Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-01-16 12:10 -0500 (Thu, 16 Jan 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4387 |
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 1632/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qsea 1.32.0 (landing page) Matthias Lienhard
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the qsea package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qsea.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: qsea |
Version: 1.32.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qsea_1.32.0.tar.gz |
StartedAt: 2025-01-15 05:27:58 -0500 (Wed, 15 Jan 2025) |
EndedAt: 2025-01-15 05:33:16 -0500 (Wed, 15 Jan 2025) |
EllapsedTime: 318.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: qsea.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qsea_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/qsea.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘qsea/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘qsea’ version ‘1.32.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘qsea’ can be installed ... WARNING Found the following significant warnings: lm.c:64:14: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/qsea.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... NOTE checkRd: (-1) fitNBglm.Rd:16: Lost braces 16 | dQuote{log} link function is implemented. } | ^ checkRd: (-1) fitNBglm.Rd:19: Lost braces 19 | Allowed values are dQuote{region_wise} for independent window wise estimates, | ^ checkRd: (-1) fitNBglm.Rd:20: Lost braces 20 | dQuote{common} for a single estimate for all windows, | ^ checkRd: (-1) fitNBglm.Rd:21: Lost braces 21 | dQuote{cutAtQuantiles} for window wise estimates trimmed at the 25\% and 75\% | ^ checkRd: (-1) fitNBglm.Rd:23: Lost braces 23 | or dQuote{initial} for using the dispersion parameters provided with the | ^ checkRd: (-1) plotCNV.Rd:20: Lost braces 20 | \item{dist}{distance measure for clustering. dQuote{euclid}ian | ^ checkRd: (-1) plotCNV.Rd:21: Lost braces 21 | or dQuote{cor}relation based (1-cor)} | ^ * 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 R/sysdata.rda ... 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 addNewSamples 21.141 1.032 22.248 addPatternDensity 7.629 0.436 8.075 addCNV 7.425 0.238 7.710 * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/qsea.Rcheck/00check.log’ for details.
qsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qsea ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘qsea’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lm.c -o lm.o lm.c:64:14: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat] n,p, XLENGTH(y)); ^~~~~~~~~~ 1 warning generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o qsea.so lm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-qsea/00new/qsea/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (qsea)
qsea.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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(qsea) > > test_check("qsea") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] > > proc.time() user system elapsed 14.220 0.501 14.725
qsea.Rcheck/qsea-Ex.timings
name | user | system | elapsed | |
addCNV | 7.425 | 0.238 | 7.710 | |
addContrast | 1.327 | 0.030 | 1.357 | |
addCoverage | 3.854 | 0.116 | 3.974 | |
addEnrichmentParameters | 0.354 | 0.008 | 0.361 | |
addLibraryFactors | 1.003 | 0.090 | 1.094 | |
addNewSamples | 21.141 | 1.032 | 22.248 | |
addOffset | 0.293 | 0.013 | 0.307 | |
addPatternDensity | 7.629 | 0.436 | 8.075 | |
createQseaSet | 0.195 | 0.017 | 0.212 | |
example | 0.210 | 0.006 | 0.215 | |
fitNBglm | 0.805 | 0.066 | 0.872 | |
getPCA | 0.799 | 0.030 | 0.829 | |
isSignificant | 0.993 | 0.052 | 1.047 | |
makeTable | 1.246 | 0.093 | 1.339 | |
normMethod | 0.001 | 0.001 | 0.002 | |
plotCNV | 0.268 | 0.007 | 0.274 | |
plotCoverage | 0.631 | 0.028 | 0.659 | |
plotEnrichmentProfile | 0.329 | 0.039 | 0.368 | |
plotPCA | 0.611 | 0.111 | 0.723 | |
qseaGLM-class | 0.001 | 0.000 | 0.001 | |
qseaPCA-class | 0.000 | 0.000 | 0.001 | |
qseaSet-class | 0.000 | 0.000 | 0.001 | |
regionStats | 0.550 | 0.011 | 0.562 | |