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This page was generated on 2021-10-15 15:06:23 -0400 (Fri, 15 Oct 2021).

CHECK results for SpatialDecon on tokay2

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? here 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 1815/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialDecon 1.2.0  (landing page)
Patrick Danaher
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/SpatialDecon
git_branch: RELEASE_3_13
git_last_commit: df6b718
git_last_commit_date: 2021-05-19 12:56:38 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: SpatialDecon
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpatialDecon.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SpatialDecon_1.2.0.tar.gz
StartedAt: 2021-10-15 06:00:49 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 06:02:52 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 123.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: SpatialDecon.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpatialDecon.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SpatialDecon_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SpatialDecon.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SpatialDecon/DESCRIPTION' ... OK
* this is package 'SpatialDecon' version '1.2.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
reverseDecon 7.37   0.01    7.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
reverseDecon 8.64      0    8.64
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  `expected`: TRUE 
  -- Failure (test-integration-testing.R:130:5): reverseDecon is as expected:  ---
  all(abs(rdres.test$yhat - rdres$yhat) < 1) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  -- Failure (test-integration-testing.R:131:5): reverseDecon is as expected:  ---
  all(abs(rdres.test$coefs - rdres$coefs) < 100) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 10 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  `expected`: TRUE 
  -- Failure (test-integration-testing.R:130:5): reverseDecon is as expected:  ---
  all(abs(rdres.test$yhat - rdres$yhat) < 1) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  -- Failure (test-integration-testing.R:131:5): reverseDecon is as expected:  ---
  all(abs(rdres.test$coefs - rdres$coefs) < 100) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 10 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/SpatialDecon.Rcheck/00check.log'
for details.

Installation output

SpatialDecon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SpatialDecon_1.2.0.tar.gz && rm -rf SpatialDecon.buildbin-libdir && mkdir SpatialDecon.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpatialDecon.buildbin-libdir SpatialDecon_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SpatialDecon_1.2.0.zip && rm SpatialDecon_1.2.0.tar.gz SpatialDecon_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1619k  100 1619k    0     0  3770k      0 --:--:-- --:--:-- --:--:-- 3782k

install for i386

* 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
  converting help for package 'SpatialDecon'
    finding HTML links ... done
    SpatialDecon-package                    html  
    TIL_barplot                             html  
    algorithm2                              html  
    cellcols                                html  
    collapseCellTypes                       html  
    convertCellScoresToCounts               html  
    convertCellTypes                        html  
    deconLNR                                html  
    deriveWeights                           html  
    derive_GeoMx_background                 html  
    download_profile_matrix                 html  
    flagOutliers                            html  
    florets                                 html  
    mean.resid.sd                           html  
    mergeTumorIntoX                         html  
    mini_geomx_dataset                      html  
    reverseDecon                            html  
    runErrorModel                           html  
    safeTME                                 html  
    safeTME.matches                         html  
    spatialdecon                            html  
    tidy_X_and_Y                            html  
** 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

install for x64

* installing *source* package 'SpatialDecon' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpatialDecon' as SpatialDecon_1.2.0.zip
* DONE (SpatialDecon)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'SpatialDecon' successfully unpacked and MD5 sums checked

Tests output

SpatialDecon.Rcheck/tests_i386/testthat.Rout.fail


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
== Failed tests ================================================================
-- Failure (test-integration-testing.R:57:3): spatialdecon is as expected: beta --
all(abs(ires.test$beta - gres$beta) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:61:3): spatialdecon is as expected: sigma --
all(abs(ires.test$sigmas - gres$sigmas) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:74:3): spatialdecon is as expected: p ---
all(abs(ires.test$p - gres$p) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:96:3): spatialdeconTILs is as expected: beta --
all(abs(res.test$beta - res$beta) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:100:3): spatialdeconTILs is as expected: sigma --
all(abs(res.test$sigma - res$sigma) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:104:3): spatialdeconTILs is as expected: yhat --
mean(abs(res.test$yhat - res$yhat)) < 0.001 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:108:3): spatialdeconTILs is as expected: resids --
all(...) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:113:3): spatialdeconTILs is as expected: p --
all(abs(res.test$p - res$p) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:130:5): reverseDecon is as expected:  ---
all(abs(rdres.test$yhat - rdres$yhat) < 1) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:131:5): reverseDecon is as expected:  ---
all(abs(rdres.test$coefs - rdres$coefs) < 100) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 10 | WARN 0 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted

SpatialDecon.Rcheck/tests_x64/testthat.Rout.fail


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
== Failed tests ================================================================
-- Failure (test-integration-testing.R:57:3): spatialdecon is as expected: beta --
all(abs(ires.test$beta - gres$beta) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:61:3): spatialdecon is as expected: sigma --
all(abs(ires.test$sigmas - gres$sigmas) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:74:3): spatialdecon is as expected: p ---
all(abs(ires.test$p - gres$p) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:96:3): spatialdeconTILs is as expected: beta --
all(abs(res.test$beta - res$beta) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:100:3): spatialdeconTILs is as expected: sigma --
all(abs(res.test$sigma - res$sigma) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:104:3): spatialdeconTILs is as expected: yhat --
mean(abs(res.test$yhat - res$yhat)) < 0.001 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:108:3): spatialdeconTILs is as expected: resids --
all(...) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:113:3): spatialdeconTILs is as expected: p --
all(abs(res.test$p - res$p) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:130:5): reverseDecon is as expected:  ---
all(abs(rdres.test$yhat - rdres$yhat) < 1) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
-- Failure (test-integration-testing.R:131:5): reverseDecon is as expected:  ---
all(abs(rdres.test$coefs - rdres$coefs) < 100) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 10 | WARN 0 | SKIP 0 | PASS 18 ]
Error: Test failures
Execution halted

Example timings

SpatialDecon.Rcheck/examples_i386/SpatialDecon-Ex.timings

nameusersystemelapsed
SpatialDecon-package4.810.034.84
TIL_barplot1.610.021.63
collapseCellTypes1.560.001.57
derive_GeoMx_background0.020.000.01
download_profile_matrix0.860.041.21
florets1.750.001.75
mergeTumorIntoX0.000.020.01
reverseDecon7.370.017.39
spatialdecon4.470.004.47

SpatialDecon.Rcheck/examples_x64/SpatialDecon-Ex.timings

nameusersystemelapsed
SpatialDecon-package4.900.074.97
TIL_barplot1.720.011.73
collapseCellTypes1.740.001.75
derive_GeoMx_background0.000.020.01
download_profile_matrix0.780.000.93
florets1.870.011.89
mergeTumorIntoX0.020.020.03
reverseDecon8.640.008.64
spatialdecon4.810.024.83