##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD check --install=check:orthos.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc-gpu/R/site-library --timings orthos_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/orthos.Rcheck’
* using R Under development (unstable) (2025-11-17 r89032)
* 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 ‘orthos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘orthos’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/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 whether startup messages can be suppressed ... 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
queryWithContrasts     27.823 10.071  33.423
plotQueryResultsManh   27.868  9.481  33.305
plotQueryResultsViolin 28.036  9.298  31.452
decomposeVar           15.944  5.470  30.618
loadContrastDatabase    2.633  0.095   7.970
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/orthos.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD INSTALL orthos
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/R/site-library’
* installing *source* package ‘orthos’ ...
** this is package ‘orthos’ version ‘1.9.0’
** 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) (2025-11-17 r89032) -- "Unsuffered Consequences"
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.

> # 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: 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

> 
> test_check("orthos")
demo_decomposed_contrasts_mouse_rds  already present in cache at: /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
demo_decomposed_contrasts_human_rds  already present in cache at: /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
demo_decomposed_contrasts_mouse_rds  already present in cache at: /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
demo_decomposed_contrasts_human_rds  already present in cache at: /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
demo_decomposed_contrasts_mouse_rds  already present in cache at: /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
demo_decomposed_contrasts_human_rds  already present in cache at: /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
see ?orthosData and browseVignettes('orthosData') for documentation
loading from cache
require("keras")
2025-12-19 11:06:33.211572: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:467] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
E0000 00:00:1766160393.228192   32071 cuda_dnn.cc:8579] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
E0000 00:00:1766160393.233272   32071 cuda_blas.cc:1407] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
W0000 00:00:1766160393.247530   32071 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
W0000 00:00:1766160393.247548   32071 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
W0000 00:00:1766160393.247552   32071 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
W0000 00:00:1766160393.247556   32071 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
2025-12-19 11:06:33.251664: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
W0000 00:00:1766160395.173486   32071 gpu_device.cc:2341] Cannot dlopen some GPU libraries. Please make sure the missing libraries mentioned above are installed properly if you would like to use GPU. Follow the guide at https://www.tensorflow.org/install/gpu for how to download and setup the required libraries for your platform.
Skipping registering GPU devices...
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 75ms/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 49ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 43ms/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 38ms/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 0x76c05c559580> 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 46ms/step
WARNING:tensorflow:6 out of the last 6 calls to <function Model.make_predict_function.<locals>.predict_function at 0x76c07956e8e0> 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 43ms/step
Checking input...
demo_decomposed_contrasts_human_rds  already present in cache at: /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
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
Error while performing HEAD request.
   Proceeding without cache information.
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 37ms/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 45ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 46ms/step
Preparing output...
Done!
Checking input...
demo_decomposed_contrasts_mouse_rds  already present in cache at: /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
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 37ms/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 52ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 45ms/step
Preparing output...
Done!
demo_decomposed_contrasts_human_rds  already present in cache at: /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
demo_decomposed_contrasts_mouse_rds  already present in cache at: /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
demo_decomposed_contrasts_human_rds  already present in cache at: /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
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 42ms/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 48ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 49ms/step
demo_decomposed_contrasts_human_rds  already present in cache at: /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
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
demo_decomposed_contrasts_human_hdf5  already present in cache at: /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!
=== TensorFlow/Keras Diagnostic ===
TF Version:  2.19.0 
LD_LIBRARY_PATH:
 /media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib:/home/biocbuild/.pyenv/versions/3.12.12/lib:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server 
Build Info:
$cpu_compiler
[1] "/usr/lib/llvm-18/bin/clang"

$cuda_compute_capabilities
[1] "sm_60"      "sm_70"      "sm_80"      "sm_89"      "compute_90"

$cuda_version
[1] "12.5.1"

$cudnn_version
[1] "9"

$is_cuda_build
[1] TRUE

$is_rocm_build
[1] FALSE

$is_tensorrt_build
[1] FALSE

Physical Devices:
[[1]]
PhysicalDevice(name='/physical_device:CPU:0', device_type='CPU')

Keras Available:  TRUE 
===================================
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 229 ]

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 229 ]
> 
> proc.time()
   user  system elapsed 
 92.821  24.935 182.038 
     32493:	find library=libc.so.6 [0]; searching
     32493:	 search path=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/glibc-hwcaps/x86-64-v3:/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/glibc-hwcaps/x86-64-v2:/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib:/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.pyenv/versions/3.12.12/lib:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib:/usr/local/lib/glibc-hwcaps/x86-64-v3:/usr/local/lib/glibc-hwcaps/x86-64-v2:/usr/local/lib		(LD_LIBRARY_PATH)
     32493:	  trying file=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     32493:	  trying file=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     32493:	  trying file=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/libc.so.6
     32493:	  trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     32493:	  trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     32493:	  trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/libc.so.6
     32493:	  trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     32493:	  trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     32493:	  trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/libc.so.6
     32493:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     32493:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     32493:	  trying file=/usr/local/lib/libc.so.6
     32493:	 search path=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3:/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2:/usr/lib/x86_64-linux-gnu		(system search path)
     32493:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
     32493:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
     32493:	  trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
     32493:	
     32493:	
     32493:	calling init: /lib64/ld-linux-x86-64.so.2
     32493:	
     32493:	
     32493:	calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
     32493:	
     32493:	
     32493:	initialize program: sh
     32493:	
     32493:	
     32493:	transferring control: sh
     32493:	
     32494:	find library=libc.so.6 [0]; searching
     32494:	 search path=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/glibc-hwcaps/x86-64-v3:/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/glibc-hwcaps/x86-64-v2:/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib:/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.pyenv/versions/3.12.12/lib:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.23-bioc-gpu/R/lib:/usr/local/lib/glibc-hwcaps/x86-64-v3:/usr/local/lib/glibc-hwcaps/x86-64-v2:/usr/local/lib		(LD_LIBRARY_PATH)
     32494:	  trying file=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     32494:	  trying file=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     32494:	  trying file=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/libc.so.6
     32494:	  trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     32494:	  trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     32494:	  trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/libc.so.6
     32494:	  trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     32494:	  trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     32494:	  trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/libc.so.6
     32494:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     32494:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     32494:	  trying file=/usr/local/lib/libc.so.6
     32494:	 search path=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3:/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2:/usr/lib/x86_64-linux-gnu		(system search path)
     32494:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
     32494:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
     32494:	  trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
     32494:	
     32494:	
     32494:	calling init: /lib64/ld-linux-x86-64.so.2
     32494:	
     32494:	
     32494:	calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
     32494:	
     32494:	
     32494:	initialize program: rm
     32494:	
     32494:	
     32494:	transferring control: rm
     32494: