Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:00 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 Cardinal package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Cardinal.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 254/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Cardinal 3.0.1 (landing page) Kylie A. Bemis
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: Cardinal |
Version: 3.0.1 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings Cardinal_3.0.1.tar.gz |
StartedAt: 2023-04-10 19:30:09 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:35:22 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 312.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Cardinal.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings Cardinal_3.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/Cardinal.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘Cardinal/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Cardinal’ version ‘3.0.1’ * 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 ‘Cardinal’ 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 loading without being on the library search path ... 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 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 * 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 ... ‘Cardinal-3-guide.Rmd’ using ‘UTF-8’... OK ‘Cardinal-3-stats.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.16-bioc/meat/Cardinal.Rcheck/00check.log’ for details.
Cardinal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL Cardinal ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘Cardinal’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DIP.cpp -o DIP.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c imzML.cpp -o imzML.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pugixml.cpp -o pugixml.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c spatial.cpp -o spatial.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o Cardinal.so DIP.o imzML.o init.o pugixml.o spatial.o utils.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-Cardinal/00new/Cardinal/libs ** R ** 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 ** 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 (Cardinal)
Cardinal.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-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(Cardinal) Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: BiocParallel Loading required package: EBImage Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname > > test_check("Cardinal") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 282 ] > > proc.time() user system elapsed 48.687 0.819 49.493
Cardinal.Rcheck/Cardinal-Ex.timings
name | user | system | elapsed | |
ImageList-class | 0.077 | 0.004 | 0.081 | |
ImagingExperiment-class | 0.036 | 0.000 | 0.036 | |
MSImagingExperiment-class | 0.105 | 0.000 | 0.106 | |
MSImagingInfo-class | 0.226 | 0.012 | 0.238 | |
MassDataFrame-class | 0.003 | 0.004 | 0.007 | |
PCA-methods | 0.687 | 0.071 | 0.759 | |
PLS-methods | 0.670 | 0.004 | 0.675 | |
PositionDataFrame-class | 0.015 | 0.000 | 0.016 | |
SparseImagingExperiment-class | 0.033 | 0.000 | 0.034 | |
XDataFrame-class | 0.009 | 0.000 | 0.010 | |
aggregate-methods | 1.354 | 0.040 | 1.394 | |
colocalized-methods | 0.834 | 0.028 | 0.862 | |
colors-functions | 0.593 | 0.016 | 0.608 | |
findNeighbors-methods | 0.043 | 0.008 | 0.051 | |
image-methods | 0.569 | 0.016 | 0.585 | |
meansTest-methods | 3.242 | 0.100 | 3.342 | |
mz-methods | 0.000 | 0.001 | 0.001 | |
mzAlign-methods | 0.406 | 0.003 | 0.409 | |
mzBin-methods | 0.274 | 0.008 | 0.283 | |
mzFilter-methods | 0.786 | 0.000 | 0.786 | |
normalize-methods | 0.257 | 0.000 | 0.256 | |
peakAlign-methods | 0.487 | 0.048 | 0.534 | |
peakBin-methods | 0.262 | 0.016 | 0.278 | |
peakPick-methods | 0.267 | 0.000 | 0.268 | |
pixelApply-methods | 0.329 | 0.008 | 0.338 | |
plot-methods | 0.785 | 0.000 | 0.785 | |
process-methods | 0.714 | 0.004 | 0.718 | |
reduceBaseline-methods | 0.308 | 0.004 | 0.311 | |
simulateSpectrum | 0.443 | 0.008 | 0.452 | |
slice-methods | 0.339 | 0.004 | 0.344 | |
smoothSignal-methods | 0.282 | 0.000 | 0.282 | |
spatialDGMM-methods | 1.317 | 0.000 | 1.316 | |
spatialFastmap-methods | 0.502 | 0.000 | 0.502 | |
spatialKMeans-methods | 1.192 | 0.040 | 1.232 | |
spatialShrunkenCentroids-methods | 2.483 | 0.031 | 2.515 | |
subset-methods | 0.409 | 0.039 | 0.449 | |
topFeatures-methods | 0.767 | 0.017 | 0.783 | |