##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TileDBArray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TileDBArray_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TileDBArray.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TileDBArray/DESCRIPTION’ ... OK
* this is package ‘TileDBArray’ version ‘1.4.0’
* 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 ‘TileDBArray’ 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 ... NOTE
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
':::' call which should be '::': ‘tiledb:::tiledb_datatype_R_type’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
* checking Rd \usage sections ... NOTE
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 4 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/TileDBArray.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘TileDBArray’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c remap_indices.cpp -o remap_indices.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o TileDBArray.so RcppExports.o remap_indices.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-TileDBArray/00new/TileDBArray/libs
** R
** byte-compile and prepare package for lazy loading
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Warning in system2(pkgcfg, c("tiledb", "--cflags"), stdout = TRUE) :
  running command ''/usr/local/bin/pkg-config' tiledb --cflags' had status 1
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Warning in system2(pkgcfg, c("tiledb", "--libs"), stdout = TRUE) :
  running command ''/usr/local/bin/pkg-config' tiledb --libs' had status 1
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Warning in system2(pkgcfg, c("tiledb", "--cflags"), stdout = TRUE) :
  running command ''/usr/local/bin/pkg-config' tiledb --cflags' had status 1
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Warning in system2(pkgcfg, c("tiledb", "--libs"), stdout = TRUE) :
  running command ''/usr/local/bin/pkg-config' tiledb --libs' had status 1
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Warning in system2(pkgcfg, c("tiledb", "--cflags"), stdout = TRUE) :
  running command ''/usr/local/bin/pkg-config' tiledb --cflags' had status 1
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Warning in system2(pkgcfg, c("tiledb", "--libs"), stdout = TRUE) :
  running command ''/usr/local/bin/pkg-config' tiledb --libs' had status 1
** testing if installed package keeps a record of temporary installation path
* DONE (TileDBArray)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(TileDBArray)
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
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, 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: 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: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep

Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Package tiledb was not found in the pkg-config search path.
Perhaps you should add the directory containing `tiledb.pc'
to the PKG_CONFIG_PATH environment variable
No package 'tiledb' found
Warning messages:
1: In system2(pkgcfg, c("tiledb", "--cflags"), stdout = TRUE) :
  running command ''/usr/local/bin/pkg-config' tiledb --cflags' had status 1
2: In system2(pkgcfg, c("tiledb", "--libs"), stdout = TRUE) :
  running command ''/usr/local/bin/pkg-config' tiledb --libs' had status 1
> test_check("TileDBArray")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 224 ]
> 
> proc.time()
   user  system elapsed 
 20.057   3.472  22.211