##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialDE_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/spatialDE.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialDE/DESCRIPTION’ ... OK
* this is package ‘spatialDE’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘spatialDE’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.16-bioc/meat/spatialDE.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
spatial_patterns 17.818  1.303   9.681
FSV_sig           7.660  2.068  10.428
* 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
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/spatialDE.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialDE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘spatialDE’ ...
** using non-staged installation via StagedInstall field
** R
** data
** 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
* DONE (spatialDE)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(spatialDE)
> 
> test_check("spatialDE")
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Note: spatialData and spatialDataNames have been deprecated; all columns should be stored in colData and spatialCoords
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:56: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:476: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only.
  ms_results = ms_results.drop(transfer_columns, 1) \
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:56: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
Note: spatialData and spatialDataNames have been deprecated; all columns should be stored in colData and spatialCoords
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:56: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:476: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only.
  ms_results = ms_results.drop(transfer_columns, 1) \
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:56: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:476: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only.
  ms_results = ms_results.drop(transfer_columns, 1) \
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:56: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:476: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only.
  ms_results = ms_results.drop(transfer_columns, 1) \
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/pandas/core/internals/blocks.py:351: RuntimeWarning: invalid value encountered in log
  result = func(self.values, **kwargs)
Note: spatialData and spatialDataNames have been deprecated; all columns should be stored in colData and spatialCoords
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:26: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/spatialDE/1.4.3/env/lib/python3.8/site-packages/SpatialDE/base.py:40: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  R2 = -2. * np.dot(X, X.T) + (Xsq[:, None] + Xsq[None, :])
> 
> proc.time()
   user  system elapsed 
 62.023   2.553  53.752