Daniel Gusenleitner
| Snapshot Date: 2018-02-28 17:00:16 -0500 (Wed, 28 Feb 2018) |
| URL: https://git.bioconductor.org/packages/IrisSpatialFeatures |
| Branch: RELEASE_3_6 |
| Last Commit: c23230e |
| Last Changed Date: 2017-10-30 12:41:36 -0500 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-03-01 14:34:43 -0500 (Thu, 01 Mar 2018).
| Package 713/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IrisSpatialFeatures 1.2.0 Daniel Gusenleitner
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: IrisSpatialFeatures |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IrisSpatialFeatures_1.2.0.tar.gz |
| StartedAt: 2018-03-01 00:53:39 -0500 (Thu, 01 Mar 2018) |
| EndedAt: 2018-03-01 01:00:22 -0500 (Thu, 01 Mar 2018) |
| EllapsedTime: 403.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IrisSpatialFeatures.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IrisSpatialFeatures_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/IrisSpatialFeatures.Rcheck’
* using R version 3.4.3 (2017-11-30)
* 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 ‘1.2.0’
* 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 5.1Mb
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 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 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 59.688 0.680 60.418
threshold_dataset 57.176 0.284 57.494
interaction_maps 19.648 0.112 19.782
extract_features 18.444 0.500 18.983
plot_interactions 13.388 0.004 13.413
extract_proximity 9.216 3.668 12.907
extract_interactions 12.712 0.000 12.727
get_all_interactions 12.560 0.008 12.581
get_interactions 11.960 0.000 11.967
extract_nearest_neighbor 4.140 3.276 7.419
plot_proximities 5.564 0.072 5.646
* 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-3.6-bioc/meat/IrisSpatialFeatures.Rcheck/00check.log’
for details.
IrisSpatialFeatures.Rcheck/00install.out
* installing *source* package ‘IrisSpatialFeatures’ ... ** libs g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c interaction.cpp -o interaction.o g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -L/usr/local/lib -o IrisSpatialFeatures.so RcppExports.o interaction.o masking.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.6-bioc/meat/IrisSpatialFeatures.Rcheck/IrisSpatialFeatures/libs ** R ** data *** moving datasets to lazyload DB ** inst ** preparing 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 version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 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
61.912 0.836 62.784
IrisSpatialFeatures.Rcheck/IrisSpatialFeatures-Ex.timings
| name | user | system | elapsed | |
| Coordinate-class | 0.000 | 0.000 | 0.001 | |
| as.data.frame | 1.256 | 0.860 | 2.115 | |
| collapse_markers | 0.004 | 0.000 | 0.004 | |
| extract_ROI | 0.096 | 0.028 | 0.124 | |
| extract_features | 18.444 | 0.500 | 18.983 | |
| extract_interactions | 12.712 | 0.000 | 12.727 | |
| extract_mask | 0.168 | 0.156 | 0.343 | |
| extract_nearest_neighbor | 4.140 | 3.276 | 7.419 | |
| extract_proximity | 9.216 | 3.668 | 12.907 | |
| feature_selection | 0.04 | 0.00 | 0.04 | |
| get_all_interactions | 12.560 | 0.008 | 12.581 | |
| get_all_nearest_neighbors | 0.412 | 0.000 | 0.412 | |
| get_all_proximities | 0.000 | 0.000 | 0.001 | |
| get_count_ratios | 0.004 | 0.000 | 0.001 | |
| get_counts_per_mm2 | 0.016 | 0.000 | 0.016 | |
| get_counts_per_mm2_noncollapsed | 0.000 | 0.000 | 0.001 | |
| get_interactions | 11.960 | 0.000 | 11.967 | |
| get_nearest_neighbors | 0.592 | 0.000 | 0.593 | |
| interaction_maps | 19.648 | 0.112 | 19.782 | |
| neighbor_ray_plot | 0.456 | 0.000 | 0.455 | |
| overview_plot | 0.688 | 0.000 | 0.690 | |
| plot | 2.112 | 0.000 | 2.116 | |
| plot_interactions | 13.388 | 0.004 | 13.413 | |
| plot_nearest_neighbor | 0.676 | 0.000 | 0.680 | |
| plot_proximities | 5.564 | 0.072 | 5.646 | |
| rayplot_single_coordinate | 0.412 | 0.000 | 0.415 | |
| read_raw | 59.688 | 0.680 | 60.418 | |
| threshold_dataset | 57.176 | 0.284 | 57.494 | |