| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:25 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 809/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenProSeq 1.3.0 (landing page) Dongmin Jung
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| Package: GenProSeq |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenProSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenProSeq_1.3.0.tar.gz |
| StartedAt: 2023-04-11 20:34:12 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 20:38:10 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 238.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenProSeq.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenProSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenProSeq_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenProSeq.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GenProSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenProSeq’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenProSeq’ can be installed ... OK
* 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 R 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 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 ... NOTE
fit_VAE: no visible binding for global variable ‘z_mean’
fit_VAE: no visible binding for global variable ‘z_log_stddev’
fit_VAE : vae_loss: no visible binding for global variable
‘z_log_stddev’
fit_VAE : vae_loss: no visible binding for global variable ‘z_mean’
layer_embedding_token_position : <anonymous>: no visible global
function definition for ‘super’
layer_embedding_token_position : <anonymous>: no visible binding for
global variable ‘self’
layer_transformer_encoder : <anonymous>: no visible global function
definition for ‘super’
layer_transformer_encoder : <anonymous>: no visible binding for global
variable ‘self’
Undefined global functions or variables:
self super z_log_stddev z_mean
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ART 54.332 5.599 54.343
VAE 41.335 11.259 42.706
GAN 17.201 1.736 15.143
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘GenProSeq.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘GenProSeq.Rmd’ using rmarkdown
2023-04-11 20:37:31.497018: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-04-11 20:37:31.729877: I tensorflow/core/util/util.cc:169] 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`.
2023-04-11 20:37:31.736467: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-04-11 20:37:31.736531: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
2023-04-11 20:37:31.768716: E tensorflow/stream_executor/cuda/cuda_blas.cc:2981] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2023-04-11 20:37:32.673276: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-04-11 20:37:32.673428: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-04-11 20:37:32.673450: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
2023-04-11 20:37:35.981069: E tensorflow/stream_executor/cuda/cuda_driver.cc:265] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2023-04-11 20:37:35.981150: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (nebbiolo1): /proc/driver/nvidia/version does not exist
2023-04-11 20:37:35.981638: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 3ms/step
1/5 [=====>........................] - ETA: 5s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 2s 133ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 137ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 141ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 1s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 138ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 2ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 185ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 207ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 3ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 229ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 156ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 133ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 1s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 135ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 2ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 149ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 210ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 150ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 3ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 235ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 152ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 3ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 153ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 129ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 137ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 1s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 3ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 201ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
1/5 [=====>........................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
2/5 [===========>..................] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
3/5 [=================>............] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
4/5 [=======================>......] - ETA: 0s
1/2 [==============>...............] - ETA: 0s
2/2 [==============================] - 0s 2ms/step
5/5 [==============================] - 1s 218ms/step
1/11 [=>............................] - ETA: 0s
11/11 [==============================] - 0s 1ms/step
1/4 [======>.......................] - ETA: 0s
4/4 [==============================] - 0s 2ms/step
Quitting from lines 102-107 (GenProSeq.Rmd)
Error: processing vignette 'GenProSeq.Rmd' failed with diagnostics:
there is no package called 'ggseqlogo'
--- failed re-building ‘GenProSeq.Rmd’
SUMMARY: processing the following file failed:
‘GenProSeq.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/GenProSeq.Rcheck/00check.log’
for details.
GenProSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenProSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘GenProSeq’ ... ** using staged installation ** R ** data ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenProSeq)
GenProSeq.Rcheck/tests/testthat.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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.
> library(testthat)
> library(GenProSeq)
Loading required package: keras
Loading required package: mclust
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
>
> test_check("GenProSeq")
2023-04-11 20:37:24.433535: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-04-11 20:37:24.700214: I tensorflow/core/util/util.cc:169] 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`.
2023-04-11 20:37:24.707471: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-04-11 20:37:24.707563: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
2023-04-11 20:37:24.741741: E tensorflow/stream_executor/cuda/cuda_blas.cc:2981] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2023-04-11 20:37:25.654216: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-04-11 20:37:25.654330: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-04-11 20:37:25.654351: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 26 ]
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 26 ]
>
> proc.time()
user system elapsed
6.593 0.608 7.096
GenProSeq.Rcheck/GenProSeq-Ex.timings
| name | user | system | elapsed | |
| ART | 54.332 | 5.599 | 54.343 | |
| GAN | 17.201 | 1.736 | 15.143 | |
| VAE | 41.335 | 11.259 | 42.706 | |
| prot_seq_check | 0.013 | 0.000 | 0.014 | |
| prot_vec | 0.332 | 0.004 | 0.337 | |
| transformer | 1.056 | 0.026 | 1.082 | |