Kylie A. Bemis
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/Cardinal |
| git_branch: RELEASE_3_13 |
| git_last_commit: 174f14c |
| git_last_commit_date: 2021-05-19 12:10:59 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 241/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Cardinal 2.10.0 (landing page) Kylie A. Bemis
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Cardinal |
| Version: 2.10.0 |
| 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_2.10.0.tar.gz |
| StartedAt: 2021-10-14 17:04:31 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:12:08 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 457.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Cardinal.Rcheck |
| Warnings: 0 |
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### 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_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Cardinal.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 11.801 0.048 11.869
spatialKMeans-methods 8.626 0.024 8.656
* 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-3.13-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/4.1/Resources/library’ * installing *source* package ‘Cardinal’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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++14 -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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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You are welcome to redistribute it under certain conditions.
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 objects are masked from 'package:base':
I, expand.grid, unname
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
192.968 1.915 195.092
Cardinal.Rcheck/Cardinal-Ex.timings
| name | user | system | elapsed | |
| AnnotatedImagingExperiment-class | 0.000 | 0.000 | 0.001 | |
| ImageList-class | 0.117 | 0.003 | 0.119 | |
| ImagingExperiment-class | 0.068 | 0.001 | 0.070 | |
| MSImagingExperiment-class | 0.166 | 0.002 | 0.169 | |
| MSImagingInfo-class | 0.547 | 0.006 | 0.553 | |
| MassDataFrame-class | 0.013 | 0.001 | 0.014 | |
| PCA-methods | 1.062 | 0.019 | 1.082 | |
| PLS-methods | 1.071 | 0.017 | 1.087 | |
| PositionDataFrame-class | 0.020 | 0.001 | 0.020 | |
| SparseImagingExperiment-class | 0.059 | 0.002 | 0.060 | |
| XDataFrame-class | 0.015 | 0.001 | 0.015 | |
| aggregate-methods | 2.821 | 0.031 | 2.853 | |
| colocalized-methods | 1.342 | 0.065 | 1.409 | |
| colors-functions | 1.385 | 0.072 | 1.458 | |
| findNeighbors-methods | 0.072 | 0.042 | 0.113 | |
| image-methods | 1.293 | 0.038 | 1.334 | |
| meansTest-methods | 4.402 | 0.232 | 4.637 | |
| mz-methods | 0.001 | 0.003 | 0.004 | |
| mzAlign-methods | 0.858 | 0.007 | 0.866 | |
| mzBin-methods | 0.507 | 0.002 | 0.508 | |
| mzFilter-methods | 1.237 | 0.008 | 1.246 | |
| normalize-methods | 0.519 | 0.003 | 0.522 | |
| peakAlign-methods | 0.831 | 0.004 | 0.836 | |
| peakBin-methods | 0.471 | 0.003 | 0.474 | |
| peakPick-methods | 0.419 | 0.003 | 0.421 | |
| pixelApply-methods | 1.183 | 0.020 | 1.203 | |
| plot-methods | 1.500 | 0.029 | 1.533 | |
| process-methods | 1.524 | 0.020 | 1.545 | |
| reduceBaseline-methods | 0.558 | 0.003 | 0.562 | |
| simulateSpectrum | 0.976 | 0.018 | 0.995 | |
| slice-methods | 0.674 | 0.012 | 0.686 | |
| smoothSignal-methods | 0.623 | 0.006 | 0.630 | |
| spatialDGMM-methods | 3.435 | 0.062 | 3.503 | |
| spatialFastmap-methods | 2.837 | 0.015 | 2.855 | |
| spatialKMeans-methods | 8.626 | 0.024 | 8.656 | |
| spatialShrunkenCentroids-methods | 11.801 | 0.048 | 11.869 | |
| subset-methods | 0.665 | 0.012 | 0.681 | |
| topFeatures-methods | 2.853 | 0.023 | 2.883 | |