Kylie A. Bemis
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Cardinal |
| Branch: RELEASE_3_10 |
| Last Commit: 5f5c0c9 |
| Last Changed Date: 2019-10-29 13:09:08 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:41:24 -0400 (Wed, 15 Apr 2020).
| Package 226/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Cardinal 2.4.0 Kylie A. Bemis
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Cardinal |
| Version: 2.4.0 |
| 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_2.4.0.tar.gz |
| StartedAt: 2020-04-15 00:56:52 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:01:53 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 301.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_2.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/Cardinal.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-apple-darwin15.6.0 (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 ‘2.4.0’ * 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 * 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-3.10-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/3.6/Resources/library’ * installing *source* package ‘Cardinal’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c DIP.cpp -o DIP.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c dynAlign.cpp -o dynAlign.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c imzML.cpp -o imzML.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pugixml.cpp -o pugixml.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c spatial.cpp -o spatial.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -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/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
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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, 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")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 479 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
64.155 1.645 66.434
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| AnnotatedImagingExperiment-class | 0.484 | 0.018 | 0.507 | |
| Hashmat-class | 0.452 | 0.012 | 0.467 | |
| IAnnotatedDataFrame-class | 0.150 | 0.004 | 0.154 | |
| ImageData-class | 0.032 | 0.001 | 0.034 | |
| ImageList-class | 0.087 | 0.003 | 0.089 | |
| ImagingExperiment-class | 0.050 | 0.003 | 0.053 | |
| MIAPE-Imaging-class | 0.003 | 0.001 | 0.005 | |
| MSImageData-class | 0.172 | 0.022 | 0.195 | |
| MSImageProcess-class | 0.001 | 0.001 | 0.001 | |
| MSImageSet-class | 0.326 | 0.039 | 0.366 | |
| MSImagingExperiment-class | 0.129 | 0.015 | 0.144 | |
| MSImagingInfo-class | 0.419 | 0.059 | 0.479 | |
| MassDataFrame-class | 0.011 | 0.002 | 0.012 | |
| PCA-methods | 1.793 | 0.077 | 1.883 | |
| PLS-methods | 0.980 | 0.033 | 1.035 | |
| PositionDataFrame-class | 0.019 | 0.001 | 0.019 | |
| SImageData-class | 0.044 | 0.001 | 0.045 | |
| SImageSet-class | 0.110 | 0.002 | 0.113 | |
| SparseImagingExperiment-class | 0.029 | 0.000 | 0.030 | |
| XDataFrame-class | 0.005 | 0.000 | 0.006 | |
| colocalized-methods | 1.090 | 0.062 | 1.156 | |
| colors-functions | 1.061 | 0.010 | 1.073 | |
| dplyr-methods | 1.059 | 0.033 | 1.101 | |
| findNeighbors-methods | 0.077 | 0.022 | 0.098 | |
| iSet-class | 0.041 | 0.001 | 0.042 | |
| image-methods | 0.870 | 0.012 | 0.884 | |
| meansTest-methods | 3.348 | 0.125 | 3.482 | |
| mz-methods | 0.002 | 0.001 | 0.002 | |
| mzAlign-methods | 0.443 | 0.020 | 0.463 | |
| mzBin-methods | 0.424 | 0.010 | 0.434 | |
| mzFilter-methods | 0.882 | 0.007 | 0.891 | |
| normalize-methods | 0.347 | 0.003 | 0.353 | |
| peakAlign-methods | 0.664 | 0.005 | 0.672 | |
| peakBin-methods | 0.410 | 0.003 | 0.413 | |
| peakPick-methods | 0.433 | 0.003 | 0.436 | |
| pixelApply-methods | 1.568 | 0.023 | 1.598 | |
| plot-methods | 1.222 | 0.028 | 1.270 | |
| process-methods | 1.071 | 0.046 | 1.123 | |
| reduceBaseline-methods | 0.502 | 0.003 | 0.505 | |
| simulateSpectrum | 1.065 | 0.013 | 1.083 | |
| slice-methods | 0.481 | 0.010 | 0.493 | |
| smoothSignal-methods | 0.414 | 0.002 | 0.416 | |
| spatialDGMM-methods | 1.935 | 0.033 | 1.974 | |
| spatialFastmap-methods | 0.621 | 0.040 | 0.664 | |
| spatialKMeans-methods | 1.346 | 0.030 | 1.381 | |
| spatialShrunkenCentroids-methods | 1.545 | 0.017 | 1.571 | |
| topFeatures-methods | 0.745 | 0.014 | 0.761 | |