Dongmin Jung
| Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 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 2024-05-30 11:36:00 -0400 (Thu, 30 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 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: /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_1.12.0.tar.gz |
| StartedAt: 2024-05-30 00:25:40 -0400 (Thu, 30 May 2024) |
| EndedAt: 2024-05-30 00:28:34 -0400 (Thu, 30 May 2024) |
| EllapsedTime: 173.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ttgsea.Rcheck |
| Warnings: 0 |
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###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ttgsea.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.12.0’
* 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 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 23.356 5.611 17.218
predict_model 22.279 6.209 15.108
bi_gru 10.243 2.130 14.123
token_vector 9.470 0.712 6.399
text_token 9.252 0.627 6.146
* 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 (2024-04-24) -- "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")
2024-05-30 00:28:08.901906: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
/Library/Python/3.9/site-packages/urllib3/__init__.py:34: NotOpenSSLWarning: urllib3 v2 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'LibreSSL 2.8.3'. See: https://github.com/urllib3/urllib3/issues/3020
warnings.warn(
1/45 [..............................] - ETA: 2:58 - loss: 1.6066 - pearson_correlation: -0.3365
3/45 [=>............................] - ETA: 1s - loss: 1.6163 - pearson_correlation: -0.0969
5/45 [==>...........................] - ETA: 1s - loss: 1.5967 - pearson_correlation: -0.0084
7/45 [===>..........................] - ETA: 1s - loss: 1.6292 - pearson_correlation: 0.0445
9/45 [=====>........................] - ETA: 1s - loss: 1.5914 - pearson_correlation: 0.0309
12/45 [=======>......................] - ETA: 0s - loss: 1.6117 - pearson_correlation: 0.0480
14/45 [========>.....................] - ETA: 0s - loss: 1.6074 - pearson_correlation: 0.0423
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18/45 [===========>..................] - ETA: 0s - loss: 1.5816 - pearson_correlation: 0.0717
20/45 [============>.................] - ETA: 0s - loss: 1.5955 - pearson_correlation: 0.0734
22/45 [=============>................] - ETA: 0s - loss: 1.5691 - pearson_correlation: 0.0837
24/45 [===============>..............] - ETA: 0s - loss: 1.5657 - pearson_correlation: 0.0840
26/45 [================>.............] - ETA: 0s - loss: 1.5769 - pearson_correlation: 0.1065
28/45 [=================>............] - ETA: 0s - loss: 1.5606 - pearson_correlation: 0.1074
31/45 [===================>..........] - ETA: 0s - loss: 1.5489 - pearson_correlation: 0.1081
33/45 [=====================>........] - ETA: 0s - loss: 1.5470 - pearson_correlation: 0.1117
35/45 [======================>.......] - ETA: 0s - loss: 1.5466 - pearson_correlation: 0.1111
37/45 [=======================>......] - ETA: 0s - loss: 1.5614 - pearson_correlation: 0.1127
39/45 [=========================>....] - ETA: 0s - loss: 1.5692 - pearson_correlation: 0.1195
41/45 [==========================>...] - ETA: 0s - loss: 1.5643 - pearson_correlation: 0.1228
44/45 [============================>.] - ETA: 0s - loss: 1.5631 - pearson_correlation: 0.1237
45/45 [==============================] - 5s 29ms/step - loss: 1.5608 - pearson_correlation: 0.1257
1/4 [======>.......................] - ETA: 1s
4/4 [==============================] - 1s 9ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 25ms/step
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32/32 [==============================] - 0s 8ms/step
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
32.450 11.283 28.707
ttgsea.Rcheck/ttgsea-Ex.timings
| name | user | system | elapsed | |
| bi_gru | 10.243 | 2.130 | 14.123 | |
| bi_lstm | 0.297 | 0.026 | 0.322 | |
| fit_model | 23.356 | 5.611 | 17.218 | |
| metric_pearson_correlation | 0.020 | 0.002 | 0.022 | |
| plot_model | 0.256 | 0.043 | 0.293 | |
| predict_model | 22.279 | 6.209 | 15.108 | |
| sampling_generator | 0.000 | 0.000 | 0.001 | |
| text_token | 9.252 | 0.627 | 6.146 | |
| token_vector | 9.470 | 0.712 | 6.399 | |