Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-04-17 11:47 -0400 (Thu, 17 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4667
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 1687/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ramr 1.16.0  (landing page)
Oleksii Nikolaienko
Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025)
git_url: https://git.bioconductor.org/packages/ramr
git_branch: RELEASE_3_21
git_last_commit: a19305b
git_last_commit_date: 2025-04-15 12:17:05 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  

CHECK results for ramr on kunpeng2

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.

raw results


Summary

Package: ramr
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2025-04-17 10:28:27 -0000 (Thu, 17 Apr 2025)
EndedAt: 2025-04-17 11:08:28 -0000 (Thu, 17 Apr 2025)
EllapsedTime: 2400.7 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: ramr.Rcheck
Warnings: NA

Command output

##############################################################################
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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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ramr.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ramr/DESCRIPTION’ ... OK
* this is package ‘ramr’ version ‘1.16.0’
* 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 21.715  1.548   13.60
plotAMR          5.098  0.455    5.56
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’

Installation output

ramr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ramr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘ramr’ ...
** this is package ‘ramr’ version ‘1.16.0’
** 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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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/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/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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)

Tests output

ramr.Rcheck/tests/runTests.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("ramr")
Preprocessing data [0.142s]
Computing IQR [0.010s]
Creating genomic ranges [0.053s]
Preprocessing data [0.134s]
Computing IQR [0.006s]
Creating genomic ranges [0.024s]
Preprocessing data [0.132s]
Fitting beta distribution [0.180s]
Creating genomic ranges [0.021s]
Preprocessing data [0.131s]
Fitting beta distribution [0.210s]
Creating genomic ranges [0.021s]
Preprocessing data [0.137s]
Computing IQR [0.005s]
Creating genomic ranges [0.021s]
Preprocessing data [0.132s]
Computing IQR [0.011s]
Creating genomic ranges [0.020s]
Preprocessing data [0.123s]
Computing IQR [0.005s]
Creating genomic ranges [0.020s]
Preprocessing data [0.133s]
Fitting beta distribution [0.177s]
Creating genomic ranges [0.022s]
Preprocessing data [0.135s]
Computing IQR [0.012s]
Creating genomic ranges [0.024s]
Preprocessing data [0.133s]
Fitting beta distribution [0.175s]
Creating genomic ranges [0.020s]
Preprocessing data [0.127s]
Fitting beta distribution [0.198s]
Creating genomic ranges [0.020s]
Preprocessing data [0.126s]
Fitting beta distribution [0.212s]
Creating genomic ranges [0.024s]
Preprocessing data [0.129s]
Fitting beta distribution [0.215s]
Creating genomic ranges [0.035s]
Preprocessing data [0.130s]
Fitting beta distribution [0.185s]
Creating genomic ranges [0.021s]
Preprocessing data [0.130s]
Fitting beta distribution [0.201s]
Creating genomic ranges [0.021s]
Preprocessing data [0.181s]
Fitting beta distribution [0.224s]
Creating genomic ranges [0.032s]
Preprocessing data [0.126s]
Fitting beta distribution [0.116s]
Creating genomic ranges [0.036s]
Preprocessing data [0.123s]
Fitting beta distribution [0.104s]
Creating genomic ranges [0.036s]
Identifying AMRsLoading required package: foreach
Loading required package: rngtools
 [9.082s]
Identifying AMRs [5.494s]
Identifying AMRs [10.572s]
Identifying AMRs

Example timings

ramr.Rcheck/ramr-Ex.timings

nameusersystemelapsed
getAMR0.6110.0400.652
getAMR.obsolete21.715 1.54813.600
getUniverse0.3320.0240.356
plotAMR5.0980.4555.560
ramr.data1.8190.0481.868
simulateAMR0.5220.0120.534
simulateData1.2840.0241.310
simulateData.obsolete3.3050.6123.061