Package: IrisSpatialFeatures

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IrisSpatialFeatures_1.2.0.tar.gz

StartedAt: 2018-03-01 05:57:33 -0500 (Thu, 01 Mar 2018)

EndedAt: 2018-03-01 06:08:16 -0500 (Thu, 01 Mar 2018)

EllapsedTime: 642.7 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/IrisSpatialFeatures.Rcheck’
* using R version 3.4.3 (2017-11-30)
* 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 ‘1.2.0’
* 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 ... 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         85.431  0.876  89.344
threshold_dataset        80.662  0.605  83.036
read_raw                 78.825  0.525  81.129
extract_features         27.806  0.847  29.428
plot_interactions        23.037  0.161  23.689
extract_interactions     22.821  0.197  23.941
get_all_interactions     22.719  0.221  23.743
get_interactions         22.399  0.157  23.124
extract_proximity        11.017  8.125  19.854
extract_nearest_neighbor  6.464  6.828  13.696
plot_proximities          4.399  0.581   5.085
* 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/3.4/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/3.4/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/3.4/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-3.6-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)

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 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 
 84.606   0.625  87.090 

name	user	system	elapsed
Coordinate-class	0.001	0.000	0.001
as.data.frame	1.243	0.295	1.570
collapse_markers	0.005	0.000	0.006
extract_ROI	0.142	0.021	0.165
extract_features	27.806	0.847	29.428
extract_interactions	22.821	0.197	23.941
extract_mask	0.257	0.293	0.568
extract_nearest_neighbor	6.464	6.828	13.696
extract_proximity	11.017	8.125	19.854
feature_selection	0.036	0.001	0.038
get_all_interactions	22.719	0.221	23.743
get_all_nearest_neighbors	0.714	0.014	0.794
get_all_proximities	0.001	0.001	0.001
get_count_ratios	0.002	0.000	0.002
get_counts_per_mm2	0.017	0.000	0.017
get_counts_per_mm2_noncollapsed	0.002	0.001	0.001
get_interactions	22.399	0.157	23.124
get_nearest_neighbors	0.640	0.001	0.646
interaction_maps	85.431	0.876	89.344
neighbor_ray_plot	0.740	0.048	0.794
overview_plot	0.904	0.014	0.951
plot	2.666	0.020	2.739
plot_interactions	23.037	0.161	23.689
plot_nearest_neighbor	0.588	0.004	0.607
plot_proximities	4.399	0.581	5.085
rayplot_single_coordinate	0.605	0.010	0.626
read_raw	78.825	0.525	81.129
threshold_dataset	80.662	0.605	83.036