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This page was generated on 2024-03-27 11:36:35 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 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 523/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DegNorm 1.12.0  (landing page)
Ji-Ping Wang
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/DegNorm
git_branch: RELEASE_3_18
git_last_commit: 405e5cb
git_last_commit_date: 2023-10-24 11:22:52 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for DegNorm on palomino4


To the developers/maintainers of the DegNorm package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DegNorm.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: DegNorm
Version: 1.12.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DegNorm.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings DegNorm_1.12.0.tar.gz
StartedAt: 2024-03-26 00:05:13 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 00:12:48 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 455.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DegNorm.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DegNorm.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings DegNorm_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/DegNorm.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DegNorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DegNorm' version '1.12.0'
* 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 'DegNorm' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
    libs      1.2Mb
* 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 R 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 ... 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
read_coverage_batch 4.84   0.22  107.94
degnorm             0.55   0.10   48.35
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/DegNorm.Rcheck/00check.log'
for details.



Installation output

DegNorm.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL DegNorm
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'DegNorm' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c degnormCPP.cpp -o degnormCPP.o
g++ -shared -s -static-libgcc -o DegNorm.dll tmp.def RcppExports.o degnormCPP.o -fopenmp -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-DegNorm/00new/DegNorm/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DegNorm)

Tests output


Example timings

DegNorm.Rcheck/DegNorm-Ex.timings

nameusersystemelapsed
PlotFunctions2.110.083.47
coverage_res_chr210.110.000.11
degnorm 0.55 0.1048.35
plot_coverage1.670.031.70
read_coverage_batch 4.84 0.22107.94
res_DegNorm_chr210.060.000.06
summary_CoverageClass0.100.000.09
summary_DegNormClass0.080.000.08