Dongmin Jung
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/ttgsea |
| git_branch: devel |
| git_last_commit: 23e12ac |
| git_last_commit_date: 2024-04-30 11:30:06 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 2158/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ttgsea 1.13.0 (landing page) Dongmin Jung
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ttgsea_1.13.0.tar.gz |
| StartedAt: 2024-06-10 11:32:02 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 11:37:16 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 313.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ttgsea.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ttgsea_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ttgsea.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.13.0’
* 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 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 39.748 3.607 31.271
predict_model 38.759 3.694 30.347
bi_gru 16.956 2.911 24.672
token_vector 15.494 0.978 11.794
text_token 15.454 0.814 11.291
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
ttgsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ttgsea ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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")
1/45 [..............................] - ETA: 7:48 - loss: 1.4907 - pearson_correlation: -0.2977
2/45 [>.............................] - ETA: 2s - loss: 1.5717 - pearson_correlation: -0.2999
4/45 [=>............................] - ETA: 1s - loss: 1.5730 - pearson_correlation: -0.2838
6/45 [===>..........................] - ETA: 1s - loss: 1.6171 - pearson_correlation: -0.2281
8/45 [====>.........................] - ETA: 1s - loss: 1.5538 - pearson_correlation: -0.1853
10/45 [=====>........................] - ETA: 1s - loss: 1.5789 - pearson_correlation: -0.1222
12/45 [=======>......................] - ETA: 1s - loss: 1.5526 - pearson_correlation: -0.0995
14/45 [========>.....................] - ETA: 1s - loss: 1.5569 - pearson_correlation: -0.0755
16/45 [=========>....................] - ETA: 1s - loss: 1.5407 - pearson_correlation: -0.0719
18/45 [===========>..................] - ETA: 0s - loss: 1.5689 - pearson_correlation: -0.0646
20/45 [============>.................] - ETA: 0s - loss: 1.5736 - pearson_correlation: -0.0480
22/45 [=============>................] - ETA: 0s - loss: 1.5729 - pearson_correlation: -0.0452
24/45 [===============>..............] - ETA: 0s - loss: 1.5827 - pearson_correlation: -0.0397
26/45 [================>.............] - ETA: 0s - loss: 1.5751 - pearson_correlation: -0.0429
28/45 [=================>............] - ETA: 0s - loss: 1.5907 - pearson_correlation: -0.0329
30/45 [===================>..........] - ETA: 0s - loss: 1.5863 - pearson_correlation: -0.0132
32/45 [====================>.........] - ETA: 0s - loss: 1.5768 - pearson_correlation: -0.0156
34/45 [=====================>........] - ETA: 0s - loss: 1.5660 - pearson_correlation: -0.0146
36/45 [=======================>......] - ETA: 0s - loss: 1.5555 - pearson_correlation: -0.0059
38/45 [========================>.....] - ETA: 0s - loss: 1.5691 - pearson_correlation: -1.2729e-04
40/45 [=========================>....] - ETA: 0s - loss: 1.5692 - pearson_correlation: 0.0044
42/45 [===========================>..] - ETA: 0s - loss: 1.5649 - pearson_correlation: 0.0094
44/45 [============================>.] - ETA: 0s - loss: 1.5605 - pearson_correlation: 0.0225
45/45 [==============================] - 12s 35ms/step - loss: 1.5643 - pearson_correlation: 0.0247
1/4 [======>.......................] - ETA: 3s
4/4 [==============================] - 1s 10ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 52ms/step
1/32 [..............................] - ETA: 1s
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1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 52ms/step
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32/32 [==============================] - 0s 10ms/step
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
56.506 6.976 57.296
ttgsea.Rcheck/ttgsea-Ex.timings
| name | user | system | elapsed | |
| bi_gru | 16.956 | 2.911 | 24.672 | |
| bi_lstm | 0.557 | 0.029 | 0.585 | |
| fit_model | 39.748 | 3.607 | 31.271 | |
| metric_pearson_correlation | 0.022 | 0.002 | 0.025 | |
| plot_model | 0.448 | 0.048 | 0.524 | |
| predict_model | 38.759 | 3.694 | 30.347 | |
| sampling_generator | 0.000 | 0.000 | 0.002 | |
| text_token | 15.454 | 0.814 | 11.291 | |
| token_vector | 15.494 | 0.978 | 11.794 | |