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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IrisSpatialFeatures_1.3.0.tar.gz
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* 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

* 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)

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 

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