ‘ramr’ version ‘1.17.1’ * 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 ‘ramr’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... OK Not all R platforms support C++20 * checking installed package size ... INFO installed size is 9.9Mb sub-directories of 1Mb or more: data 2.0Mb libs 7.7Mb * 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 whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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 ... OK * 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 getAMR.obsolete 16.064 2.102 11.199 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/ramr.Rcheck/00check.log’ for details.
ramr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ramr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ramr’ ... ** this is package ‘ramr’ version ‘1.17.1’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++20 g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_compute_logp.cpp -o rcpp_compute_logp.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_compute_xiqr.cpp -o rcpp_compute_xiqr.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_create_granges.cpp -o rcpp_create_granges.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_filter_threshold.cpp -o rcpp_filter_threshold.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_fit_beta.cpp -o rcpp_fit_beta.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_fit_betabinom.cpp -o rcpp_fit_betabinom.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_fit_binom.cpp -o rcpp_fit_binom.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_generate_random_values.cpp -o rcpp_generate_random_values.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_get_iqr.cpp -o rcpp_get_iqr.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_get_meanvar.cpp -o rcpp_get_meanvar.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_helper_functions.cpp -o rcpp_helper_functions.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_prepare_data.cpp -o rcpp_prepare_data.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c rcpp_test_omp.cpp -o rcpp_test_omp.o g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o ramr.so RcppExports.o rcpp_compute_logp.o rcpp_compute_xiqr.o rcpp_create_granges.o rcpp_filter_threshold.o rcpp_fit_beta.o rcpp_fit_betabinom.o rcpp_fit_binom.o rcpp_generate_random_values.o rcpp_get_iqr.o rcpp_get_meanvar.o rcpp_helper_functions.o rcpp_prepare_data.o rcpp_test_omp.o -fopenmp -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-ramr/00new/ramr/libs ** R ** data ** 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 (ramr)
ramr.Rcheck/tests/runTests.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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. > BiocGenerics:::testPackage("ramr") Preprocessing data [0.092s] Computing IQR [0.007s] Creating genomic ranges [0.037s] Preprocessing data [0.085s] Computing IQR [0.004s] Creating genomic ranges [0.014s] Loading required namespace: GenomeInfoDb Preprocessing data [0.087s] Fitting beta distribution [0.095s] Creating genomic ranges [0.016s] Preprocessing data [0.085s] Fitting beta distribution [0.109s] Creating genomic ranges [0.014s] Preprocessing data [0.090s] Computing IQR [0.002s] Creating genomic ranges [0.015s] Preprocessing data [0.087s] Computing IQR [0.006s] Creating genomic ranges [0.014s] Preprocessing data [0.086s] Computing IQR [0.004s] Creating genomic ranges [0.015s] Preprocessing data [0.090s] Fitting beta distribution [0.094s] Creating genomic ranges [0.015s] Preprocessing data [0.087s] Computing IQR [0.007s] Creating genomic ranges [0.020s] Preprocessing data [0.084s] Fitting beta distribution [0.093s] Creating genomic ranges [0.014s] Preprocessing data [0.082s] Fitting beta distribution [0.104s] Creating genomic ranges [0.015s] Preprocessing data [0.083s] Fitting beta distribution [0.109s] Creating genomic ranges [0.017s] Preprocessing data [0.086s] Fitting beta distribution [0.111s] Creating genomic ranges [0.023s] Preprocessing data [0.082s] Fitting beta distribution [0.097s] Creating genomic ranges [0.015s] Preprocessing data [0.082s] Fitting beta distribution [0.105s] Creating genomic ranges [0.014s] Preprocessing data [0.114s] Fitting beta distribution [0.117s] Creating genomic ranges [0.023s] Preprocessing data [0.087s] Fitting beta distribution [0.066s] Creating genomic ranges [0.024s] Preprocessing data [0.082s] Fitting beta distribution [0.059s] Creating genomic ranges [0.024s] Identifying AMRsLoading required package: foreach Loading required package: rngtools [6.246s] Identifying AMRs [4.224s] Identifying AMRs [7.718s] Identifying AMRs [7.109s] Identifying AMRs [3.465s] Identifying AMRs [75.237s] Preprocessing data [0.101s] Plotting 5 genomic ranges Plotting 5 genomic ranges 20% 40% 60% 80%100%[0.568s] Plotting 6 genomic ranges 17% 33% 50% 67% 83%100%[0.658s] 'nsamples' has been set to the maximum possible value of 143 'regions.per.sample' has been set to the maximum possible value of 1 'samples.per.region' has been set to the maximum possible value of 143 'regions.per.sample' has been set to the maximum possible value of 4 'regions.per.sample' has been set to the maximum possible value of 15 Preprocessing data [0.091s] Simulating data [0.004s] Introducing epimutations[0.059s] Preprocessing data [0.095s] Simulating data [0.005s] Introducing epimutations[0.056s] Preprocessing data [0.111s] Simulating data [0.041s] Preprocessing data [0.118s] Simulating data [0.041s] Preprocessing data [0.159s] Simulating data [0.040s] Preprocessing data [0.099s] Simulating data [0.041s] Simulating data [0.950s] Introducing epimutations [0.066s] Simulating data [0.937s] Introducing epimutations [0.082s] RUNIT TEST PROTOCOL -- Sat Aug 2 01:53:26 2025 *********************************************** Number of test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : ramr RUnit Tests - 8 test functions, 0 errors, 0 failures Number of test functions: 8 Number of errors: 0 Number of failures: 0 Warning messages: 1: In foreach::foreach(chunk = chunks, .combine = c) %dorng% matrixStats::rowMedians(betas[chunk, : Foreach loop (doParallelMC) had changed the current RNG type: RNG was restored to same type, next state 2: In foreach::foreach(chunk = chunks, .combine = c) %dorng% matrixStats::rowIQRs(betas[chunk, : Foreach loop (doParallelMC) had changed the current RNG type: RNG was restored to same type, next state 3: In foreach::foreach(column = colnames(betas.filtered)) %dorng% getMergedRanges(column) : Foreach loop (doParallelMC) had changed the current RNG type: RNG was restored to same type, next state > > proc.time() user system elapsed 211.490 7.999 125.733
ramr.Rcheck/ramr-Ex.timings
name | user | system | elapsed | |
getAMR | 0.486 | 0.041 | 0.528 | |
getAMR.obsolete | 16.064 | 2.102 | 11.199 | |
getUniverse | 0.305 | 0.024 | 0.331 | |
plotAMR | 4.208 | 0.178 | 4.328 | |
ramr.data | 1.414 | 0.043 | 1.417 | |
simulateAMR | 0.45 | 0.01 | 0.46 | |
simulateData | 1.033 | 0.052 | 1.072 | |
simulateData.obsolete | 1.972 | 0.705 | 2.096 | |