Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:49 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1476/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qsea 1.18.0 (landing page) Matthias Lienhard
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: qsea |
Version: 1.18.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings qsea_1.18.0.tar.gz |
StartedAt: 2021-10-14 11:11:15 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:15:16 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 240.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qsea.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:qsea.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings qsea_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/qsea.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’ * 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 ... NOTE Namespaces in Imports field not imported from: ‘KernSmooth’ ‘MASS’ All declared Imports should be used. * 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 ... 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 18.267 1.556 19.856 addPatternDensity 6.622 0.672 7.294 addCNV 5.916 0.323 6.248 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/qsea.Rcheck/00check.log’ for details.
qsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL qsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘qsea’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c lm.c -o lm.o gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o qsea.so lm.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-qsea/00new/qsea/libs ** R ** inst ** preparing package for lazy loading No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘qsea’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘qsea’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘qsea’ ** testing if installed package keeps a record of temporary installation path * DONE (qsea)
qsea.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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) No methods found in package 'IRanges' for request: 'values' when loading 'qsea' > > test_check("qsea") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ] > > proc.time() user system elapsed 12.324 0.562 12.871
qsea.Rcheck/qsea-Ex.timings
name | user | system | elapsed | |
addCNV | 5.916 | 0.323 | 6.248 | |
addContrast | 1.351 | 0.024 | 1.376 | |
addCoverage | 2.167 | 0.056 | 2.223 | |
addEnrichmentParameters | 0.421 | 0.016 | 0.437 | |
addLibraryFactors | 1.788 | 0.028 | 1.816 | |
addNewSamples | 18.267 | 1.556 | 19.856 | |
addOffset | 0.388 | 0.012 | 0.400 | |
addPatternDensity | 6.622 | 0.672 | 7.294 | |
createQseaSet | 0.170 | 0.008 | 0.179 | |
example | 0.262 | 0.020 | 0.282 | |
fitNBglm | 0.771 | 0.164 | 0.934 | |
getPCA | 0.616 | 0.032 | 0.648 | |
isSignificant | 0.97 | 0.00 | 0.97 | |
makeTable | 1.215 | 0.028 | 1.243 | |
normMethod | 0.001 | 0.000 | 0.001 | |
plotCNV | 0.323 | 0.004 | 0.328 | |
plotCoverage | 0.710 | 0.008 | 0.719 | |
plotEnrichmentProfile | 0.358 | 0.140 | 0.499 | |
plotPCA | 0.571 | 0.084 | 0.655 | |
qseaGLM-class | 0.001 | 0.000 | 0.001 | |
qseaPCA-class | 0 | 0 | 0 | |
qseaSet-class | 0.000 | 0.001 | 0.001 | |
regionStats | 0.657 | 0.062 | 0.718 | |