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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:philr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings philr_1.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/philr.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘philr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘philr’ version ‘1.35.0’
* 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 ‘philr’ 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) philr.Rd:48: Lost braces
    48 | weightings (code{p}), ilr weightings (code{ilr.weights}), contrast matrix (\code{V})) as a list
       |                 ^
checkRd: (-1) philr.Rd:48: Lost braces
    48 | weightings (code{p}), ilr weightings (code{ilr.weights}), contrast matrix (\code{V})) as a list
       |                                           ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘philr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: philr
> ### Title: Data transformation and driver of PhILR.
> ### Aliases: philr build.phylo.ilr
> 
> ### ** Examples
> 
> # Prepare example data
> tr <- named_rtree(5)
> x <- t(rmultinom(10,100,c(.1,.6,.2,.3,.2))) + 0.65 # add a small pseudocount
> colnames(x) <- tr$tip.label
> philr(x, tr, part.weights='enorm.x.gm.counts',
+                ilr.weights='blw.sqrt', return.all=FALSE)
Building Sequential Binary Partition from Tree...
Building Contrast Matrix...
Transforming the Data...
Calculating ILR Weights...
               n1           n2          n3          n4
 [1,]  0.54249790  0.804450241  0.13128922  0.69261304
 [2,]  0.08297088  1.166649275 -0.18291107 -0.80710027
 [3,] -0.15038015 -0.610943864 -0.98971565 -0.10401441
 [4,] -0.04390273 -0.355678151  0.04706121  0.48508839
 [5,] -0.46119543  0.125319890  0.54040042  0.58606755
 [6,]  0.16614802 -0.008687729  1.03530810  0.04866846
 [7,]  0.08050414 -0.012289070 -0.78951207 -1.14052888
 [8,] -0.16583104 -0.054863409  0.22362213 -0.36998049
 [9,] -0.15935905 -0.697233050 -0.24125826 -0.02211077
[10,] -0.15622637 -0.082074431  0.54357406  0.91192001
> 
> # Running philr on a TreeSummarizedExperiment object
> 
> ## Prepare example data
> library(mia)
Loading required package: MultiAssayExperiment
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
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: S4Vectors

Attaching package: ‘S4Vectors’

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: Seqinfo
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

Loading required package: SingleCellExperiment
Loading required package: TreeSummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

This is mia version 1.17.9
- Online documentation and vignettes: https://microbiome.github.io/mia/
- Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/
> library(tidyr)

Attaching package: ‘tidyr’

The following object is masked from ‘package:S4Vectors’:

    expand

> data(GlobalPatterns, package="mia")
> 
> ## Select prevalent taxa 
> tse <-  GlobalPatterns %>% subsetByPrevalentTaxa(
+                                detection = 3,
+                                prevalence = 20/100,
+                                as_relative = FALSE)
Warning in subsetByPrevalentTaxa(., detection = 3, prevalence = 20/100,  :
  'subsetByPrevalentTaxa' is deprecated. Use 
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: %>% ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 ‘philr-intro.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from philr-intro.Rmd:95-113 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─GlobalPatterns %>% ...
  2. ├─mia::subsetByPrevalentTaxa(...)
  3. ├─mia::subsetByPrevalentTaxa(...)
  4. │ ├─mia::subsetByPrevalent(x, ...)
  5. │ └─mia::subsetByPrevalent(x, ...)
  6. │   └─mia (local) .local(x, ...)
  7. │     ├─methods::callNextMethod(x, ...)
  8. │     │ └─base::eval(call, callEnv)
  9. │     │   └─base::eval(call, callEnv)
 10. │     └─mia (local) .nextMethod(x, ...)
 11. │       └─mia (local) .local(x, ...)
 12. │         ├─x[prevalent_indices, ]
 13. │         └─x[prevalent_indices, ]
 14. │           ├─BiocGenerics::updateObject(x)
 15. │           └─TreeSummarizedExperiment::updateObject(x)
 16. │             ├─methods::callNextMethod()
 17. │             └─SingleCellExperiment (local) .nextMethod(object = object)
 18. │               ├─methods::callNextMethod()
 19. │               └─SummarizedExperiment (local) .nextMethod(object = object)
 20. │                 ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 21. │                 └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 22. │                   ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 23. │                   └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 24. │                     └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 25. └─methods:::.extendsForS3(`<chr>`)
 26.   └─methods::extends(Class, maybe = FALSE)
 27.     └─methods::getClassDef(class1)
 28.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'philr-intro.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘philr-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘philr-intro.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/philr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL philr
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘philr’ ...
** this is package ‘philr’ version ‘1.35.0’
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (philr)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.

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(philr)
> 
> test_check("philr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  2.975   0.241   3.207