| Back to --- experimental! --- GPU-enabled build/check report for BioC 3.22 Report updated every 6 hours |
This page was generated on 2025-06-06 10:45 -0400 (Fri, 06 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| biocgpu | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 Patched (2025-05-01 r88189) -- "How About a Twenty-Six" | 280 |
| amarone | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (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 1/3 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| orthos 1.7.2 (landing page) Panagiotis Papasaikas
| biocgpu | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||||
| amarone | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
|
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. |
| Package: orthos |
| Version: 1.7.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:orthos.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings orthos_1.7.2.tar.gz |
| StartedAt: 2025-06-06 14:15:18 -0000 (Fri, 06 Jun 2025) |
| EndedAt: 2025-06-06 14:24:56 -0000 (Fri, 06 Jun 2025) |
| EllapsedTime: 577.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: orthos.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:orthos.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings orthos_1.7.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc-gpu/meat/orthos.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘/home/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/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/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/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/usr/local/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
9425: find library=libc.so.6 [0]; searching
9425: search path=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v4:/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-v4:/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/R/lib/glibc-hwcaps/x86-64-v4:/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib/glibc-hwcaps/x86-64-v4:/usr/local/lib/glibc-hwcaps/x86-64-v3:/usr/local/lib/glibc-hwcaps/x86-64-v2:/usr/local/lib (LD_LIBRARY_PATH)
9425: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9425: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9425: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9425: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/libc.so.6
9425: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9425: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9425: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9425: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/libc.so.6
9425: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9425: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9425: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9425: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/libc.so.6
9425: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9425: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9425: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9425: trying file=/usr/local/lib/libc.so.6
9425: search path=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v4:/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)
9425: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v4/libc.so.6
9425: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
9425: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
9425: trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
9425:
9425:
9425: calling init: /lib64/ld-linux-x86-64.so.2
9425:
9425:
9425: calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
9425:
9425:
9425: initialize program: sh
9425:
9425:
9425: transferring control: sh
9425:
9426: find library=libc.so.6 [0]; searching
9426: search path=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v4:/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-v4:/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/R/lib/glibc-hwcaps/x86-64-v4:/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib/glibc-hwcaps/x86-64-v4:/usr/local/lib/glibc-hwcaps/x86-64-v3:/usr/local/lib/glibc-hwcaps/x86-64-v2:/usr/local/lib (LD_LIBRARY_PATH)
9426: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9426: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9426: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9426: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/libc.so.6
9426: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9426: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9426: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9426: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/libc.so.6
9426: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9426: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9426: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9426: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/libc.so.6
9426: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9426: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9426: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9426: trying file=/usr/local/lib/libc.so.6
9426: search path=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v4:/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)
9426: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v4/libc.so.6
9426: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
9426: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
9426: trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
9426:
9426:
9426: calling init: /lib64/ld-linux-x86-64.so.2
9426:
9426:
9426: calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
9426:
9426:
9426: initialize program: rm
9426:
9426:
9426: transferring control: rm
9426:
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotQueryResultsViolin 28.985 10.868 32.787
queryWithContrasts 27.404 11.173 33.710
plotQueryResultsManh 24.475 10.179 32.346
decomposeVar 12.252 5.764 29.359
loadContrastDatabase 2.974 0.275 8.642
* 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:
9747: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
9747: trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
9747:
9747:
9747: calling init: /lib64/ld-linux-x86-64.so.2
9747:
9747:
9747: calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
9747:
9747:
9747: initialize program: rm
9747:
9747:
9747: transferring control: rm
9747:
* 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
‘/home/biocbuild/bbs-3.22-bioc-gpu/meat/orthos.Rcheck/00check.log’
for details.
orthos.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL orthos ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/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)
orthos.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 (2025-04-11) -- "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")
2025-06-06 14:20:58.208774: I tensorflow/core/util/port.cc:113] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2025-06-06 14:20:58.356691: 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
2025-06-06 14:20:58.356992: 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
2025-06-06 14:20:58.381670: 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
2025-06-06 14:20:58.432520: 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 AVX512F AVX512_VNNI AVX512_BF16 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2025-06-06 14:20:59.658342: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
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 88ms/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 44ms/step
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.
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 34ms/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 0x764b2439d3a0> 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 41ms/step
WARNING:tensorflow:6 out of the last 6 calls to <function Model.make_predict_function.<locals>.predict_function at 0x764b242511c0> 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 37ms/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 34ms/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 61ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 57ms/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 50ms/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 63ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 81ms/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 51ms/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 72ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 59ms/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/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/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/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/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/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-21-openjdk-amd64/lib/server:/usr/local/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 0 | 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 0 | SKIP 1 | PASS 228 ]
Error: Test failures
Execution halted
9746: find library=libc.so.6 [0]; searching
9746: search path=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v4:/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-v4:/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/R/lib/glibc-hwcaps/x86-64-v4:/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib/glibc-hwcaps/x86-64-v4:/usr/local/lib/glibc-hwcaps/x86-64-v3:/usr/local/lib/glibc-hwcaps/x86-64-v2:/usr/local/lib (LD_LIBRARY_PATH)
9746: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9746: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9746: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9746: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/libc.so.6
9746: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9746: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9746: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9746: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/libc.so.6
9746: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9746: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9746: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9746: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/libc.so.6
9746: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9746: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9746: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9746: trying file=/usr/local/lib/libc.so.6
9746: search path=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v4:/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)
9746: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v4/libc.so.6
9746: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
9746: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
9746: trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
9746:
9746:
9746: calling init: /lib64/ld-linux-x86-64.so.2
9746:
9746:
9746: calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
9746:
9746:
9746: initialize program: sh
9746:
9746:
9746: transferring control: sh
9746:
9747: find library=libc.so.6 [0]; searching
9747: search path=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v4:/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-v4:/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/R/lib/glibc-hwcaps/x86-64-v4:/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v3:/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v2:/home/biocbuild/bbs-3.22-bioc/R/lib:/usr/local/lib/glibc-hwcaps/x86-64-v4:/usr/local/lib/glibc-hwcaps/x86-64-v3:/usr/local/lib/glibc-hwcaps/x86-64-v2:/usr/local/lib (LD_LIBRARY_PATH)
9747: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9747: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9747: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9747: trying file=/home/biocbuild/.cache/R/basilisk/1.21.5/orthos/1.7.2/orthos/lib/libc.so.6
9747: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9747: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9747: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9747: trying file=/home/biocbuild/.pyenv/versions/3.11.11/lib/libc.so.6
9747: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9747: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9747: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9747: trying file=/home/biocbuild/bbs-3.22-bioc/R/lib/libc.so.6
9747: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v4/libc.so.6
9747: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v3/libc.so.6
9747: trying file=/usr/local/lib/glibc-hwcaps/x86-64-v2/libc.so.6
9747: trying file=/usr/local/lib/libc.so.6
9747: search path=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v4:/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)
9747: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v4/libc.so.6
9747: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v3/libc.so.6
9747: trying file=/usr/lib/x86_64-linux-gnu/glibc-hwcaps/x86-64-v2/libc.so.6
9747: trying file=/usr/lib/x86_64-linux-gnu/libc.so.6
9747:
9747:
9747: calling init: /lib64/ld-linux-x86-64.so.2
9747:
9747:
9747: calling init: /usr/lib/x86_64-linux-gnu/libc.so.6
9747:
9747:
9747: initialize program: rm
9747:
9747:
9747: transferring control: rm
9747:
orthos.Rcheck/orthos-Ex.timings
| name | user | system | elapsed | |
| decomposeVar | 12.252 | 5.764 | 29.359 | |
| loadContrastDatabase | 2.974 | 0.275 | 8.642 | |
| plotQueryResultsManh | 24.475 | 10.179 | 32.346 | |
| plotQueryResultsViolin | 28.985 | 10.868 | 32.787 | |
| queryWithContrasts | 27.404 | 11.173 | 33.710 | |