Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:50 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SpatialDecon on machv2


To the developers/maintainers of the SpatialDecon package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialDecon.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1846/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialDecon 1.4.3  (landing page)
Nicole Ortogero
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/SpatialDecon
git_branch: RELEASE_3_14
git_last_commit: 72c2c83
git_last_commit_date: 2021-11-02 16:28:16 -0400 (Tue, 02 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SpatialDecon
Version: 1.4.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialDecon_1.4.3.tar.gz
StartedAt: 2022-04-12 18:50:54 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:17:41 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 1607.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SpatialDecon.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialDecon_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/SpatialDecon.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialDecon/DESCRIPTION’ ... OK
* this is package ‘SpatialDecon’ version ‘1.4.3’
* package encoding: UTF-8
* 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 ‘SpatialDecon’ 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 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 ... NOTE
download_profile_matrix: no visible binding for global variable
  ‘profile_matrix’
Undefined global functions or variables:
  profile_matrix
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
runCollapseCellTypes-NanoStringGeoMxSet-method 174.711  3.203 178.072
runCollapseCellTypes                           174.706  3.193 178.017
runReverseDecon-NanoStringGeoMxSet-method      169.097  2.834 172.073
runReverseDecon                                167.842  2.811 170.810
runspatialdecon                                 86.506  7.638  94.745
runspatialdecon-Seurat-method                   51.739  5.452  58.033
runspatialdecon-NanoStringGeoMxSet-method       37.868  0.979  38.880
runMergeTumorIntoX                              27.426  0.100  27.545
runMergeTumorIntoX-NanoStringGeoMxSet-method    27.339  0.158  27.512
runErrorModel                                   27.251  0.117  27.390
reverseDecon                                    15.685  0.320  16.019
SpatialDecon-package                             9.212  0.807  10.028
spatialdecon                                     8.233  1.196   9.434
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/SpatialDecon.Rcheck/00check.log’
for details.



Installation output

SpatialDecon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialDecon
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘SpatialDecon’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpatialDecon)

Tests output

SpatialDecon.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(SpatialDecon)
> 
> test_check("SpatialDecon")
[1] "Creating Atlas"
[1] "1 / 4 : B"
[1] "2 / 4 : C"
[1] "3 / 4 : A"
[1] "4 / 4 : D"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
> 
> proc.time()
   user  system elapsed 
359.832   7.311 368.877 

Example timings

SpatialDecon.Rcheck/SpatialDecon-Ex.timings

nameusersystemelapsed
SpatialDecon-package 9.212 0.80710.028
TIL_barplot2.7730.1302.905
collapseCellTypes2.7280.1142.844
create_profile_matrix0.8140.0480.862
derive_GeoMx_background0.0050.0020.005
download_profile_matrix0.6721.1483.258
florets2.6120.1552.770
mergeTumorIntoX0.0160.0020.018
reverseDecon15.685 0.32016.019
runCollapseCellTypes-NanoStringGeoMxSet-method174.711 3.203178.072
runCollapseCellTypes174.706 3.193178.017
runErrorModel27.251 0.11727.390
runMergeTumorIntoX-NanoStringGeoMxSet-method27.339 0.15827.512
runMergeTumorIntoX27.426 0.10027.545
runReverseDecon-NanoStringGeoMxSet-method169.097 2.834172.073
runReverseDecon167.842 2.811170.810
runspatialdecon-NanoStringGeoMxSet-method37.868 0.97938.880
runspatialdecon-Seurat-method51.739 5.45258.033
runspatialdecon86.506 7.63894.745
spatialdecon8.2331.1969.434