##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:orthos.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings orthos_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/orthos.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘orthos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘orthos’ version ‘1.3.0’
* 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 ‘orthos’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/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 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 ... 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: queryWithContrasts
> ### Title: Query the contrast database with a set of contrasts
> ### Aliases: queryWithContrasts
> 
> ### ** Examples
> 
> MKL1_human <- readRDS(system.file("extdata", "GSE215150_MKL1_Human.rds",
+ package = "orthos"))
> 
> # Decompose contrasts:
> dec_MKL1_human <- decomposeVar(M = MKL1_human, treatm = c(2, 3), cntr = c(1, 1), 
+                                organism = "Human", verbose = FALSE)
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 76ms/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 156ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 203ms/step
> 
> # Perform query against contrast DB with the decomposed fractions.
> # !!!Note!!! mode="DEMO" for demonstration purposes only.                             
> params <- BiocParallel::MulticoreParam(workers = 2)                              
> query.res.human <- queryWithContrasts(dec_MKL1_human, organism = "Human", 
+                                       BPPARAM = params, verbose = FALSE, 
+                                       mode = "DEMO")
demo_decomposed_contrasts_human_rds  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
updating resource /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
Error in vapply(urls, FUN = function(url) { : values must be length 1,
 but FUN(X[[1]]) result is length 0
Calls: queryWithContrasts ... <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("Mouse", mustWork = FALSE) at test-decomposeVar.R:151:5
   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 0 | PASS 186 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/orthos.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL orthos
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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.

> # 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, 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_human_rds  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
updating resource /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_human_hdf5  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
updating resource /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
demo_decomposed_contrasts_mouse_rds  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds
updating resource /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_mouse_hdf5  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5
updating resource /home/biocbuild/.cache/R/ExperimentHub/mouse_v212_NDF_c100_DEMOassays.h5
demo_decomposed_contrasts_human_rds  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
updating resource /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_human_hdf5  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
updating resource /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
2024-07-06 01:45:26.259637: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-07-06 01:45:26.830731: I tensorflow/core/util/util.cc:169] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
see ?orthosData and browseVignettes('orthosData') for documentation
loading from cache
require("keras")
2024-07-06 01:45:35.739305: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
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 225ms/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 110ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 105ms/step
demo_decomposed_contrasts_human_rds  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
updating resource /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_human_hdf5  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
updating resource /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
provided contrast:  INPUT_CONTRASTS
provided contrast:  DECODED_CONTRASTS
provided contrast:  RESIDUAL_CONTRASTS
Loading contrast database...
demo_decomposed_contrasts_human_rds  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
updating resource /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
demo_decomposed_contrasts_human_hdf5  already present in cache at: /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
updating resource /home/biocbuild/.cache/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5
Thresholding genes...
Querying contrast database with INPUT_CONTRASTS...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%

Querying contrast database with DECODED_CONTRASTS...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%

Querying contrast database with RESIDUAL_CONTRASTS...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%

Compiling query statistics...
Done!
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 186 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-decomposeVar.R:55:5'): .readGeneInformation works ──────────────
Error in `vapply(urls, FUN = function(url) {
    tryCatch({
        headers(HEAD(url))$`content-length`
    }, error = function(err) {
        NA_character_
    })
}, FUN.VALUE = character(1), USE.NAMES = FALSE)`: values must be length 1,
 but FUN(X[[1]]) result is length 0
Backtrace:
    ▆
 1. └─orthos:::.readGeneInformation("Mouse", mustWork = FALSE) at test-decomposeVar.R:55:5
 2.   └─orthosData::GetorthosContrastDB(...)
 3.     ├─AnnotationHub::getInfoOnIds(rds_hubObj)
 4.     └─AnnotationHub::getInfoOnIds(rds_hubObj)
 5.       ├─AnnotationHub::getInfoOnIds(hub, ids)
 6.       └─AnnotationHub::getInfoOnIds(hub, ids)
 7.         └─AnnotationHub:::getSize(hub, res)
 8.           └─base::vapply(...)
── Error ('test-decomposeVar.R:78:5'): .detectFeatureIdType works ──────────────
Error in `vapply(urls, FUN = function(url) {
    tryCatch({
        headers(HEAD(url))$`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("Mouse", mustWork = FALSE) at test-decomposeVar.R:78:5
 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(...)
── Error ('test-decomposeVar.R:151:5'): 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:::.readGeneInformation("Mouse", mustWork = FALSE) at test-decomposeVar.R:151:5
 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 0 | PASS 186 ]
Error: Test failures
Execution halted