| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-08 11:41:26 -0400 (Wed, 08 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4707 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 2071/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| srnadiff 1.24.0 (landing page) Zytnicki Matthias
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: srnadiff |
| Version: 1.24.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings srnadiff_1.24.0.tar.gz |
| StartedAt: 2024-05-08 12:21:43 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 12:32:29 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 645.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: srnadiff.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:srnadiff.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings srnadiff_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/srnadiff.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘srnadiff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘srnadiff’ version ‘1.24.0’
* 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-3.19-bioc/meat/srnadiff.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
extdata 2.0Mb
libs 4.7Mb
* 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotRegions 16.022 1.639 16.558
parameters 14.816 2.479 16.456
countMatrix 13.457 1.049 13.375
srnadiff 6.947 1.035 6.974
regions 6.866 0.968 6.871
srnadiffDefaultParameters 6.792 0.987 6.833
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/srnadiff.Rcheck/00check.log’
for details.
srnadiff.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL srnadiff ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘srnadiff’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_utils.cpp -o rcpp_utils.o gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 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.
> library(testthat)
> library(srnadiff)
There were 21 warnings (use warnings() to see them)
>
> test_check("srnadiff")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
>
> proc.time()
user system elapsed
120.100 14.791 122.969
srnadiff.Rcheck/srnadiff-Ex.timings
| name | user | system | elapsed | |
| annotReg | 0.167 | 0.004 | 0.183 | |
| bamFiles | 0.262 | 0.000 | 0.263 | |
| chromosomeSizes | 0.048 | 0.000 | 0.048 | |
| countMatrix | 13.457 | 1.049 | 13.375 | |
| coverages | 0.095 | 0.008 | 0.103 | |
| normFactors | 0.053 | 0.000 | 0.052 | |
| parameters | 14.816 | 2.479 | 16.456 | |
| plotRegions | 16.022 | 1.639 | 16.558 | |
| readAnnotation | 1.476 | 0.039 | 1.520 | |
| regions | 6.866 | 0.968 | 6.871 | |
| sampleInfo | 0.079 | 0.020 | 0.099 | |
| srnadiff | 6.947 | 1.035 | 6.974 | |
| srnadiffDefaultParameters | 6.792 | 0.987 | 6.833 | |
| srnadiffExample | 0.053 | 0.000 | 0.053 | |
| srnadiffExp | 1.721 | 0.076 | 1.801 | |