##############################################################################
##############################################################################
###
### 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/orthos.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘orthos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘orthos’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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-3.21-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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
plotQueryResultsViolin 13.147  5.405  15.795
queryWithContrasts     12.979  5.487  15.435
plotQueryResultsManh   13.503  3.223  15.858
decomposeVar           10.506  4.518  21.697
loadContrastDatabase    1.527  0.095   5.541
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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
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: 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
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
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
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
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
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
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
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
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
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
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
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
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 32ms/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 24ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 23ms/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.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 19ms/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.
WARNING:tensorflow:5 out of the last 5 calls to <function Model.make_predict_function.<locals>.predict_function at 0x2ea2b7d00> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 24ms/step
WARNING:tensorflow:6 out of the last 6 calls to <function Model.make_predict_function.<locals>.predict_function at 0x2ea2b6d40> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 25ms/step
Checking input...
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
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
Detecting feature ids-type...
Feature ids-type detected: GENE_SYMBOL
18051/18051 provided input features mapped against a total of 20411 model features.
2360 missing features will be set to 0.
--> Missing features corresponding to non/lowly expressed genes in your context(s) are of no consequence.
--> The model is robust to small fractions (<10%) of missing genes that are expressed in your context(s).
--> Increased numbers of missing expressed genes in your input might result in model performance decline.
Preparing input...
Encoding context...
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 20ms/step
Encoding and decoding contrasts...
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 24ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 22ms/step
Preparing output...
Done!
Checking input...
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
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
Detecting feature ids-type...
Feature ids-type detected: GENE_SYMBOL
19774/19776 provided input features mapped against a total of 20339 model features.
565 missing features will be set to 0.
--> Missing features corresponding to non/lowly expressed genes in your context(s) are of no consequence.
--> The model is robust to small fractions (<10%) of missing genes that are expressed in your context(s).
--> Increased numbers of missing expressed genes in your input might result in model performance decline.
Preparing input...
Encoding context...
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 18ms/step
Encoding and decoding contrasts...
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 23ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 22ms/step
Preparing output...
Done!
2024-12-12 02:26:53.631 R[76965:88078788] XType: Using static font registry.
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
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
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
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
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
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
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 20ms/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 27ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 22ms/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
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
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: /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
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 0 | WARN 2 | SKIP 1 | PASS 229 ]

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

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 229 ]
> 
> proc.time()
   user  system elapsed 
 49.988  13.074  95.781