Kylie A. Bemis
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/Cardinal |
| Branch: RELEASE_3_12 |
| Last Commit: 2df8fad |
| Last Changed Date: 2020-10-27 11:02:20 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:28 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the Cardinal package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 234/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Cardinal 2.8.0 (landing page) Kylie A. Bemis
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Cardinal |
| Version: 2.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Cardinal_2.8.0.tar.gz |
| StartedAt: 2021-05-05 23:57:17 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-06 00:04:38 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 441.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Cardinal_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/Cardinal.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Cardinal/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Cardinal’ version ‘2.8.0’
* 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
* 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 ... 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
spatialShrunkenCentroids-methods 10.115 0.073 10.225
spatialKMeans-methods 6.528 0.036 6.585
* 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-3.12-bioc/meat/Cardinal.Rcheck/00check.log’
for details.
Cardinal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Cardinal ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘Cardinal’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c dynAlign.cpp -o dynAlign.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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++11 -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++11 -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++11 -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++11 -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++11 -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 dynAlign.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/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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Type 'license()' or 'licence()' for distribution details.
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> library(testthat)
> library(Cardinal)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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:base':
expand.grid
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
Attaching package: 'Cardinal'
The following object is masked from 'package:stats':
filter
>
> test_check("Cardinal")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 304 ]
>
> proc.time()
user system elapsed
185.759 1.793 187.803
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| AnnotatedImagingExperiment-class | 0.001 | 0.001 | 0.001 | |
| ImageList-class | 0.122 | 0.003 | 0.126 | |
| ImagingExperiment-class | 0.059 | 0.002 | 0.061 | |
| MSImagingExperiment-class | 0.116 | 0.002 | 0.118 | |
| MSImagingInfo-class | 0.699 | 0.005 | 0.706 | |
| MassDataFrame-class | 0.008 | 0.001 | 0.009 | |
| PCA-methods | 0.835 | 0.051 | 0.888 | |
| PLS-methods | 0.944 | 0.013 | 0.959 | |
| PositionDataFrame-class | 0.018 | 0.000 | 0.019 | |
| SparseImagingExperiment-class | 0.042 | 0.001 | 0.043 | |
| XDataFrame-class | 0.012 | 0.000 | 0.012 | |
| aggregate-methods | 2.300 | 0.055 | 2.359 | |
| colocalized-methods | 1.284 | 0.036 | 1.321 | |
| colors-functions | 1.365 | 0.036 | 1.404 | |
| findNeighbors-methods | 0.080 | 0.050 | 0.131 | |
| image-methods | 1.451 | 0.037 | 1.622 | |
| meansTest-methods | 3.054 | 0.164 | 3.218 | |
| mz-methods | 0.002 | 0.002 | 0.004 | |
| mzAlign-methods | 0.595 | 0.002 | 0.597 | |
| mzBin-methods | 0.658 | 0.005 | 0.663 | |
| mzFilter-methods | 1.091 | 0.011 | 1.101 | |
| normalize-methods | 0.391 | 0.003 | 0.394 | |
| peakAlign-methods | 0.687 | 0.004 | 0.692 | |
| peakBin-methods | 0.354 | 0.002 | 0.356 | |
| peakPick-methods | 0.384 | 0.009 | 0.398 | |
| pixelApply-methods | 0.730 | 0.011 | 0.742 | |
| plot-methods | 1.196 | 0.024 | 1.225 | |
| process-methods | 1.832 | 0.026 | 1.864 | |
| reduceBaseline-methods | 0.598 | 0.006 | 0.607 | |
| simulateSpectrum | 0.779 | 0.019 | 0.803 | |
| slice-methods | 0.705 | 0.015 | 0.722 | |
| smoothSignal-methods | 0.581 | 0.005 | 0.588 | |
| spatialDGMM-methods | 3.628 | 0.060 | 3.702 | |
| spatialFastmap-methods | 2.000 | 0.024 | 2.032 | |
| spatialKMeans-methods | 6.528 | 0.036 | 6.585 | |
| spatialShrunkenCentroids-methods | 10.115 | 0.073 | 10.225 | |
| subset-methods | 0.577 | 0.007 | 0.585 | |
| topFeatures-methods | 2.835 | 0.033 | 2.884 | |