##############################################################################
##############################################################################
###
### 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年11月17日 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
plotQueryResultsViolin 31.665 10.680 36.960
plotQueryResultsManh 31.135 11.168 38.169
queryWithContrasts 26.407 9.600 31.340
decomposeVar 17.018 5.819 32.618
loadContrastDatabase 2.619 0.100 8.006
* 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年11月17日 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年12月03日 17:06:01.927550: 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 00:00:1764799561.944361 64486 cuda_dnn.cc:8579] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
E0000 00:00:1764799561.950191 64486 cuda_blas.cc:1407] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
W0000 00:00:1764799561.964610 64486 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
W0000 00:00:1764799561.964630 64486 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
W0000 00:00:1764799561.964634 64486 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
W0000 00:00:1764799561.964638 64486 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
2025年12月03日 17:06:01.968782: 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 00:00:1764799563.934556 64486 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 73ms/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 54ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 46ms/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 37ms/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 0x76493c2ad580> 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 52ms/step
WARNING:tensorflow:6 out of the last 6 calls to <function Model.make_predict_function.<locals>.predict_function at 0x76493c3ea8e0> 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
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
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
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 49ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 45ms/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 48ms/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 39ms/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 51ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 46ms/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 
 85.478 21.295 167.140 
 64973:	find library=libc.so.6 [0]; searching
 64973:	 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)
 64973:	 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
 64973:	 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
 64973:	 trying file=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/libc.so.6
 64973:	 trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v3/libc.so.6
 64973:	 trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v2/libc.so.6
 64973:	 trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/libc.so.6
 64973:	 trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
 64973:	 trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
 64973:	 trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/libc.so.6
 64973:	 trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
 64973:	 trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
 64973:	 trying file=/usr/local/lib/libc.so.6
 64973:	 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)
 64973:	 trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
 64973:	 trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
 64973:	 trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
 64973:	
 64973:	
 64973:	calling init: /lib64/ld-linux-x86-64.so.2
 64973:	
 64973:	
 64973:	calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
 64973:	
 64973:	
 64973:	initialize program: sh
 64973:	
 64973:	
 64973:	transferring control: sh
 64973:	
 64974:	find library=libc.so.6 [0]; searching
 64974:	 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)
 64974:	 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
 64974:	 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
 64974:	 trying file=/media/volume/biocgpu2/biocbuild/.cache/R/basilisk/1.23.0/orthos/1.9.0/orthos/lib/libc.so.6
 64974:	 trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v3/libc.so.6
 64974:	 trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/glibc-hwcaps/x86-64-v2/libc.so.6
 64974:	 trying file=/home/biocbuild/.pyenv/versions/3.12.12/lib/libc.so.6
 64974:	 trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
 64974:	 trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
 64974:	 trying file=/home/biocbuild/bbs-3.23-bioc-gpu/R/lib/libc.so.6
 64974:	 trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
 64974:	 trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
 64974:	 trying file=/usr/local/lib/libc.so.6
 64974:	 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)
 64974:	 trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
 64974:	 trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
 64974:	 trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
 64974:	
 64974:	
 64974:	calling init: /lib64/ld-linux-x86-64.so.2
 64974:	
 64974:	
 64974:	calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
 64974:	
 64974:	
 64974:	initialize program: rm
 64974:	
 64974:	
 64974:	transferring control: rm
 64974: