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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SQLDataFrame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SQLDataFrame_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SQLDataFrame.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 ‘SQLDataFrame/DESCRIPTION’ ... OK
* this is package ‘SQLDataFrame’ version ‘1.23.0’
* 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 ‘SQLDataFrame’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  LGPL (>= 3); File LICENSE
Standardizable: FALSE
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SQLColumnSeed.Rd: DelayedArray-class, DataFrame-class
  SQLDataFrame.Rd: DataFrame-class, DFrame-class
  acquireConn.Rd: DataFrame-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘DuckDBColumnSeed’ ‘DuckDBColumnVector’ ‘DuckDBDataFrame’
  ‘SQLiteColumnSeed’ ‘SQLiteColumnVector’ ‘SQLiteDataFrame’ ‘dbtype’
  ‘sqltable’
Undocumented S4 methods:
  generic 'dbtype' and siglist 'SQLColumnSeed'
  generic 'dbtype' and siglist 'SQLDataFrame'
  generic 'extract_array' and siglist 'DuckDBColumnSeed'
  generic 'extract_array' and siglist 'SQLiteColumnSeed'
  generic 'sqltable' and siglist 'SQLDataFrame'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
SQL_extensions 8.831  0.373   8.989
* 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:
  as.data.frame(copy) not identical to `ref`.
  Component "mpg": Mean relative difference: 0.08571429
  Component "cyl": Mean relative difference: 0.3333333
  Component "disp": Mean relative difference: 0.12
  Component "hp": Mean relative difference: 0.1363636
  Component "drat": Mean relative difference: 0.005128205
  Component "wt": Mean relative difference: 0.09565217
  Component "qsec": Mean relative difference: 0.3454759
  Component "vs": Mean absolute difference: 1
  Component "am": Mean relative difference: 1
  ...
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 154 ]
  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, 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SQLDataFrame.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SQLDataFrame
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SQLDataFrame’ ...
** this is package ‘SQLDataFrame’ version ‘1.23.0’
** using staged installation
** R
** 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 (SQLDataFrame)

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.

> library(testthat)
> library(SQLDataFrame)
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep

> 
> test_check("SQLDataFrame")
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 154 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_SQLColumnSeed.R:20:9'): extraction methods work as expected for a SQLColumnSeed ──
as.vector(extract_array(y, list(keep))) not identical to example_df$wt[keep].
1/16 mismatches
[5] 2.88 - 3.15 == -0.275
── Failure ('test_SQLColumnSeed.R:24:9'): extraction methods work as expected for a SQLColumnSeed ──
as.vector(extract_array(y, list(keep))) not identical to example_df$wt[keep].
4/32 mismatches (average diff: 0.607)
[11] 3.15 - 2.78 ==  0.370
[19] 2.88 - 3.15 == -0.275
[21] 1.94 - 2.88 == -0.940
[22] 2.78 - 1.94 ==  0.845
── Failure ('test_SQLColumnSeed.R:28:9'): extraction methods work as expected for a SQLColumnSeed ──
as.vector(extract_array(y, list(keep))) not identical to example_df$wt[keep].
2/9 mismatches (average diff: 0.94)
[2] 1.94 - 2.88 == -0.94
[7] 1.94 - 2.88 == -0.94
── Failure ('test_SQLDataFrame.R:102:9'): slicing by rows collapses to an ordinary DFrame ──
as.vector(copy[[1]]) not identical to example_df[[1]][i].
4/32 mismatches (average diff: 3.85)
[2]  22.8 - 21.4 ==  1.4
[4]  21.0 - 22.8 == -1.8
[10] 21.4 - 27.3 == -5.9
[30] 27.3 - 21.0 ==  6.3
── Failure ('test_SQLDataFrame.R:122:9'): subset assignment usually collapses to an ordinary DFrame ──
as.data.frame(copy) not identical to `ref`.
Component "mpg": Mean relative difference: 0.08571429
Component "cyl": Mean relative difference: 0.3333333
Component "disp": Mean relative difference: 0.12
Component "hp": Mean relative difference: 0.1363636
Component "drat": Mean relative difference: 0.005128205
Component "wt": Mean relative difference: 0.09565217
Component "qsec": Mean relative difference: 0.3454759
Component "vs": Mean absolute difference: 1
Component "am": Mean relative difference: 1
...

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 154 ]
Error: Test failures
Execution halted