Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-03-01 07:13:59 -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: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --no-vignettes --timings IrisSpatialFeatures_1.3.0.tar.gz |
StartedAt: 2018-03-01 00:50:31 -0500 (Thu, 01 Mar 2018) |
EndedAt: 2018-03-01 00:56:52 -0500 (Thu, 01 Mar 2018) |
EllapsedTime: 380.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IrisSpatialFeatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --no-vignettes --timings IrisSpatialFeatures_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/IrisSpatialFeatures.Rcheck’ * using R Under development (unstable) (2018-01-28 r74177) * using platform: x86_64-pc-linux-gnu (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 ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 1.4Mb extdata 1.9Mb libs 1.2Mb * 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 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed read_raw 63.832 0.060 63.932 threshold_dataset 63.600 0.028 63.678 interaction_maps 17.596 0.028 17.635 extract_features 16.192 0.164 16.381 extract_interactions 11.956 0.000 11.965 plot_interactions 11.732 0.004 11.747 get_all_interactions 11.440 0.000 11.447 get_interactions 11.244 0.000 11.249 extract_proximity 8.012 3.072 11.087 extract_nearest_neighbor 4.180 2.760 6.945 * 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 ‘/home/biocbuild/bbs-3.7-bioc/meat/IrisSpatialFeatures.Rcheck/00check.log’ for details.
IrisSpatialFeatures.Rcheck/00install.out
* installing *source* package ‘IrisSpatialFeatures’ ... ** libs g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c interaction.cpp -o interaction.o g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c masking.cpp -o masking.o g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o IrisSpatialFeatures.so RcppExports.o interaction.o masking.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/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) (2018-01-28 r74177) -- "Unsuffered Consequences" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 65.264 0.180 65.486
IrisSpatialFeatures.Rcheck/IrisSpatialFeatures-Ex.timings
name | user | system | elapsed | |
Coordinate-class | 0.004 | 0.000 | 0.001 | |
as.data.frame | 1.228 | 0.040 | 1.267 | |
collapse_markers | 0.004 | 0.000 | 0.004 | |
extract_ROI | 0.096 | 0.012 | 0.108 | |
extract_features | 16.192 | 0.164 | 16.381 | |
extract_interactions | 11.956 | 0.000 | 11.965 | |
extract_mask | 0.120 | 0.140 | 0.259 | |
extract_nearest_neighbor | 4.180 | 2.760 | 6.945 | |
extract_proximity | 8.012 | 3.072 | 11.087 | |
feature_selection | 0.024 | 0.000 | 0.025 | |
get_all_interactions | 11.440 | 0.000 | 11.447 | |
get_all_nearest_neighbors | 0.364 | 0.000 | 0.364 | |
get_all_proximities | 0.000 | 0.000 | 0.001 | |
get_count_ratios | 0.004 | 0.000 | 0.001 | |
get_counts_per_mm2 | 0.012 | 0.000 | 0.012 | |
get_counts_per_mm2_noncollapsed | 0.000 | 0.000 | 0.001 | |
get_interactions | 11.244 | 0.000 | 11.249 | |
get_nearest_neighbors | 0.448 | 0.000 | 0.447 | |
interaction_maps | 17.596 | 0.028 | 17.635 | |
neighbor_ray_plot | 0.376 | 0.000 | 0.377 | |
overview_plot | 0.152 | 0.000 | 0.152 | |
plot | 0.820 | 0.004 | 0.825 | |
plot_interactions | 11.732 | 0.004 | 11.747 | |
plot_nearest_neighbor | 0.360 | 0.004 | 0.363 | |
plot_proximities | 4.444 | 0.000 | 4.445 | |
rayplot_single_coordinate | 0.372 | 0.000 | 0.373 | |
read_raw | 63.832 | 0.060 | 63.932 | |
threshold_dataset | 63.600 | 0.028 | 63.678 | |