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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpatialDecon_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialDecon.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘1.14.0’
* 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 ... WARNING
Error: package or namespace load failed for ‘SpatialDecon’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Biobase’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.lo
Execution halted
* checking Rd \usage sections ... NOTE
Error: there is no package called ‘Biobase’
Call sequence:
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
  Failed with error:  'package 'Biobase' required by 'GeomxTools' could not be found'
  Error loading dataset 'nsclc':
   Error in .requirePackage(package) : 
    unable to find required package 'GeomxTools'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
* 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 occurred in:


R version 4.4.0 beta (2024-04-15 r86425) -- "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.

  Natural language support but running in an English locale

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.

> pkgname <- "SpatialDecon"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> base::assign(".ExTimings", "SpatialDecon-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+   if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+   if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+   options(OutDec = '.')
+   format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
> 
> ### * </HEADER>
> library('SpatialDecon')
Error: package or namespace load failed for ‘SpatialDecon’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Biobase’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SpatialDecon)
  Error: package or namespace load failed for 'SpatialDecon' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   there is no package called 'Biobase'
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘SpatialDecon_vignette_NSCLC.Rmd’ using rmarkdown

Quitting from lines  at lines 51-53 [setup] (SpatialDecon_vignette_NSCLC.Rmd)
Error: processing vignette 'SpatialDecon_vignette_NSCLC.Rmd' failed with diagnostics:
package or namespace load failed for 'SpatialDecon' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'Biobase'
--- failed re-building ‘SpatialDecon_vignette_NSCLC.Rmd’

--- re-building ‘SpatialDecon_vignette.Rmd’ using rmarkdown

Quitting from lines  at lines 51-52 [setup] (SpatialDecon_vignette.Rmd)
Error: processing vignette 'SpatialDecon_vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'SpatialDecon' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'Biobase'
--- failed re-building ‘SpatialDecon_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘SpatialDecon_vignette_NSCLC.Rmd’ ‘SpatialDecon_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialDecon.Rcheck/00check.log’
for details.