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CHECK report for IrisSpatialFeatures on malbec2

This page was generated on 2018-03-01 07:13:59 -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: /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

Command output

##############################################################################
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###
### 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.



Installation output

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)

Tests output

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 

Example timings

IrisSpatialFeatures.Rcheck/IrisSpatialFeatures-Ex.timings

nameusersystemelapsed
Coordinate-class0.0040.0000.001
as.data.frame1.2280.0401.267
collapse_markers0.0040.0000.004
extract_ROI0.0960.0120.108
extract_features16.192 0.16416.381
extract_interactions11.956 0.00011.965
extract_mask0.1200.1400.259
extract_nearest_neighbor4.1802.7606.945
extract_proximity 8.012 3.07211.087
feature_selection0.0240.0000.025
get_all_interactions11.440 0.00011.447
get_all_nearest_neighbors0.3640.0000.364
get_all_proximities0.0000.0000.001
get_count_ratios0.0040.0000.001
get_counts_per_mm20.0120.0000.012
get_counts_per_mm2_noncollapsed0.0000.0000.001
get_interactions11.244 0.00011.249
get_nearest_neighbors0.4480.0000.447
interaction_maps17.596 0.02817.635
neighbor_ray_plot0.3760.0000.377
overview_plot0.1520.0000.152
plot0.8200.0040.825
plot_interactions11.732 0.00411.747
plot_nearest_neighbor0.3600.0040.363
plot_proximities4.4440.0004.445
rayplot_single_coordinate0.3720.0000.373
read_raw63.832 0.06063.932
threshold_dataset63.600 0.02863.678