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This page was generated on 2024-06-20 12:14 -0400 (Thu, 20 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4687
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4402
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

Package 1978/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialDecon 1.15.0  (landing page)
Maddy Griswold
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/SpatialDecon
git_branch: devel
git_last_commit: 091cec3
git_last_commit_date: 2024-04-30 11:28:11 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped


CHECK results for SpatialDecon on nebbiolo2

To the developers/maintainers of the SpatialDecon package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SpatialDecon
Version: 1.15.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SpatialDecon_1.15.0.tar.gz
StartedAt: 2024-06-20 03:56:03 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 04:10:38 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 875.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SpatialDecon.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SpatialDecon_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SpatialDecon.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SpatialDecon/DESCRIPTION’ ... OK
* this is package ‘SpatialDecon’ version ‘1.15.0’
* 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... 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
runReverseDecon      98.818  0.403  99.376
runspatialdecon      63.834  1.896  66.338
runCollapseCellTypes 63.273  0.672  63.944
runMergeTumorIntoX   20.068  0.116  20.211
runErrorModel        13.763  0.096  13.864
reverseDecon          5.741  0.251   5.993
spatialdecon          5.182  0.312   5.499
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/SpatialDecon.Rcheck/00check.log’
for details.


Installation output

SpatialDecon.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SpatialDecon
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 96 ]
> 
> proc.time()
   user  system elapsed 
224.329   2.827 228.704 

Example timings

SpatialDecon.Rcheck/SpatialDecon-Ex.timings

nameusersystemelapsed
SpatialDecon-package3.7950.1043.899
TIL_barplot1.1380.0041.141
collapseCellTypes1.1310.0001.131
create_profile_matrix0.6160.0560.672
derive_GeoMx_background0.0030.0000.003
download_profile_matrix0.5430.2891.644
florets1.1520.1281.280
mergeTumorIntoX0.0070.0040.011
reverseDecon5.7410.2515.993
runCollapseCellTypes63.273 0.67263.944
runErrorModel13.763 0.09613.864
runMergeTumorIntoX20.068 0.11620.211
runReverseDecon98.818 0.40399.376
runspatialdecon63.834 1.89666.338
spatialdecon5.1820.3125.499