Multiple platform build/check report for BioC 3.19 - BUILD results for GenProSeq on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4747
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4489
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4518
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4467
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*

BUILD results for GenProSeq on palomino7

To the developers/maintainers of the GenProSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenProSeq.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: GenProSeq

Version: 1.8.0

Command: chmod a+r GenProSeq -R && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data GenProSeq

StartedAt: 2024-07-21 19:33:35 -0400 (Sun, 21 Jul 2024)

EndedAt: 2024-07-21 19:35:37 -0400 (Sun, 21 Jul 2024)

EllapsedTime: 122.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   chmod a+r GenProSeq -R && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data GenProSeq
###
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* checking for file 'GenProSeq/DESCRIPTION' ... OK
* preparing 'GenProSeq':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'GenProSeq.Rmd' using rmarkdown
2024-07-21 19:34:13.880928: 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`.
2024-07-21 19:34:28.980537: 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`.
2024-07-21 19:35:36.504122: 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 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
C:\PYTHON~1\Lib\site-packages\keras\src\layers\reshaping\flatten.py:37: UserWarning: Do not pass an `input_shape`/`input_dim` argument to a layer. When using Sequential models, prefer using an `Input(shape)` object as the first layer in the model instead.
  super().__init__(**kwargs)

Quitting from lines 55-81 [unnamed-chunk-1] (GenProSeq.Rmd)
Error: processing vignette 'GenProSeq.Rmd' failed with diagnostics:
object 'combined' not found
--- failed re-building 'GenProSeq.Rmd'

SUMMARY: processing the following file failed:
  'GenProSeq.Rmd'

Error: Vignette re-building failed.
Execution halted