Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:21 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the qsea package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1567/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qsea 1.24.0 (landing page) Matthias Lienhard
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: qsea |
Version: 1.24.0 |
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_1.24.0.tar.gz |
StartedAt: 2023-04-10 22:02:29 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 22:06:28 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 238.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: qsea.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### 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_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/qsea.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘qsea/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘qsea’ version ‘1.24.0’ * 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 ... OK * 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 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 ... NOTE subdivideRegions: no visible global function definition for ‘metadata’ Undefined global functions or variables: metadata * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'getPCA': getPCA Code: function(qs, chr = getChrNames(qs), ROIs, minRowSum = 20, keep, norm_method = normMethod(logRPM = c("log", "library_size", "cnv", "preference", "psC10")), topVar = 1000, samples = getSampleNames(qs), minEnrichment = 0) Docs: function(qs, chr = getChrNames(qs), ROIs, minRowSum = 20, keep, norm_method = normMethod(logRPM = c("log", "library_size", "cnv", "preference", "psC10")), topVar = 1000, samples = getSampleNames(qs)) Argument names in code not in docs: minEnrichment * checking Rd \usage sections ... WARNING Documented arguments not in \usage in documentation object 'getPCA': ‘minEnrichment’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 16.556 0.791 17.411 addCNV 4.848 0.270 5.145 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.16-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/4.2/Resources/library’ * installing *source* package ‘qsea’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c lm.c -o lm.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o qsea.so lm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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 11.109 0.505 11.635
qsea.Rcheck/qsea-Ex.timings
name | user | system | elapsed | |
addCNV | 4.848 | 0.270 | 5.145 | |
addContrast | 1.224 | 0.053 | 1.285 | |
addCoverage | 2.895 | 0.099 | 3.011 | |
addEnrichmentParameters | 0.327 | 0.012 | 0.339 | |
addLibraryFactors | 0.755 | 0.091 | 0.851 | |
addNewSamples | 16.556 | 0.791 | 17.411 | |
addOffset | 0.229 | 0.007 | 0.237 | |
addPatternDensity | 4.252 | 0.397 | 4.665 | |
createQseaSet | 0.210 | 0.016 | 0.226 | |
example | 0.162 | 0.003 | 0.166 | |
fitNBglm | 0.651 | 0.074 | 0.730 | |
getPCA | 0.523 | 0.018 | 0.542 | |
isSignificant | 0.876 | 0.023 | 0.902 | |
makeTable | 0.956 | 0.072 | 1.029 | |
normMethod | 0.001 | 0.000 | 0.002 | |
plotCNV | 0.205 | 0.002 | 0.207 | |
plotCoverage | 0.564 | 0.078 | 0.648 | |
plotEnrichmentProfile | 0.277 | 0.004 | 0.283 | |
plotPCA | 0.457 | 0.010 | 0.469 | |
qseaGLM-class | 0.001 | 0.000 | 0.001 | |
qseaPCA-class | 0.001 | 0.001 | 0.001 | |
qseaSet-class | 0.001 | 0.000 | 0.001 | |
regionStats | 0.535 | 0.015 | 0.552 | |