Dongmin Jung
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ttgsea |
| git_branch: RELEASE_3_21 |
| git_last_commit: f73271e |
| git_last_commit_date: 2025-04-15 12:16:26 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 2254/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ttgsea 1.16.0 (landing page) Dongmin Jung
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2025-10-14 11:59:35 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 12:04:25 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 290.0 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ttgsea.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.16.0’
* 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 40.339 3.306 32.554
predict_model 38.547 3.500 29.423
bi_gru 16.685 2.416 21.070
token_vector 15.730 1.012 11.886
text_token 15.601 0.872 11.314
* 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/4.5-x86_64/Resources/library’ * installing *source* package ‘ttgsea’ ... ** this is package ‘ttgsea’ version ‘1.16.0’ ** 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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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
The keras package is deprecated. Use the keras3 package instead.
>
> test_check("ttgsea")
1/45 [..............................] - ETA: 7:20 - loss: 1.6096 - pearson_correlation: -0.1446
2/45 [>.............................] - ETA: 3s - loss: 1.6030 - pearson_correlation: 0.0368
3/45 [=>............................] - ETA: 2s - loss: 1.5283 - pearson_correlation: 0.0768
5/45 [==>...........................] - ETA: 2s - loss: 1.5894 - pearson_correlation: 0.1335
7/45 [===>..........................] - ETA: 1s - loss: 1.5899 - pearson_correlation: 0.0786
9/45 [=====>........................] - ETA: 1s - loss: 1.5783 - pearson_correlation: 0.0614
11/45 [======>.......................] - ETA: 1s - loss: 1.6293 - pearson_correlation: 0.0978
13/45 [=======>......................] - ETA: 1s - loss: 1.6268 - pearson_correlation: 0.1090
15/45 [=========>....................] - ETA: 1s - loss: 1.6080 - pearson_correlation: 0.1111
17/45 [==========>...................] - ETA: 1s - loss: 1.5746 - pearson_correlation: 0.0985
19/45 [===========>..................] - ETA: 0s - loss: 1.5721 - pearson_correlation: 0.0962
21/45 [=============>................] - ETA: 0s - loss: 1.5613 - pearson_correlation: 0.0891
23/45 [==============>...............] - ETA: 0s - loss: 1.5523 - pearson_correlation: 0.1020
25/45 [===============>..............] - ETA: 0s - loss: 1.5339 - pearson_correlation: 0.1226
27/45 [=================>............] - ETA: 0s - loss: 1.5266 - pearson_correlation: 0.1110
29/45 [==================>...........] - ETA: 0s - loss: 1.5229 - pearson_correlation: 0.1077
31/45 [===================>..........] - ETA: 0s - loss: 1.5378 - pearson_correlation: 0.1109
33/45 [=====================>........] - ETA: 0s - loss: 1.5509 - pearson_correlation: 0.1204
35/45 [======================>.......] - ETA: 0s - loss: 1.5567 - pearson_correlation: 0.1215
37/45 [=======================>......] - ETA: 0s - loss: 1.5526 - pearson_correlation: 0.1270
39/45 [=========================>....] - ETA: 0s - loss: 1.5467 - pearson_correlation: 0.1289
41/45 [==========================>...] - ETA: 0s - loss: 1.5451 - pearson_correlation: 0.1343
43/45 [===========================>..] - ETA: 0s - loss: 1.5524 - pearson_correlation: 0.1348
45/45 [==============================] - ETA: 0s - loss: 1.5638 - pearson_correlation: 0.1341
45/45 [==============================] - 11s 34ms/step - loss: 1.5638 - pearson_correlation: 0.1341
1/4 [======>.......................] - ETA: 3s
4/4 [==============================] - 1s 12ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 46ms/step
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1/1 [==============================] - 0s 52ms/step
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32/32 [==============================] - 0s 12ms/step
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
56.984 7.115 54.850
ttgsea.Rcheck/ttgsea-Ex.timings
| name | user | system | elapsed | |
| bi_gru | 16.685 | 2.416 | 21.070 | |
| bi_lstm | 0.569 | 0.030 | 0.610 | |
| fit_model | 40.339 | 3.306 | 32.554 | |
| metric_pearson_correlation | 0.021 | 0.002 | 0.025 | |
| plot_model | 0.444 | 0.048 | 0.530 | |
| predict_model | 38.547 | 3.500 | 29.423 | |
| sampling_generator | 0.001 | 0.000 | 0.002 | |
| text_token | 15.601 | 0.872 | 11.314 | |
| token_vector | 15.730 | 1.012 | 11.886 | |