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This page was generated on 2022-01-18 11:08:26 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 riesling1


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 1839/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialDecon 1.5.4  (landing page)
Nicole Ortogero
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/SpatialDecon
git_branch: master
git_last_commit: 5099a40
git_last_commit_date: 2022-01-07 16:50:55 -0500 (Fri, 07 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SpatialDecon
Version: 1.5.4
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialDecon.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SpatialDecon_1.5.4.tar.gz
StartedAt: 2022-01-17 20:13:12 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 20:25:26 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 734.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SpatialDecon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialDecon.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SpatialDecon_1.5.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/SpatialDecon.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.5.4'
* 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
* 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 72.53   0.60   73.16
runCollapseCellTypes                           71.61   0.35   71.95
runReverseDecon-NanoStringGeoMxSet-method      65.80   0.16   65.95
runReverseDecon                                64.73   0.34   65.08
runspatialdecon                                46.64   2.33   49.39
runspatialdecon-Seurat-method                  29.49   3.08   33.39
runspatialdecon-NanoStringGeoMxSet-method      15.78   0.28   16.06
runMergeTumorIntoX                             13.67   0.05   13.72
runMergeTumorIntoX-NanoStringGeoMxSet-method   12.67   0.04   12.72
runErrorModel                                  11.33   0.08   11.41
SpatialDecon-package                            6.04   0.61    6.65
reverseDecon                                    6.33   0.15    6.47
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/SpatialDecon.Rcheck/00check.log'
for details.



Installation output

SpatialDecon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SpatialDecon
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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
  converting help for package 'SpatialDecon'
    finding HTML links ... done
    SpatialDecon-package                    html  
    TIL_barplot                             html  
    cellcols                                html  
    collapseCellTypes                       html  
    create_profile_matrix                   html  
    derive_GeoMx_background                 html  
    download_profile_matrix                 html  
    florets                                 html  
    mean.resid.sd                           html  
    mergeTumorIntoX                         html  
    mini_geomx_dataset                      html  
    mini_singleCell_dataset                 html  
    nsclc                                   html  
    reverseDecon                            html  
    runCollapseCellTypes-NanoStringGeoMxSet-method
                                            html  
    runCollapseCellTypes                    html  
    runErrorModel                           html  
    runMergeTumorIntoX-NanoStringGeoMxSet-method
                                            html  
    runMergeTumorIntoX                      html  
    runReverseDecon-NanoStringGeoMxSet-method
                                            html  
    runReverseDecon                         html  
    runspatialdecon-NanoStringGeoMxSet-method
                                            html  
    runspatialdecon-Seurat-method           html  
    runspatialdecon                         html  
    safeTME                                 html  
    safeTME.matches                         html  
    spatialdecon                            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
* DONE (SpatialDecon)
Making 'packages.html' ... done

Tests output

SpatialDecon.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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")
[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 
 162.48    2.62  166.71 

Example timings

SpatialDecon.Rcheck/SpatialDecon-Ex.timings

nameusersystemelapsed
SpatialDecon-package6.040.616.65
TIL_barplot1.550.091.64
collapseCellTypes2.040.062.09
create_profile_matrix0.930.221.16
derive_GeoMx_background0.000.020.02
download_profile_matrix0.360.341.84
florets1.50.31.8
mergeTumorIntoX0.000.010.01
reverseDecon6.330.156.47
runCollapseCellTypes-NanoStringGeoMxSet-method72.53 0.6073.16
runCollapseCellTypes71.61 0.3571.95
runErrorModel11.33 0.0811.41
runMergeTumorIntoX-NanoStringGeoMxSet-method12.67 0.0412.72
runMergeTumorIntoX13.67 0.0513.72
runReverseDecon-NanoStringGeoMxSet-method65.80 0.1665.95
runReverseDecon64.73 0.3465.08
runspatialdecon-NanoStringGeoMxSet-method15.78 0.2816.06
runspatialdecon-Seurat-method29.49 3.0833.39
runspatialdecon46.64 2.3349.39
spatialdecon4.160.484.64