Dongmin Jung
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/ttgsea |
| git_branch: RELEASE_3_16 |
| git_last_commit: 5b3d6a6 |
| git_last_commit_date: 2022-11-11 07:10:28 -0400 (Fri, 11 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:22 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 ttgsea package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2107/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ttgsea 1.6.3 (landing page) Dongmin Jung
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ttgsea |
| Version: 1.6.3 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ttgsea_1.6.3.tar.gz |
| StartedAt: 2023-04-11 00:42:14 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 00:44:53 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 159.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ttgsea.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings ttgsea_1.6.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/ttgsea.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.6.3’
* 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 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 ... 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
predict_model 23.704 3.235 12.911
fit_model 22.659 2.722 13.382
text_token 11.106 0.746 6.532
token_vector 10.815 0.800 6.431
* 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 ...
‘ttgsea.Rmd’ using ‘UTF-8’... OK
NONE
* 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-3.16-bioc/R/bin/R CMD INSTALL ttgsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
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(ttgsea)
Loading required package: keras
>
> test_check("ttgsea")
2023-04-11 00:44:05.984359: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] 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-3.16-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.16-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.16-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.16-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.16-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-04-11 00:44:05.984411: 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 00:44:08.688770: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
2023-04-11 00:44:08.689961: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
2023-04-11 00:44:08.731841: E tensorflow/stream_executor/cuda/cuda_driver.cc:328] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2023-04-11 00:44:08.731880: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (nebbiolo2): /proc/driver/nvidia/version does not exist
2023-04-11 00:44:08.732305: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-04-11 00:44:08.735166: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
2023-04-11 00:44:09.069447: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
2023-04-11 00:44:09.070365: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2200000000 Hz
1/45 [..............................] - ETA: 2:10 - loss: 1.6961 - pearson_correlation: 0.2385
3/45 [=>............................] - ETA: 1s - loss: 1.5880 - pearson_correlation: 0.0935
6/45 [===>..........................] - ETA: 1s - loss: 1.5648 - pearson_correlation: 0.0482
9/45 [=====>........................] - ETA: 0s - loss: 1.5697 - pearson_correlation: 0.0330
11/45 [======>.......................] - ETA: 0s - loss: 1.5688 - pearson_correlation: 0.0356
13/45 [=======>......................] - ETA: 0s - loss: 1.5714 - pearson_correlation: 0.0375
16/45 [=========>....................] - ETA: 0s - loss: 1.5787 - pearson_correlation: 0.0375
18/45 [===========>..................] - ETA: 0s - loss: 1.5824 - pearson_correlation: 0.0398
20/45 [============>.................] - ETA: 0s - loss: 1.5859 - pearson_correlation: 0.0408
22/45 [=============>................] - ETA: 0s - loss: 1.5881 - pearson_correlation: 0.0421
24/45 [===============>..............] - ETA: 0s - loss: 1.5886 - pearson_correlation: 0.0429
26/45 [================>.............] - ETA: 0s - loss: 1.5886 - pearson_correlation: 0.0444
28/45 [=================>............] - ETA: 0s - loss: 1.5880 - pearson_correlation: 0.0456
30/45 [===================>..........] - ETA: 0s - loss: 1.5869 - pearson_correlation: 0.0469
32/45 [====================>.........] - ETA: 0s - loss: 1.5863 - pearson_correlation: 0.0474
34/45 [=====================>........] - ETA: 0s - loss: 1.5857 - pearson_correlation: 0.0481
37/45 [=======================>......] - ETA: 0s - loss: 1.5849 - pearson_correlation: 0.0492
40/45 [=========================>....] - ETA: 0s - loss: 1.5832 - pearson_correlation: 0.0506
43/45 [===========================>..] - ETA: 0s - loss: 1.5820 - pearson_correlation: 0.0518
45/45 [==============================] - 4s 26ms/step - loss: 1.5806 - pearson_correlation: 0.0535
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
22.870 3.958 16.739
ttgsea.Rcheck/ttgsea-Ex.timings
| name | user | system | elapsed | |
| bi_gru | 2.833 | 0.641 | 3.142 | |
| bi_lstm | 0.209 | 0.004 | 0.213 | |
| fit_model | 22.659 | 2.722 | 13.382 | |
| metric_pearson_correlation | 0.018 | 0.000 | 0.019 | |
| plot_model | 0.180 | 0.000 | 0.173 | |
| predict_model | 23.704 | 3.235 | 12.911 | |
| sampling_generator | 0.01 | 0.00 | 0.01 | |
| text_token | 11.106 | 0.746 | 6.532 | |
| token_vector | 10.815 | 0.800 | 6.431 | |