Oleksii Nikolaienko
| Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/ramr |
| git_branch: devel |
| git_last_commit: 87b137f |
| git_last_commit_date: 2025-07-06 07:03:47 -0400 (Sun, 06 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-20 12:07 -0400 (Sat, 20 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
| 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 1682/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ramr 1.17.1 (landing page) Oleksii Nikolaienko
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ramr |
| Version: 1.17.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ramr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ramr_1.17.1.tar.gz |
| StartedAt: 2025-09-19 12:00:13 -0000 (Fri, 19 Sep 2025) |
| EndedAt: 2025-09-19 12:40:13 -0000 (Fri, 19 Sep 2025) |
| EllapsedTime: 2400.1 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: ramr.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:ramr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ramr_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ramr.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 22.688 1.630 24.916
plotAMR 6.722 0.285 10.095
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ramr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ramr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘ramr’ ... ** this is package ‘ramr’ version ‘1.17.1’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++20 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++20 -shared -L/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
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Type 'q()' to quit R.
> BiocGenerics:::testPackage("ramr")
Preprocessing data [0.252s]
Computing IQR [0.009s]
Creating genomic ranges [0.052s]
Preprocessing data [0.137s]
Computing IQR [0.012s]
Creating genomic ranges [0.021s]
Loading required namespace: GenomeInfoDb
Preprocessing data [0.132s]
Fitting beta distribution [0.176s]
Creating genomic ranges [0.020s]
Preprocessing data [0.130s]
Fitting beta distribution [0.207s]
Creating genomic ranges [0.021s]
Preprocessing data [0.137s]
Computing IQR [0.003s]
Creating genomic ranges [0.033s]
Preprocessing data [0.129s]
Computing IQR [0.009s]
Creating genomic ranges [0.021s]
Preprocessing data [0.127s]
Computing IQR [0.005s]
Creating genomic ranges [0.021s]
Preprocessing data [0.138s]
Fitting beta distribution [0.252s]
Creating genomic ranges [0.022s]
Preprocessing data [0.137s]
Computing IQR [0.009s]
Creating genomic ranges [0.030s]
Preprocessing data [0.126s]
Fitting beta distribution [0.172s]
Creating genomic ranges [0.022s]
Preprocessing data [0.162s]
Fitting beta distribution [0.195s]
Creating genomic ranges [0.023s]
Preprocessing data [0.160s]
Fitting beta distribution [0.263s]
Creating genomic ranges [0.029s]
Preprocessing data [0.132s]
Fitting beta distribution [0.216s]
Creating genomic ranges [0.034s]
Preprocessing data [0.125s]
Fitting beta distribution [0.186s]
Creating genomic ranges [0.026s]
Preprocessing data [0.189s]
Fitting beta distribution [0.232s]
Creating genomic ranges [0.022s]
Preprocessing data [0.212s]
Fitting beta distribution [0.284s]
Creating genomic ranges [0.064s]
Preprocessing data [0.168s]
Fitting beta distribution [0.111s]
Creating genomic ranges [0.034s]
Preprocessing data [0.125s]
Fitting beta distribution [0.100s]
Creating genomic ranges [0.034s]
Identifying AMRsLoading required package: foreach
Loading required package: rngtools
[11.485s]
Identifying AMRs [7.552s]
Identifying AMRs [17.770s]
Identifying AMRs [17.168s]
Identifying AMRs [6.195s]
Identifying AMRs [171.808s]
Preprocessing data [0.329s]
Plotting 5 genomic ranges Plotting 5 genomic ranges 20% 40% 60% 80%100%[1.514s]
Plotting 6 genomic ranges 17% 33% 50% 67% 83%100%[2.341s]
'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 [0.134s]
Simulating data [0.005s]
Introducing epimutations[0.107s]
Preprocessing data [0.144s]
Simulating data [0.006s]
Introducing epimutations[0.118s]
Preprocessing data [0.141s]
Simulating data [0.053s]
Preprocessing data [0.140s]
Simulating data [0.052s]
Preprocessing data [0.147s]
Simulating data [0.055s]
Preprocessing data [0.137s]
Simulating data [0.051s]
Simulating data
ramr.Rcheck/ramr-Ex.timings
| name | user | system | elapsed | |
| getAMR | 0.630 | 0.028 | 0.686 | |
| getAMR.obsolete | 22.688 | 1.630 | 24.916 | |
| getUniverse | 0.317 | 0.008 | 0.650 | |
| plotAMR | 6.722 | 0.285 | 10.095 | |
| ramr.data | 2.277 | 0.025 | 4.158 | |
| simulateAMR | 0.551 | 0.016 | 0.571 | |
| simulateData | 1.502 | 0.075 | 1.612 | |
| simulateData.obsolete | 3.165 | 0.590 | 4.760 | |