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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SpatialDecon_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SpatialDecon.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SpatialDecon/DESCRIPTION’ ... OK
* this is package ‘SpatialDecon’ version ‘1.9.0’
* 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 ... 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 ... ERROR
Running examples in ‘SpatialDecon-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runspatialdecon
> ### Title: Run spatialdecon
> ### Aliases: runspatialdecon runspatialdecon,NanoStringGeoMxSet-method
> ###   runspatialdecon,Seurat-method
> 
> ### ** Examples
> 
> 
> ## GeoMxSet Object ##
> library(GeomxTools)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: NanoStringNCTools
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: ggplot2
> datadir <- system.file("extdata", "DSP_NGS_Example_Data", package = "GeomxTools")
> demoData <- readRDS(file.path(datadir, "/demoData.rds"))
> 
> demoData <- shiftCountsOne(demoData)
> target_demoData <- aggregateCounts(demoData)
> 
> target_demoData <- normalize(target_demoData, "quant")
> 
> demoData <- runspatialdecon(object = target_demoData, 
+                             norm_elt = "exprs_norm",
+                             raw_elt = "exprs")
> 
> ## Seurat Object ##
> # get dataset
> con <- gzcon(url("https://github.com/almaan/her2st/raw/master/data/ST-cnts/G1.tsv.gz"))
> txt <- readLines(con)
> temp <- read.table(textConnection(txt), sep = "\t", header = TRUE, row.names = 1)
> # parse data
> raw = t(as.matrix(temp))
> norm = sweep(raw, 2, colSums(raw), "/") * mean(colSums(raw))
> x = as.numeric(substr(rownames(temp), 1, unlist(gregexpr("x", rownames(temp))) - 1))
> y = -as.numeric(substr(rownames(temp), 
+                  unlist(gregexpr("x", rownames(temp))) + 1, nchar(rownames(temp))))
> # put into a seurat object:
> andersson_g1 = SeuratObject::CreateSeuratObject(counts = raw, assay="Spatial")
> andersson_g1@meta.data$x = x
> andersson_g1@meta.data$y = y
> 
> res <- runspatialdecon(andersson_g1)
Killed
* 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 ...
  ‘SpatialDecon_vignette.Rmd’ using ‘UTF-8’... OK
  ‘SpatialDecon_vignette_NSCLC.Rmd’ using ‘UTF-8’... OK
  ‘SpatialDecon_vignette_ST.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘SpatialDecon_vignette.Rmd’ using rmarkdown
Killed
--- re-building ‘SpatialDecon_vignette_NSCLC.Rmd’ using rmarkdown
Killed
--- re-building ‘SpatialDecon_vignette_ST.Rmd’ using rmarkdown
Killed
SUMMARY: processing the following files failed:
  ‘SpatialDecon_vignette.Rmd’ ‘SpatialDecon_vignette_NSCLC.Rmd’
  ‘SpatialDecon_vignette_ST.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/SpatialDecon.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SpatialDecon
###
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* installing to library ‘/home/biocbuild/bbs-3.17-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
** 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)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 
280.808   5.316 311.180