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CHECK report for IrisSpatialFeatures on merida2

This page was generated on 2018-03-01 07:39:36 -0500 (Thu, 01 Mar 2018).

Package 723/1499HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IrisSpatialFeatures 1.3.0
Daniel Gusenleitner
Snapshot Date: 2018-02-28 17:01:29 -0500 (Wed, 28 Feb 2018)
URL: https://git.bioconductor.org/packages/IrisSpatialFeatures
Branch: master
Last Commit: 5bc531a
Last Changed Date: 2017-10-30 12:54:32 -0500 (Mon, 30 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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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


Installation output

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)

Tests output

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 

Example timings

IrisSpatialFeatures.Rcheck/IrisSpatialFeatures-Ex.timings

nameusersystemelapsed
Coordinate-class0.0010.0010.003
as.data.frame1.6000.3952.048
collapse_markers0.0070.0010.007
extract_ROI0.1970.0160.221
extract_features34.908 1.08737.642
extract_interactions28.643 0.34730.733
extract_mask0.3190.3890.729
extract_nearest_neighbor 8.544 8.92618.365
extract_proximity14.26410.77826.320
feature_selection0.0560.0020.061
get_all_interactions29.012 0.31530.849
get_all_nearest_neighbors0.7030.0050.746
get_all_proximities0.0010.0000.001
get_count_ratios0.0020.0010.003
get_counts_per_mm20.0270.0000.028
get_counts_per_mm2_noncollapsed0.0030.0000.002
get_interactions29.025 0.25230.961
get_nearest_neighbors0.8900.0060.959
interaction_maps117.439 1.662125.533
neighbor_ray_plot0.7170.0160.780
overview_plot2.4070.1032.684
plot3.7280.0423.981
plot_interactions28.846 0.27730.226
plot_nearest_neighbor0.6660.0050.690
plot_proximities5.0780.6465.934
rayplot_single_coordinate0.7300.0050.755
read_raw113.503 1.236121.352
threshold_dataset112.668 1.349120.814