Kylie A. Bemis
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/Cardinal |
| git_branch: RELEASE_3_17 |
| git_last_commit: c16ca40 |
| git_last_commit_date: 2023-05-02 20:47:36 -0400 (Tue, 02 May 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 267/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Cardinal 3.2.1 (landing page) Kylie A. Bemis
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the Cardinal package: - 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: Cardinal |
| Version: 3.2.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Cardinal_3.2.1.tar.gz |
| StartedAt: 2023-10-17 07:32:39 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 07:39:17 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 397.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Cardinal_3.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Cardinal.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘3.2.1’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
meansTest-methods 3.762 0.096 5.98
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Cardinal.Rcheck/00check.log’
for details.
Cardinal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Cardinal ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘Cardinal’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DIP.cpp -o DIP.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c imzML.cpp -o imzML.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.cpp -o init.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pugixml.cpp -o pugixml.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spatial.cpp -o spatial.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Cardinal.so DIP.o imzML.o init.o pugixml.o spatial.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
>
> test_check("Cardinal")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 282 ]
>
> proc.time()
user system elapsed
62.871 1.548 99.174
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| ImageList-class | 0.072 | 0.001 | 0.111 | |
| ImagingExperiment-class | 0.042 | 0.001 | 0.066 | |
| MSImagingExperiment-class | 0.123 | 0.003 | 0.191 | |
| MSImagingInfo-class | 0.282 | 0.015 | 0.472 | |
| MassDataFrame-class | 0.008 | 0.001 | 0.017 | |
| PCA-methods | 0.866 | 0.037 | 1.389 | |
| PLS-methods | 0.843 | 0.012 | 1.324 | |
| PositionDataFrame-class | 0.022 | 0.001 | 0.036 | |
| SparseImagingExperiment-class | 0.042 | 0.002 | 0.068 | |
| XDataFrame-class | 0.010 | 0.001 | 0.018 | |
| aggregate-methods | 1.397 | 0.032 | 2.219 | |
| colocalized-methods | 1.153 | 0.017 | 1.809 | |
| colors-functions | 0.765 | 0.017 | 1.222 | |
| findNeighbors-methods | 0.052 | 0.028 | 0.127 | |
| image-methods | 0.773 | 0.019 | 1.230 | |
| meansTest-methods | 3.762 | 0.096 | 5.980 | |
| mz-methods | 0.001 | 0.002 | 0.005 | |
| mzAlign-methods | 0.539 | 0.016 | 0.861 | |
| mzBin-methods | 0.361 | 0.005 | 0.568 | |
| mzFilter-methods | 0.963 | 0.013 | 1.499 | |
| normalize-methods | 0.340 | 0.004 | 0.528 | |
| peakAlign-methods | 0.605 | 0.006 | 0.933 | |
| peakBin-methods | 0.370 | 0.004 | 0.585 | |
| peakPick-methods | 0.387 | 0.004 | 0.604 | |
| pixelApply-methods | 0.421 | 0.006 | 0.664 | |
| plot-methods | 1.334 | 0.033 | 2.062 | |
| process-methods | 0.975 | 0.023 | 1.535 | |
| reduceBaseline-methods | 0.363 | 0.004 | 0.569 | |
| simulateSpectrum | 0.562 | 0.013 | 0.886 | |
| slice-methods | 0.455 | 0.008 | 0.710 | |
| smoothSignal-methods | 0.402 | 0.005 | 0.630 | |
| spatialDGMM-methods | 2.278 | 0.048 | 3.575 | |
| spatialFastmap-methods | 0.632 | 0.009 | 0.988 | |
| spatialKMeans-methods | 1.546 | 0.019 | 2.417 | |
| spatialShrunkenCentroids-methods | 3.025 | 0.033 | 4.768 | |
| subset-methods | 0.552 | 0.009 | 0.878 | |
| topFeatures-methods | 0.956 | 0.012 | 1.494 | |