Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1409/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
normr 1.31.0 (landing page) Johannes Helmuth
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the normr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/normr.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: normr |
Version: 1.31.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:normr.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings normr_1.31.0.tar.gz |
StartedAt: 2024-08-21 03:22:09 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 03:27:51 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 342.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: normr.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:normr.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings normr_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/normr.Rcheck' * using R version 4.4.1 (2024-06-14 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 'normr/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'normr' version '1.31.0' * 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 'normr' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr' See 'F:/biocbuild/bbs-3.20-bioc/meat/normr.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 ... 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 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 ... NOTE Invalid package aliases in Rd file 'normR.Rd': 'normR-package' * checking Rd cross-references ... WARNING Missing link or links in Rd file 'normR-diffR.Rd': '[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}' Missing link or links in Rd file 'normR-enrichR.Rd': '[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}' Missing link or links in Rd file 'normR-regimeR.Rd': '[GenomeInfoDb]{fetchExtendedChromInfoFromUCSC}' See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 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 files in 'vignettes' ... OK * checking examples ... OK * 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, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/normr.Rcheck/00check.log' for details.
normr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL normr ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'normr' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'F:/biocbuild/bbs-3.20-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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em.cpp -o em.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c normr_init.c -o normr_init.o g++ -shared -s -static-libgcc -o normr.dll tmp.def RcppExports.o em.o normr_init.o -fopenmp -D_GLIBCXX_USE_C99 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-normr/00new/normr/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr' Creating a new generic function for 'getClasses' in package 'normr' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr' ** testing if installed package can be loaded from final location Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr' ** testing if installed package keeps a record of temporary installation path * DONE (normr)
normr.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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(testthat) > library(normr) Attaching package: 'normr' The following object is masked from 'package:methods': getClasses Warning message: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr' > > test_check("normr") [ FAIL 0 | WARN 0 | SKIP 2 | PASS 439 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test-CLI.R:4:1', 'test-CLI.R:7:1' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 439 ] > > proc.time() user system elapsed 57.78 1.98 60.03
normr.Rcheck/normr-Ex.timings
name | user | system | elapsed | |
NormRCountConfig-class | 0 | 0 | 0 | |
NormRFit-class | 0.25 | 0.03 | 0.28 | |
normR-diffR | 1.55 | 0.11 | 1.67 | |
normR-enrichR | 1.99 | 0.13 | 2.14 | |
normR-regimeR | 1.14 | 0.09 | 1.24 | |
normR | 1.21 | 0.08 | 1.31 | |