##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPOTlight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPOTlight_1.13.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SPOTlight.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPOTlight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPOTlight’ version ‘1.13.1’
* 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 ‘SPOTlight’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 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 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
.extract_coord: no visible global function definition for ‘is’
.extract_counts: no visible global function definition for ‘is’
.extract_image: no visible global function definition for ‘is’
.pred_hp: no visible global function definition for ‘as’
.set_groups_if_null: no visible global function definition for ‘is’
plotImage: no visible global function definition for ‘is’
plotSpatialScatterpie: no visible global function definition for ‘is’
plotSpatialScatterpie: no visible global function definition for ‘as’
plotTopicProfiles: no visible global function definition for ‘is’
runDeconvolution: no visible global function definition for ‘is’
runDeconvolution: no visible global function definition for ‘as’
trainNMF: no visible global function definition for ‘is’
trainNMF: no visible global function definition for ‘as’
Undefined global functions or variables:
  as is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) dot-filter.Rd:11-56: Lost braces
    11 |     weight_id = "weight") {
       |                           ^
checkRd: (-1) dot-filter.Rd:13-15: Lost braces
    13 |     if (is.null(n_top)) {
       |                         ^
checkRd: (-1) dot-filter.Rd:29-33: Lost braces
    29 |     mgs <- lapply(mgs, function(df) {
       |                                     ^
checkRd: (-1) dot-filter.Rd:36-40: Lost braces
    36 |     mgs <- lapply(ks, function(k) {
       |                                   ^
checkRd: (-1) dot-filter.Rd:44-50: Lost braces
    44 |     W <- vapply(ks, function(k) {
       |                                 ^
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
SPOTlight 5.89  0.239   6.159
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  y[1]: "gg"
  ── Failure ('test-utils.R:137:5'): .plot_image() SPE ───────────────────────────
  class(plt)[1] not equal to "gg".
  1/1 mismatches
  x[1]: "ggplot2::ggplot"
  y[1]: "gg"
  ── Failure ('test-utils.R:143:5'): .plot_image() SPE ───────────────────────────
  class(plt)[1] not equal to "gg".
  1/1 mismatches
  x[1]: "ggplot2::ggplot"
  y[1]: "gg"
  
  [ FAIL 13 | WARN 3 | SKIP 0 | PASS 281 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SPOTlight.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SPOTlight
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SPOTlight’ ...
** this is package ‘SPOTlight’ version ‘1.13.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC  -falign-functions=64 -Wall -g -O2   -c nmf.cpp -o nmf.o
nmf.cpp:61:13: warning: private field 'col_' is not used [-Wunused-private-field]
        int col_, index, max_index;
            ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SPOTlight.so RcppExports.o nmf.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-SPOTlight/00new/SPOTlight/libs
** R
** inst
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SPOTlight)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> set.seed(321)
> library(testthat)
> library(SPOTlight)
> # plotImage() ----
> test_check("SPOTlight")

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 3.70e-01
   2 | 3.51e-03
   3 | 6.06e-05
   4 | 2.98e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 3.70e-01
   2 | 3.51e-03
   3 | 6.06e-05
   4 | 2.98e-06
[ FAIL 13 | WARN 3 | SKIP 0 | PASS 281 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotImage.R:11:5'): plotImage path ───────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotImage.R:20:5'): plotImage array ──────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotImage.R:49:5'): plotImage SPE ────────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:20:5'): plotSpatialScatterpie with matrix and bad colnames ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:30:5'): plotSpatialScatterpie with matrix and bad colnames ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:40:5'): plotSpatialScatterpie - image ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:50:5'): plotSpatialScatterpie - type subset ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:61:5'): plotSpatialScatterpie - alpha ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:72:5'): plotSpatialScatterpie - pie_scale ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:90:5'): plotSpatialScatterpie - image ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-plotSpatialScatterpie.R:102:5'): plotSpatialScatterpie - spots on image ──
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-utils.R:137:5'): .plot_image() SPE ───────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"
── Failure ('test-utils.R:143:5'): .plot_image() SPE ───────────────────────────
class(plt)[1] not equal to "gg".
1/1 mismatches
x[1]: "ggplot2::ggplot"
y[1]: "gg"

[ FAIL 13 | WARN 3 | SKIP 0 | PASS 281 ]
Error: Test failures
Execution halted