Kylie A. Bemis
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/Cardinal |
| Branch: RELEASE_3_7 |
| Last Commit: 8885df8 |
| Last Changed Date: 2018-07-22 17:06:58 -0400 (Sun, 22 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:54:14 -0400 (Wed, 17 Oct 2018).
| Package 189/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Cardinal 1.12.1 Kylie A. Bemis
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Cardinal |
| Version: 1.12.1 |
| 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_1.12.1.tar.gz |
| StartedAt: 2018-10-16 20:15:46 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:18:27 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 160.8 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_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/Cardinal.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘1.12.1’ * 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 * 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 ... NOTE batchProcess,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ normalize,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ peakAlign,MSImageSet-numeric : <anonymous>: no visible binding for global variable ‘.Index’ peakPick,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ reduceBaseline,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ reduceDimension,MSImageSet-missing : <anonymous>: no visible binding for global variable ‘.Index’ smoothSignal,MSImageSet : <anonymous>: no visible binding for global variable ‘.Index’ Undefined global functions or variables: .Index * 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 sizes of PDF files under ‘inst/doc’ ... OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.7-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/3.5/Resources/library’ * installing *source* package ‘Cardinal’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c dynamicAlign.c -o dynamicAlign.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c fastmap.c -o fastmap.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c imzML.cpp -o imzML.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c localMaxima.c -o localMaxima.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pugixml.cpp -o pugixml.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c smooth.c -o smooth.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c spatial.c -o spatial.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o clang++ -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 dynamicAlign.o fastmap.o imzML.o localMaxima.o pugixml.o smooth.o spatial.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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 * DONE (Cardinal)
Cardinal.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
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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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: matter
Loading required package: biglm
Loading required package: DBI
Attaching package: 'matter'
The following object is masked from 'package:biglm':
biglm
The following objects are masked from 'package:base':
apply, scale
Loading required package: ProtGenerics
Welcome to Cardinal (version 1.12.1)
To get started, view the introductory vignettes with
'browseVignettes("Cardinal")'.
>
> test_check("Cardinal")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 229 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
34.911 1.230 36.344
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| Binmat-class | 0.002 | 0.000 | 0.002 | |
| Hashmat-class | 0.165 | 0.023 | 0.193 | |
| IAnnotatedDataFrame-class | 0.125 | 0.002 | 0.128 | |
| ImageData-class | 0.022 | 0.000 | 0.024 | |
| MIAPE-Imaging-class | 0.007 | 0.000 | 0.008 | |
| MSImageData-class | 0.127 | 0.009 | 0.139 | |
| MSImageProcess-class | 0.002 | 0.000 | 0.003 | |
| MSImageSet-class | 0.287 | 0.008 | 0.303 | |
| OPLS-methods | 0.141 | 0.001 | 0.142 | |
| PCA-methods | 0.062 | 0.001 | 0.063 | |
| PLS-methods | 0.103 | 0.001 | 0.107 | |
| SImageData-class | 0.060 | 0.002 | 0.064 | |
| SImageSet-class | 0.062 | 0.002 | 0.064 | |
| batchProcess-methods | 0.933 | 0.007 | 0.957 | |
| colors-functions | 1.216 | 0.005 | 1.231 | |
| generateImage | 0.925 | 0.010 | 0.944 | |
| generateSpectrum | 0.046 | 0.003 | 0.050 | |
| iSet-class | 0.050 | 0.001 | 0.051 | |
| image-methods | 0.844 | 0.014 | 0.864 | |
| normalize-methods | 0.131 | 0.001 | 0.132 | |
| peakAlign-methods | 0.357 | 0.002 | 0.360 | |
| peakFilter-methods | 0.777 | 0.007 | 0.793 | |
| peakPick-methods | 0.153 | 0.020 | 0.171 | |
| pixelApply-methods | 0.041 | 0.006 | 0.047 | |
| pixels-methods | 0.094 | 0.010 | 0.104 | |
| plot-methods | 0.670 | 0.014 | 0.693 | |
| reduceBaseline-methods | 0.141 | 0.001 | 0.144 | |
| reduceDimension-methods | 0.116 | 0.000 | 0.118 | |
| smoothSignal-methods.R | 0.102 | 0.001 | 0.102 | |
| spatialKMeans-methods | 0.393 | 0.005 | 0.397 | |
| spatialShrunkenCentroids-methods | 1.511 | 0.014 | 1.530 | |
| standardizeSamples-methods | 0.441 | 0.006 | 0.449 | |
| topLabels-methods | 0.880 | 0.010 | 0.895 | |