##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:orthos.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings orthos_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthos.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘orthos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘orthos’ version ‘1.4.1’
* 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 ‘orthos’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthos.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 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 ... 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 shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘orthos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: decomposeVar
> ### Title: Decompose input contrasts to decoded and residual fractions
> ### Aliases: decomposeVar
> 
> ### ** Examples
> 
> MKL1_human <- readRDS(system.file("extdata", "GSE215150_MKL1_Human.rds",
+ package = "orthos"))
> 
> # Specifying M, treatm and cntr:
> dec_MKL1_human <- decomposeVar(M = MKL1_human, treatm = c(2, 3), cntr = c(1, 1), 
+                               organism = "Human", verbose = FALSE)
Error in vapply(urls, FUN = function(url) { : values must be length 1,
 but FUN(X[[1]]) result is length 0
Calls: decomposeVar ... <Anonymous> -> getInfoOnIds -> getInfoOnIds -> getSize -> vapply
Execution halted
* 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:
   but FUN(X[[1]]) result is length 0
  Backtrace:
      ▆
   1. └─orthos:::.readGeneInformation("Human", mustWork = FALSE) at test-queryWithContrasts.R:48:5
   2.   └─orthosData::GetorthosContrastDB(...)
   3.     ├─AnnotationHub::getInfoOnIds(rds_hubObj)
   4.     └─AnnotationHub::getInfoOnIds(rds_hubObj)
   5.       ├─AnnotationHub::getInfoOnIds(hub, ids)
   6.       └─AnnotationHub::getInfoOnIds(hub, ids)
   7.         └─AnnotationHub:::getSize(hub, res)
   8.           └─base::vapply(...)
  
  [ FAIL 3 | WARN 2 | SKIP 1 | PASS 164 ]
  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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthos.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘orthos’ ...
** using non-staged installation via StagedInstall field
** 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
* DONE (orthos)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(orthos)
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, saveRDS, setdiff, table,
    tapply, union, 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: 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

> 
> test_check("orthos")
demo_decomposed_contrasts_mouse_rds  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_mouse_hdf5  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5
demo_decomposed_contrasts_human_rds  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_human_hdf5  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
demo_decomposed_contrasts_mouse_rds  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_mouse_hdf5  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5
demo_decomposed_contrasts_human_rds  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_human_hdf5  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
demo_decomposed_contrasts_mouse_rds  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_mouse_hdf5  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5
demo_decomposed_contrasts_human_rds  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_human_hdf5  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
2025-03-25 07:48:30.044347: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: SSE4.1 SSE4.2 AVX, in other operations, rebuild TensorFlow with the appropriate compiler flags.
see ?orthosData and browseVignettes('orthosData') for documentation
loading from cache
require("keras")
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 270ms/step
see ?orthosData and browseVignettes('orthosData') for documentation
loading from cache
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
see ?orthosData and browseVignettes('orthosData') for documentation
loading from cache
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 172ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 149ms/step
demo_decomposed_contrasts_human_rds  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_human_hdf5  already present in cache at: /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
updating resource /Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
[ FAIL 3 | WARN 2 | SKIP 1 | PASS 164 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• cannot test `mustWork` when data is available (1): 'test-decomposeVar.R:66:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-decomposeVar.R:168:5'): decomposeVar works ─────────────────────
Error in `vapply(urls, FUN = function(url) {
    tryCatch({
        headers(HEAD(url))$`content-length`
    }, error = function(err) {
        NA_character_
    })
}, FUN.VALUE = character(1), USE.NAMES = FALSE)`: values must be length 1,
 but FUN(X[[1]]) result is length 0
Backtrace:
    ▆
 1. └─orthos::decomposeVar(...) at test-decomposeVar.R:168:5
 2.   └─orthos:::.readGeneInformation(organism, verbose = verbose)
 3.     └─orthosData::GetorthosContrastDB(...)
 4.       ├─AnnotationHub:::getInfoOnIds(h5_hubObj)
 5.       └─AnnotationHub:::getInfoOnIds(h5_hubObj)
 6.         ├─AnnotationHub::getInfoOnIds(hub, ids)
 7.         └─AnnotationHub::getInfoOnIds(hub, ids)
 8.           └─AnnotationHub:::getSize(hub, res)
 9.             └─base::vapply(...)
── Error ('test-queryWithContrasts.R:10:5'): loadContrastDatabase works ────────
Error in `vapply(urls, FUN = function(url) {
    tryCatch({
        headers(HEAD(url))$`content-length`
    }, error = function(err) {
        NA_character_
    })
}, FUN.VALUE = character(1), USE.NAMES = FALSE)`: values must be length 1,
 but FUN(X[[1]]) result is length 0
Backtrace:
    ▆
 1. └─orthos::loadContrastDatabase("Mouse", mode = useMode, mustWork = FALSE) at test-queryWithContrasts.R:10:5
 2.   └─orthosData::GetorthosContrastDB(organism = organism, mode = mode)
 3.     ├─AnnotationHub::getInfoOnIds(rds_hubObj)
 4.     └─AnnotationHub::getInfoOnIds(rds_hubObj)
 5.       ├─AnnotationHub::getInfoOnIds(hub, ids)
 6.       └─AnnotationHub::getInfoOnIds(hub, ids)
 7.         └─AnnotationHub:::getSize(hub, res)
 8.           └─base::vapply(...)
── Error ('test-queryWithContrasts.R:48:5'): queryWithContrasts works ──────────
Error in `vapply(urls, FUN = function(url) {
    tryCatch({
        headers(HEAD(url))$`content-length`
    }, error = function(err) {
        NA_character_
    })
}, FUN.VALUE = character(1), USE.NAMES = FALSE)`: values must be length 1,
 but FUN(X[[1]]) result is length 0
Backtrace:
    ▆
 1. └─orthos:::.readGeneInformation("Human", mustWork = FALSE) at test-queryWithContrasts.R:48:5
 2.   └─orthosData::GetorthosContrastDB(...)
 3.     ├─AnnotationHub::getInfoOnIds(rds_hubObj)
 4.     └─AnnotationHub::getInfoOnIds(rds_hubObj)
 5.       ├─AnnotationHub::getInfoOnIds(hub, ids)
 6.       └─AnnotationHub::getInfoOnIds(hub, ids)
 7.         └─AnnotationHub:::getSize(hub, res)
 8.           └─base::vapply(...)

[ FAIL 3 | WARN 2 | SKIP 1 | PASS 164 ]
Error: Test failures
Execution halted