Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-12-23 11:43 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 2041/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
srnadiff 1.27.1  (landing page)
Zytnicki Matthias
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/srnadiff
git_branch: devel
git_last_commit: ab43752
git_last_commit_date: 2024-12-18 09:49:18 -0500 (Wed, 18 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    TIMEOUT  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    TIMEOUT    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    TIMEOUT    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    TIMEOUT  


CHECK results for srnadiff on palomino7

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.

raw results


Summary

Package: srnadiff
Version: 1.27.1
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:srnadiff.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings srnadiff_1.27.1.tar.gz
StartedAt: 2024-12-23 05:18:06 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 05:58:08 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 2401.3 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: srnadiff.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:srnadiff.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings srnadiff_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/srnadiff.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'srnadiff/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'srnadiff' version '1.27.1'
* 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 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 'E:/biocbuild/bbs-3.21-bioc/meat/srnadiff.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotRegions.Rd: GenomeAxisTrack, GeneRegionTrack, AnnotationTrack,
    DataTrack
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/srnadiff/libs/x64/srnadiff.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
parameters                20.17   0.95   72.61
plotRegions               18.00   0.53   43.72
countMatrix               14.36   0.61   40.50
regions                   10.27   0.48   35.68
srnadiffDefaultParameters 10.07   0.49   36.19
srnadiff                   9.64   0.42   35.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'

Installation output

srnadiff.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL srnadiff
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'srnadiff' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
using C++11
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c rcpp_hmm.cpp -o rcpp_hmm.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c rcpp_ir.cpp -o rcpp_ir.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c rcpp_main.cpp -o rcpp_main.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c rcpp_utils.cpp -o rcpp_utils.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c srnadiff_init.c -o srnadiff_init.o
g++ -shared -s -static-libgcc -o srnadiff.dll tmp.def RcppExports.o rcpp_hmm.o rcpp_ir.o rcpp_main.o rcpp_utils.o srnadiff_init.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-srnadiff/00new/srnadiff/libs/x64
** 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'
** 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)

Tests output

srnadiff.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(Rcpp)
> library(testthat)
> library(srnadiff)
There were 21 warnings (use warnings() to see them)
> 
> test_check("srnadiff")

Example timings

srnadiff.Rcheck/srnadiff-Ex.timings

nameusersystemelapsed
annotReg0.190.000.19
bamFiles0.340.020.36
chromosomeSizes0.050.020.06
countMatrix14.36 0.6140.50
coverages0.110.000.11
normFactors0.030.000.03
parameters20.17 0.9572.61
plotRegions18.00 0.5343.72
readAnnotation2.420.062.56
regions10.27 0.4835.68
sampleInfo0.040.000.04
srnadiff 9.64 0.4235.33
srnadiffDefaultParameters10.07 0.4936.19
srnadiffExample0.050.000.05
srnadiffExp3.970.424.39