Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-03-01 07:39:36 -0500 (Thu, 01 Mar 2018).
Package 723/1499 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
IrisSpatialFeatures 1.3.0 Daniel Gusenleitner
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK |
Package: IrisSpatialFeatures |
Version: 1.3.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IrisSpatialFeatures_1.3.0.tar.gz |
StartedAt: 2018-03-01 00:59:01 -0500 (Thu, 01 Mar 2018) |
EndedAt: 2018-03-01 01:13:48 -0500 (Thu, 01 Mar 2018) |
EllapsedTime: 886.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IrisSpatialFeatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IrisSpatialFeatures_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/IrisSpatialFeatures.Rcheck’ * using R Under development (unstable) (2018-01-26 r74169) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘IrisSpatialFeatures/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IrisSpatialFeatures’ version ‘1.3.0’ * 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 ‘IrisSpatialFeatures’ 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 loading without being on the library search path ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed interaction_maps 117.439 1.662 125.533 read_raw 113.503 1.236 121.352 threshold_dataset 112.668 1.349 120.814 extract_features 34.908 1.087 37.642 get_all_interactions 29.012 0.315 30.849 get_interactions 29.025 0.252 30.961 plot_interactions 28.846 0.277 30.226 extract_interactions 28.643 0.347 30.733 extract_proximity 14.264 10.778 26.320 extract_nearest_neighbor 8.544 8.926 18.365 plot_proximities 5.078 0.646 5.934 * 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: OK
IrisSpatialFeatures.Rcheck/00install.out
* installing *source* package ‘IrisSpatialFeatures’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c interaction.cpp -o interaction.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c masking.cpp -o masking.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 IrisSpatialFeatures.so RcppExports.o interaction.o masking.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.7-bioc/meat/IrisSpatialFeatures.Rcheck/IrisSpatialFeatures/libs ** R ** data *** moving datasets to lazyload DB ** 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 (IrisSpatialFeatures)
IrisSpatialFeatures.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-01-26 r74169) -- "Unsuffered Consequences" 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 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(IrisSpatialFeatures) > test_check("IrisSpatialFeatures") [1] "Sample: MEL2" [1] "No nuclear map found, skipping .. " [1] "No nuclear map found, skipping .. " [1] "Sample: MEL3" [1] "No nuclear map found, skipping .. " [1] "No nuclear map found, skipping .. " ══ testthat results ═══════════════════════════════════════════════════════════ OK: 2 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 119.581 1.493 129.051
IrisSpatialFeatures.Rcheck/IrisSpatialFeatures-Ex.timings
name | user | system | elapsed | |
Coordinate-class | 0.001 | 0.001 | 0.003 | |
as.data.frame | 1.600 | 0.395 | 2.048 | |
collapse_markers | 0.007 | 0.001 | 0.007 | |
extract_ROI | 0.197 | 0.016 | 0.221 | |
extract_features | 34.908 | 1.087 | 37.642 | |
extract_interactions | 28.643 | 0.347 | 30.733 | |
extract_mask | 0.319 | 0.389 | 0.729 | |
extract_nearest_neighbor | 8.544 | 8.926 | 18.365 | |
extract_proximity | 14.264 | 10.778 | 26.320 | |
feature_selection | 0.056 | 0.002 | 0.061 | |
get_all_interactions | 29.012 | 0.315 | 30.849 | |
get_all_nearest_neighbors | 0.703 | 0.005 | 0.746 | |
get_all_proximities | 0.001 | 0.000 | 0.001 | |
get_count_ratios | 0.002 | 0.001 | 0.003 | |
get_counts_per_mm2 | 0.027 | 0.000 | 0.028 | |
get_counts_per_mm2_noncollapsed | 0.003 | 0.000 | 0.002 | |
get_interactions | 29.025 | 0.252 | 30.961 | |
get_nearest_neighbors | 0.890 | 0.006 | 0.959 | |
interaction_maps | 117.439 | 1.662 | 125.533 | |
neighbor_ray_plot | 0.717 | 0.016 | 0.780 | |
overview_plot | 2.407 | 0.103 | 2.684 | |
plot | 3.728 | 0.042 | 3.981 | |
plot_interactions | 28.846 | 0.277 | 30.226 | |
plot_nearest_neighbor | 0.666 | 0.005 | 0.690 | |
plot_proximities | 5.078 | 0.646 | 5.934 | |
rayplot_single_coordinate | 0.730 | 0.005 | 0.755 | |
read_raw | 113.503 | 1.236 | 121.352 | |
threshold_dataset | 112.668 | 1.349 | 120.814 | |