Kylie A. Bemis
| Snapshot Date: 2023-03-28 14:00:22 -0400 (Tue, 28 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/Cardinal |
| git_branch: devel |
| git_last_commit: 6a786e0 |
| git_last_commit_date: 2022-11-14 15:04:46 -0400 (Mon, 14 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-29 11:06:05 -0400 (Wed, 29 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4547 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4308 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4301 |
| 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 264/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Cardinal 3.1.0 (landing page) Kylie A. Bemis
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: Cardinal |
| Version: 3.1.0 |
| 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_3.1.0.tar.gz |
| StartedAt: 2023-03-28 22:35:50 -0400 (Tue, 28 Mar 2023) |
| EndedAt: 2023-03-28 22:45:32 -0400 (Tue, 28 Mar 2023) |
| EllapsedTime: 581.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Cardinal.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_3.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Cardinal.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘3.1.0’
* 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 ‘Cardinal’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used 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 ... NOTE
checkRd: (-1) topFeatures-methods.Rd:73: Escaped LaTeX specials: \&
* 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Cardinal/libs/Cardinal.so’:
Found ‘_sprintf’, possibly from ‘sprintf’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
spatialShrunkenCentroids-methods 5.720 0.030 8.093
meansTest-methods 5.455 0.202 7.491
* 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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc/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/Resources/library’ * installing *source* package ‘Cardinal’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’ using SDK: ‘’ clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c DIP.cpp -o DIP.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c imzML.cpp -o imzML.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pugixml.cpp -o pugixml.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c spatial.cpp -o spatial.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -mmacosx-version-min=10.13 -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/usr/local/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/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
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(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
107.646 1.654 143.087
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| ImageList-class | 0.105 | 0.002 | 0.130 | |
| ImagingExperiment-class | 0.079 | 0.001 | 0.100 | |
| MSImagingExperiment-class | 0.211 | 0.003 | 0.267 | |
| MSImagingInfo-class | 0.516 | 0.021 | 0.692 | |
| MassDataFrame-class | 0.013 | 0.002 | 0.017 | |
| PCA-methods | 1.318 | 0.065 | 1.742 | |
| PLS-methods | 1.485 | 0.013 | 1.876 | |
| PositionDataFrame-class | 0.035 | 0.001 | 0.043 | |
| SparseImagingExperiment-class | 0.069 | 0.001 | 0.097 | |
| XDataFrame-class | 0.019 | 0.000 | 0.022 | |
| aggregate-methods | 2.401 | 0.041 | 3.122 | |
| colocalized-methods | 1.707 | 0.020 | 2.219 | |
| colors-functions | 1.929 | 0.025 | 2.578 | |
| findNeighbors-methods | 0.095 | 0.026 | 0.161 | |
| image-methods | 1.341 | 0.017 | 1.824 | |
| meansTest-methods | 5.455 | 0.202 | 7.491 | |
| mz-methods | 0.001 | 0.002 | 0.003 | |
| mzAlign-methods | 0.950 | 0.004 | 1.243 | |
| mzBin-methods | 0.627 | 0.002 | 0.807 | |
| mzFilter-methods | 1.832 | 0.008 | 2.511 | |
| normalize-methods | 0.606 | 0.003 | 0.839 | |
| peakAlign-methods | 1.132 | 0.004 | 1.567 | |
| peakBin-methods | 0.634 | 0.002 | 0.855 | |
| peakPick-methods | 0.668 | 0.001 | 0.917 | |
| pixelApply-methods | 1.216 | 0.017 | 1.696 | |
| plot-methods | 1.809 | 0.027 | 2.477 | |
| process-methods | 1.673 | 0.048 | 2.429 | |
| reduceBaseline-methods | 0.722 | 0.004 | 0.969 | |
| simulateSpectrum | 0.919 | 0.019 | 1.262 | |
| slice-methods | 0.770 | 0.009 | 1.047 | |
| smoothSignal-methods | 0.663 | 0.002 | 0.908 | |
| spatialDGMM-methods | 3.344 | 0.020 | 4.541 | |
| spatialFastmap-methods | 1.135 | 0.009 | 1.557 | |
| spatialKMeans-methods | 2.772 | 0.013 | 3.765 | |
| spatialShrunkenCentroids-methods | 5.720 | 0.030 | 8.093 | |
| subset-methods | 0.927 | 0.009 | 1.321 | |
| topFeatures-methods | 1.658 | 0.006 | 2.352 | |