| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:27 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 263/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Cardinal 3.3.1 (landing page) Kylie A. Bemis
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: Cardinal |
| Version: 3.3.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Cardinal_3.3.1.tar.gz |
| StartedAt: 2023-06-05 18:51:28 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 18:59:19 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 470.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Cardinal_3.3.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Cardinal.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘3.3.1’
* 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
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 startup messages can be suppressed ... 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-3.18-bioc/meat/Cardinal.Rcheck/00check.log’
for details.
Cardinal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL Cardinal ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘Cardinal’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c DIP.cpp -o DIP.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c imzML.cpp -o imzML.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pugixml.cpp -o pugixml.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c spatial.cpp -o spatial.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o Cardinal.so DIP.o imzML.o init.o pugixml.o spatial.o utils.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
>
> test_check("Cardinal")
[ FAIL 0 | WARN 396 | SKIP 0 | PASS 282 ]
[ FAIL 0 | WARN 396 | SKIP 0 | PASS 282 ]
>
> proc.time()
user system elapsed
72.561 0.898 73.684
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| ImageList-class | 0.063 | 0.004 | 0.068 | |
| ImagingExperiment-class | 0.048 | 0.000 | 0.048 | |
| MSImagingExperiment-class | 0.136 | 0.012 | 0.148 | |
| MSImagingInfo-class | 0.292 | 0.016 | 0.309 | |
| MassDataFrame-class | 0.005 | 0.004 | 0.008 | |
| PCA-methods | 0.826 | 0.072 | 0.900 | |
| PLS-methods | 0.901 | 0.040 | 0.943 | |
| PositionDataFrame-class | 0.018 | 0.004 | 0.022 | |
| SparseImagingExperiment-class | 0.047 | 0.000 | 0.048 | |
| XDataFrame-class | 0.009 | 0.004 | 0.012 | |
| aggregate-methods | 1.657 | 0.131 | 1.792 | |
| colocalized-methods | 1.120 | 0.024 | 1.147 | |
| colors-functions | 1.024 | 0.024 | 1.050 | |
| findNeighbors-methods | 0.059 | 0.008 | 0.067 | |
| image-methods | 0.889 | 0.032 | 0.923 | |
| meansTest-methods | 4.459 | 0.112 | 4.579 | |
| mz-methods | 0.002 | 0.000 | 0.001 | |
| mzAlign-methods | 0.598 | 0.016 | 0.616 | |
| mzBin-methods | 0.398 | 0.000 | 0.398 | |
| mzFilter-methods | 1.089 | 0.004 | 1.095 | |
| normalize-methods | 0.381 | 0.008 | 0.391 | |
| peakAlign-methods | 0.685 | 0.008 | 0.694 | |
| peakBin-methods | 0.378 | 0.000 | 0.379 | |
| peakPick-methods | 0.409 | 0.000 | 0.410 | |
| pixelApply-methods | 0.538 | 0.016 | 0.555 | |
| plot-methods | 1.179 | 0.008 | 1.189 | |
| process-methods | 1.526 | 0.044 | 1.573 | |
| reduceBaseline-methods | 0.432 | 0.000 | 0.432 | |
| simulateSpectrum | 0.560 | 0.000 | 0.561 | |
| slice-methods | 0.490 | 0.012 | 0.502 | |
| smoothSignal-methods | 0.409 | 0.000 | 0.409 | |
| spatialDGMM-methods | 2.340 | 0.040 | 2.386 | |
| spatialFastmap-methods | 0.745 | 0.012 | 0.758 | |
| spatialKMeans-methods | 1.790 | 0.008 | 1.801 | |
| spatialShrunkenCentroids-methods | 3.658 | 0.016 | 3.681 | |
| subset-methods | 0.588 | 0.008 | 0.597 | |
| topFeatures-methods | 1.028 | 0.004 | 1.034 | |