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This page was generated on 2022-01-19 13:07:25 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 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 1846/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialDecon 1.4.3  (landing page)
Nicole Ortogero
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 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 -0500 (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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpatialDecon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SpatialDecon_1.4.3.tar.gz
StartedAt: 2022-01-19 02:57:29 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 03:28:13 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 1844.1 seconds
RetCode: 0
Status:   OK  
CheckDir: SpatialDecon.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpatialDecon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SpatialDecon_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SpatialDecon.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.4.3'
* 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 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                user system elapsed
runCollapseCellTypes                           98.10   0.25   98.38
runCollapseCellTypes-NanoStringGeoMxSet-method 90.90   0.25   91.17
runReverseDecon                                89.89   0.01   89.90
runReverseDecon-NanoStringGeoMxSet-method      89.31   0.35   89.66
runspatialdecon                                66.90   1.28   68.24
runspatialdecon-Seurat-method                  46.38   1.27   48.28
runspatialdecon-NanoStringGeoMxSet-method      21.59   0.08   21.68
runMergeTumorIntoX                             13.28   0.01   13.29
runMergeTumorIntoX-NanoStringGeoMxSet-method   13.21   0.03   13.24
runErrorModel                                  11.89   0.08   11.97
reverseDecon                                    7.96   0.02    7.97
SpatialDecon-package                            6.36   0.03    6.39
spatialdecon                                    5.95   0.22    6.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                 user system elapsed
runCollapseCellTypes-NanoStringGeoMxSet-method 107.20   0.16  107.37
runCollapseCellTypes                           106.80   0.09  106.91
runReverseDecon                                104.74   0.07  104.85
runReverseDecon-NanoStringGeoMxSet-method      100.11   0.11  100.22
runspatialdecon                                 66.25   0.79   67.11
runspatialdecon-Seurat-method                   41.79   0.62   43.03
runspatialdecon-NanoStringGeoMxSet-method       23.46   0.06   23.53
runMergeTumorIntoX                              15.50   0.03   15.53
runErrorModel                                   14.92   0.06   14.98
runMergeTumorIntoX-NanoStringGeoMxSet-method    14.83   0.03   14.86
reverseDecon                                     8.80   0.02    8.81
SpatialDecon-package                             6.73   0.05    6.78
spatialdecon                                     5.62   0.03    5.66
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SpatialDecon.Rcheck/00check.log'
for details.



Installation output

SpatialDecon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SpatialDecon_1.4.3.tar.gz && rm -rf SpatialDecon.buildbin-libdir && mkdir SpatialDecon.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpatialDecon.buildbin-libdir SpatialDecon_1.4.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SpatialDecon_1.4.3.zip && rm SpatialDecon_1.4.3.tar.gz SpatialDecon_1.4.3.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
  5 3957k    5  226k    0     0  1236k      0  0:00:03 --:--:--  0:00:03 1238k
100 3957k  100 3957k    0     0  4698k      0 --:--:-- --:--:-- --:--:-- 4699k

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  
    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

install for x64

* installing *source* package 'SpatialDecon' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpatialDecon' as SpatialDecon_1.4.3.zip
* DONE (SpatialDecon)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SpatialDecon' successfully unpacked and MD5 sums checked

Tests output

SpatialDecon.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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")
[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 
 211.51    1.14  213.84 

SpatialDecon.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
 228.64    0.71  230.20 

Example timings

SpatialDecon.Rcheck/examples_i386/SpatialDecon-Ex.timings

nameusersystemelapsed
SpatialDecon-package6.360.036.39
TIL_barplot2.430.012.44
collapseCellTypes1.820.031.86
create_profile_matrix0.640.070.70
derive_GeoMx_background000
download_profile_matrix0.720.362.25
florets2.130.012.15
mergeTumorIntoX0.010.000.01
reverseDecon7.960.027.97
runCollapseCellTypes-NanoStringGeoMxSet-method90.90 0.2591.17
runCollapseCellTypes98.10 0.2598.38
runErrorModel11.89 0.0811.97
runMergeTumorIntoX-NanoStringGeoMxSet-method13.21 0.0313.24
runMergeTumorIntoX13.28 0.0113.29
runReverseDecon-NanoStringGeoMxSet-method89.31 0.3589.66
runReverseDecon89.89 0.0189.90
runspatialdecon-NanoStringGeoMxSet-method21.59 0.0821.68
runspatialdecon-Seurat-method46.38 1.2748.28
runspatialdecon66.90 1.2868.24
spatialdecon5.950.226.17

SpatialDecon.Rcheck/examples_x64/SpatialDecon-Ex.timings

nameusersystemelapsed
SpatialDecon-package6.730.056.78
TIL_barplot1.970.021.99
collapseCellTypes2.000.012.01
create_profile_matrix0.740.050.78
derive_GeoMx_background000
download_profile_matrix0.640.252.22
florets2.670.002.67
mergeTumorIntoX0.010.000.02
reverseDecon8.800.028.81
runCollapseCellTypes-NanoStringGeoMxSet-method107.20 0.16107.37
runCollapseCellTypes106.80 0.09106.91
runErrorModel14.92 0.0614.98
runMergeTumorIntoX-NanoStringGeoMxSet-method14.83 0.0314.86
runMergeTumorIntoX15.50 0.0315.53
runReverseDecon-NanoStringGeoMxSet-method100.11 0.11100.22
runReverseDecon104.74 0.07104.85
runspatialdecon-NanoStringGeoMxSet-method23.46 0.0623.53
runspatialdecon-Seurat-method41.79 0.6243.03
runspatialdecon66.25 0.7967.11
spatialdecon5.620.035.66