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GPU-enabled build/check report for BioC 3.22
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This page was generated on 2025-06-19 10:45 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
biocgpuLinux (Ubuntu 24.04.2 LTS)x86_644.5.0 Patched (2025-05-01 r88189) -- "How About a Twenty-Six" 280
amaroneLinux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 282
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1/3HostnameOS / ArchINSTALLBUILDCHECK
orthos 1.7.2  (landing page)
Panagiotis Papasaikas
Snapshot Date: 2025-06-19 09:00 -0400 (Thu, 19 Jun 2025)
git_url: https://git.bioconductor.org/packages/orthos
git_branch: devel
git_last_commit: 72bb5a4
git_last_commit_date: 2025-06-06 04:38:05 -0400 (Fri, 06 Jun 2025)
biocgpuLinux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    ERROR  
amaroneLinux (Ubuntu 24.04.2 LTS) / x86_64  OK    ERROR  skipped

CHECK results for orthos on biocgpu

To the developers/maintainers of the orthos package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: orthos
Version: 1.7.2
Command: /home/biocbuild/bbs-3.22-bioc-gpu/R/bin/R CMD check --install=check:orthos.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc-gpu/R/site-library --timings orthos_1.7.2.tar.gz
StartedAt: 2025-06-19 09:59:28 -0400 (Thu, 19 Jun 2025)
EndedAt: 2025-06-19 10:07:47 -0400 (Thu, 19 Jun 2025)
EllapsedTime: 499.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: orthos.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc-gpu/R/bin/R CMD check --install=check:orthos.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc-gpu/R/site-library --timings orthos_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/biocgpu/biocbuild/bbs-3.22-bioc-gpu/meat/orthos.Rcheck’
* using R version 4.5.0 Patched (2025-05-01 r88189)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘orthos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘orthos’ version ‘1.7.2’
* 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/biocgpu/biocbuild/bbs-3.22-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 ... WARNING
Found the following file with non-ASCII characters:
  R/testorthosenv.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* 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 ... ERROR
Running examples in ‘orthos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: testOrthosEnv
> ### Title: Test conda environment
> ### Aliases: testOrthosEnv
> 
> ### ** Examples
> 
> testOrthosEnv()
=== TensorFlow/Keras Diagnostic ===
TF Version:  2.15.0 
LD_LIBRARY_PATH:
 /home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib:/home/biocbuild/.pyenv/versions/3.11.11/lib:/home/biocbuild/bbs-3.22-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-3.22-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-3.22-bioc-gpu/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/comm_libs/nvshmem/lib:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/comm_libs/nccl/lib:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/math_libs/lib64:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/compilers/lib:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/compilers/extras/qd/lib:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/cuda/extras/CUPTI/lib64:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/cuda/lib64 
Build Info:
$cpu_compiler
[1] "/usr/lib/llvm-17/bin/clang"

$cuda_compute_capabilities
[1] "sm_50"      "sm_60"      "sm_70"      "sm_75"      "compute_80"

$cuda_version
[1] "12.2"

$cudnn_version
[1] "8"

$is_cuda_build
[1] TRUE

$is_rocm_build
[1] FALSE

$is_tensorrt_build
[1] TRUE

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

Keras Available:  TRUE 
---- Missing/failed libraries (ENOENT / undefined) ----
None – linker found every requested .so 
===================================
Error in close.connection(trace_con) : invalid connection
Calls: testOrthosEnv -> basiliskRun -> fun -> close -> close.connection
Execution halted
     79001:	find library=libc.so.6 [0]; searching
     79001:	 search path=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib:/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.pyenv/versions/3.11.11/lib:/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.22-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)
     79001:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79001:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79001:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/libc.so.6
     79001:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79001:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79001:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/libc.so.6
     79001:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79001:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79001:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/libc.so.6
     79001:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79001:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79001:	  trying file=/usr/local/lib/libc.so.6
     79001:	 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)
     79001:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
     79001:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
     79001:	  trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
     79001:	
     79001:	
     79001:	calling init: /lib64/ld-linux-x86-64.so.2
     79001:	
     79001:	
     79001:	calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
     79001:	
     79001:	
     79001:	initialize program: sh
     79001:	
     79001:	
     79001:	transferring control: sh
     79001:	
     79002:	find library=libc.so.6 [0]; searching
     79002:	 search path=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib:/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.pyenv/versions/3.11.11/lib:/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.22-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)
     79002:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79002:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79002:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/libc.so.6
     79002:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79002:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79002:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/libc.so.6
     79002:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79002:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79002:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/libc.so.6
     79002:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79002:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79002:	  trying file=/usr/local/lib/libc.so.6
     79002:	 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)
     79002:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
     79002:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
     79002:	  trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
     79002:	
     79002:	
     79002:	calling init: /lib64/ld-linux-x86-64.so.2
     79002:	
     79002:	
     79002:	calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
     79002:	
     79002:	
     79002:	initialize program: rm
     79002:	
     79002:	
     79002:	transferring control: rm
     79002:	
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
plotQueryResultsViolin 25.320  8.346  28.306
queryWithContrasts     24.663  8.498  28.369
plotQueryResultsManh   22.941  8.175  27.838
decomposeVar           14.178  5.191  28.055
loadContrastDatabase    2.479  0.091   7.514
* 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:
       79424:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
       79424:	  trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
       79424:	
       79424:	
       79424:	calling init: /lib64/ld-linux-x86-64.so.2
       79424:	
       79424:	
       79424:	calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
       79424:	
       79424:	
       79424:	initialize program: rm
       79424:	
       79424:	
       79424:	transferring control: rm
       79424:	
* 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 WARNING, 1 NOTE
See
  ‘/media/volume/biocgpu/biocbuild/bbs-3.22-bioc-gpu/meat/orthos.Rcheck/00check.log’
for details.

Installation output

orthos.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc-gpu/R/bin/R CMD INSTALL orthos
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/biocgpu/biocbuild/bbs-3.22-bioc-gpu/R/site-library’
* installing *source* package ‘orthos’ ...
** this is package ‘orthos’ version ‘1.7.2’
** 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)

Tests output

orthos.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 Patched (2025-05-01 r88189) -- "How About a Twenty-Six"
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: 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: /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")
2025-06-19 10:04:36.075038: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2025-06-19 10:04:36.075088: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2025-06-19 10:04:36.076433: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2025-06-19 10:04:36.081833: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2025-06-19 10:04:36.854952: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2025-06-19 10:04:37.750331: I external/local_xla/xla/stream_executor/cuda/cuda_executor.cc:901] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero. See more at https://github.com/torvalds/linux/blob/v6.0/Documentation/ABI/testing/sysfs-bus-pci#L344-L355
2025-06-19 10:04:37.829901: W tensorflow/core/common_runtime/gpu/gpu_device.cc:2256] 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 67ms/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 46ms/step

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.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 36ms/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 0x79665812b9c0> 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 44ms/step
WARNING:tensorflow:6 out of the last 6 calls to <function Model.make_predict_function.<locals>.predict_function at 0x79665815b1a0> 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 40ms/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 36ms/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 41ms/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 36ms/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 64ms/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 47ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 42ms/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:  2.15.0 
LD_LIBRARY_PATH:
 /home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib:/home/biocbuild/.pyenv/versions/3.11.11/lib:/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc-gpu/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/comm_libs/nvshmem/lib:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/comm_libs/nccl/lib:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/math_libs/lib64:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/compilers/lib:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/compilers/extras/qd/lib:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/cuda/extras/CUPTI/lib64:/software/u24/nvhpc/24.7/Linux_x86_64/24.7/cuda/lib64 
Build Info:
$cpu_compiler
[1] "/usr/lib/llvm-17/bin/clang"

$cuda_compute_capabilities
[1] "sm_50"      "sm_60"      "sm_70"      "sm_75"      "compute_80"

$cuda_version
[1] "12.2"

$cudnn_version
[1] "8"

$is_cuda_build
[1] TRUE

$is_rocm_build
[1] FALSE

$is_tensorrt_build
[1] TRUE

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

Keras Available:  TRUE 
---- Missing/failed libraries (ENOENT / undefined) ----
None – linker found every requested .so 
===================================
[ FAIL 1 | WARN 2 | SKIP 1 | PASS 228 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-testOrthosEnv.R:5:5'): testOrthosEnv works ─────────────────────
Error in `close.connection(trace_con)`: invalid connection
Backtrace:
    ▆
 1. └─orthos::testOrthosEnv() at test-testOrthosEnv.R:5:5
 2.   └─basilisk::basiliskRun(...)
 3.     └─orthos (local) fun(...)
 4.       ├─base::close(trace_con)
 5.       └─base::close.connection(trace_con)

[ FAIL 1 | WARN 2 | SKIP 1 | PASS 228 ]
Error: Test failures
Execution halted
     79423:	find library=libc.so.6 [0]; searching
     79423:	 search path=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib:/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.pyenv/versions/3.11.11/lib:/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.22-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)
     79423:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79423:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79423:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/libc.so.6
     79423:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79423:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79423:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/libc.so.6
     79423:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79423:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79423:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/libc.so.6
     79423:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79423:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79423:	  trying file=/usr/local/lib/libc.so.6
     79423:	 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)
     79423:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
     79423:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
     79423:	  trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
     79423:	
     79423:	
     79423:	calling init: /lib64/ld-linux-x86-64.so.2
     79423:	
     79423:	
     79423:	calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
     79423:	
     79423:	
     79423:	initialize program: sh
     79423:	
     79423:	
     79423:	transferring control: sh
     79423:	
     79424:	find library=libc.so.6 [0]; searching
     79424:	 search path=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib:/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/.pyenv/versions/3.11.11/lib:/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.22-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)
     79424:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79424:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79424:	  trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/libc.so.6
     79424:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79424:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79424:	  trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/libc.so.6
     79424:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79424:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79424:	  trying file=/home/biocbuild/bbs-3.22-bioc-gpu/R/lib/libc.so.6
     79424:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
     79424:	  trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
     79424:	  trying file=/usr/local/lib/libc.so.6
     79424:	 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)
     79424:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
     79424:	  trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
     79424:	  trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
     79424:	
     79424:	
     79424:	calling init: /lib64/ld-linux-x86-64.so.2
     79424:	
     79424:	
     79424:	calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
     79424:	
     79424:	
     79424:	initialize program: rm
     79424:	
     79424:	
     79424:	transferring control: rm
     79424:

Example timings

orthos.Rcheck/orthos-Ex.timings

nameusersystemelapsed
decomposeVar14.178 5.19128.055
loadContrastDatabase2.4790.0917.514
plotQueryResultsManh22.941 8.17527.838
plotQueryResultsViolin25.320 8.34628.306
queryWithContrasts24.663 8.49828.369