Dongmin Jung
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/ttgsea |
| git_branch: RELEASE_3_19 |
| git_last_commit: 15ca189 |
| git_last_commit_date: 2024-04-30 11:30:06 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:03:18 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 2220/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ttgsea 1.12.0 (landing page) Dongmin Jung
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the ttgsea package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ttgsea.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. |
| Package: ttgsea |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ttgsea_1.12.0.tar.gz |
| StartedAt: 2024-05-31 09:13:47 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 09:16:39 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 172.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ttgsea.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ttgsea_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ttgsea.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.12.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ttgsea’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fit_model 25.344 3.006 15.704
predict_model 23.799 2.555 13.775
token_vector 9.604 0.400 6.195
text_token 9.507 0.384 6.123
bi_gru 3.453 0.672 6.303
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
ttgsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ttgsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘ttgsea’ ... ** using staged installation ** R ** 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 (ttgsea)
ttgsea.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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.
> library(testthat)
> library(ttgsea)
Loading required package: keras
>
> test_check("ttgsea")
2024-05-31 09:15:41.630089: 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.
2024-05-31 09:15:41.850601: 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`.
2024-05-31 09:15:41.894129: 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
2024-05-31 09:15:42.768036: 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-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2024-05-31 09:15:42.768153: 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-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.19-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2024-05-31 09:15:42.768174: 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.
2024-05-31 09:15:44.607715: E tensorflow/stream_executor/cuda/cuda_driver.cc:265] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2024-05-31 09:15:44.607800: 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
2024-05-31 09:15:44.608183: 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.
1/45 [..............................] - ETA: 2:25 - loss: 1.3692 - pearson_correlation: -0.0698
3/45 [=>............................] - ETA: 1s - loss: 1.5624 - pearson_correlation: 0.0534
5/45 [==>...........................] - ETA: 1s - loss: 1.5480 - pearson_correlation: 0.0927
7/45 [===>..........................] - ETA: 1s - loss: 1.5587 - pearson_correlation: 0.0619
9/45 [=====>........................] - ETA: 1s - loss: 1.5649 - pearson_correlation: 0.0872
11/45 [======>.......................] - ETA: 1s - loss: 1.5646 - pearson_correlation: 0.0924
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17/45 [==========>...................] - ETA: 1s - loss: 1.5602 - pearson_correlation: 0.1102
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21/45 [=============>................] - ETA: 0s - loss: 1.5441 - pearson_correlation: 0.1250
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27/45 [=================>............] - ETA: 0s - loss: 1.5276 - pearson_correlation: 0.1299
29/45 [==================>...........] - ETA: 0s - loss: 1.5548 - pearson_correlation: 0.1339
31/45 [===================>..........] - ETA: 0s - loss: 1.5576 - pearson_correlation: 0.1422
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35/45 [======================>.......] - ETA: 0s - loss: 1.5547 - pearson_correlation: 0.1388
37/45 [=======================>......] - ETA: 0s - loss: 1.5498 - pearson_correlation: 0.1469
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41/45 [==========================>...] - ETA: 0s - loss: 1.5547 - pearson_correlation: 0.1529
43/45 [===========================>..] - ETA: 0s - loss: 1.5510 - pearson_correlation: 0.1479
45/45 [==============================] - ETA: 0s - loss: 1.5528 - pearson_correlation: 0.1538
45/45 [==============================] - 5s 38ms/step - loss: 1.5528 - pearson_correlation: 0.1538
1/4 [======>.......................] - ETA: 1s
4/4 [==============================] - 0s 9ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 25ms/step
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32/32 [==============================] - 0s 9ms/step
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
28.593 3.755 18.939
ttgsea.Rcheck/ttgsea-Ex.timings
| name | user | system | elapsed | |
| bi_gru | 3.453 | 0.672 | 6.303 | |
| bi_lstm | 0.217 | 0.004 | 0.221 | |
| fit_model | 25.344 | 3.006 | 15.704 | |
| metric_pearson_correlation | 0.01 | 0.00 | 0.01 | |
| plot_model | 0.183 | 0.012 | 0.189 | |
| predict_model | 23.799 | 2.555 | 13.775 | |
| sampling_generator | 0.000 | 0.000 | 0.001 | |
| text_token | 9.507 | 0.384 | 6.123 | |
| token_vector | 9.604 | 0.400 | 6.195 | |