| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-04-02 19:29 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 2056/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| srnadiff 1.26.0 (landing page) Zytnicki Matthias
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | TIMEOUT | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the srnadiff package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/srnadiff.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: srnadiff |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings srnadiff_1.26.0.tar.gz |
| StartedAt: 2025-04-01 02:38:50 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 03:18:51 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 2400.7 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: srnadiff.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings srnadiff_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/srnadiff.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘srnadiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘srnadiff’ version ‘1.26.0’
* 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 ‘srnadiff’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff'
Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff'
Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff'
Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff'
Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff'
See ‘/home/biocbuild/bbs-3.20-bioc/meat/srnadiff.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
extdata 2.2Mb
libs 3.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘BiocManager’ ‘BiocStyle’
A package should be listed in only one of these fields.
* 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 ... WARNING
checkRd: (5) plotRegions.Rd:115: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:116: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:117: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:118-119: \item in \describe must have non-empty label
checkRd: (5) plotRegions.Rd:120-121: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in Rd file 'srnadiffProcessedExample.Rd' but not in code:
'srnadiffProcessedExample'
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotRegions 12.923 1.862 14.013
parameters 12.071 2.625 12.913
countMatrix 11.587 1.080 11.837
srnadiff 5.998 1.200 6.420
regions 6.149 0.976 6.343
srnadiffDefaultParameters 5.888 1.141 6.245
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
srnadiff.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL srnadiff ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘srnadiff’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ 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 rcpp_hmm.cpp -o rcpp_hmm.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 rcpp_ir.cpp -o rcpp_ir.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 rcpp_main.cpp -o rcpp_main.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 rcpp_utils.cpp -o rcpp_utils.o gcc -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 srnadiff_init.c -o srnadiff_init.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o srnadiff.so RcppExports.o rcpp_hmm.o rcpp_ir.o rcpp_main.o rcpp_utils.o srnadiff_init.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-srnadiff/00new/srnadiff/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff' Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff' Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff' Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff' Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff' Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff' Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff' Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff' Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff' Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff' Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff' Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff' Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff' Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff' Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff' Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff' Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff' Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff' Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff' Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff' Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff' ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import 'IRanges::window<-' by 'stats::window<-' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::cor' by 'stats::cor' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::cov' by 'stats::cov' when loading 'srnadiff' Warning: replacing previous import 'rtracklayer::start' by 'stats::start' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::window' by 'stats::window' when loading 'srnadiff' Warning: replacing previous import 'IRanges::quantile' by 'stats::quantile' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::complete.cases' by 'stats::complete.cases' when loading 'srnadiff' Warning: replacing previous import 'rtracklayer::offset' by 'stats::offset' when loading 'srnadiff' Warning: replacing previous import 'rtracklayer::end' by 'stats::end' when loading 'srnadiff' Warning: replacing previous import 'IRanges::IQR' by 'stats::IQR' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::var' by 'stats::var' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::xtabs' by 'stats::xtabs' when loading 'srnadiff' Warning: replacing previous import 'IRanges::median' by 'stats::median' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::aggregate' by 'stats::aggregate' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::sd' by 'stats::sd' when loading 'srnadiff' Warning: replacing previous import 'IRanges::smoothEnds' by 'stats::smoothEnds' when loading 'srnadiff' Warning: replacing previous import 'S4Vectors::na.exclude' by 'stats::na.exclude' when loading 'srnadiff' Warning: replacing previous import 'IRanges::runmed' by 'stats::runmed' when loading 'srnadiff' Warning: replacing previous import 'IRanges::mad' by 'stats::mad' when loading 'srnadiff' Warning: replacing previous import 'GenomicRanges::update' by 'stats::update' when loading 'srnadiff' ** testing if installed package keeps a record of temporary installation path * DONE (srnadiff)
srnadiff.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
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.
> library(testthat)
> library(srnadiff)
There were 21 warnings (use warnings() to see them)
>
> test_check("srnadiff")
srnadiff.Rcheck/srnadiff-Ex.timings
| name | user | system | elapsed | |
| annotReg | 0.118 | 0.002 | 0.122 | |
| bamFiles | 0.156 | 0.000 | 0.158 | |
| chromosomeSizes | 0.038 | 0.001 | 0.038 | |
| countMatrix | 11.587 | 1.080 | 11.837 | |
| coverages | 0.064 | 0.004 | 0.068 | |
| normFactors | 0.037 | 0.000 | 0.037 | |
| parameters | 12.071 | 2.625 | 12.913 | |
| plotRegions | 12.923 | 1.862 | 14.013 | |
| readAnnotation | 1.069 | 0.034 | 1.103 | |
| regions | 6.149 | 0.976 | 6.343 | |
| sampleInfo | 0.037 | 0.006 | 0.043 | |
| srnadiff | 5.998 | 1.200 | 6.420 | |
| srnadiffDefaultParameters | 5.888 | 1.141 | 6.245 | |
| srnadiffExample | 0.042 | 0.004 | 0.047 | |
| srnadiffExp | 1.894 | 0.206 | 2.101 | |
| srnadiffProcessedExample | 0.037 | 0.003 | 0.041 | |