Dongmin Jung
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/ttgsea |
| git_branch: RELEASE_3_18 |
| git_last_commit: d21c96b |
| git_last_commit_date: 2023-10-24 11:28:41 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:24 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 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 2190/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ttgsea 1.10.0 (landing page) Dongmin Jung
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ttgsea |
| Version: 1.10.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ttgsea_1.10.0.tar.gz |
| StartedAt: 2023-11-02 15:06:59 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 15:09:56 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 177.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ttgsea.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ttgsea_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ttgsea.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.10.0’
* 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 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
fit_model 24.181 1.139 20.816
predict_model 23.716 0.942 19.781
token_vector 9.591 0.459 6.385
text_token 9.466 0.505 6.283
bi_gru 5.876 0.743 10.521
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
ttgsea.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL ttgsea ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
1/45 [..............................] - ETA: 4:44 - loss: 1.6682 - pearson_correlation: 0.1830
4/45 [=>............................] - ETA: 1s - loss: 1.5772 - pearson_correlation: 0.1395
5/45 [==>...........................] - ETA: 1s - loss: 1.5415 - pearson_correlation: 0.0797
6/45 [===>..........................] - ETA: 1s - loss: 1.5734 - pearson_correlation: 0.0609
7/45 [===>..........................] - ETA: 1s - loss: 1.5670 - pearson_correlation: 0.0655
8/45 [====>.........................] - ETA: 1s - loss: 1.5883 - pearson_correlation: 0.0510
9/45 [=====>........................] - ETA: 1s - loss: 1.5932 - pearson_correlation: 0.0434
10/45 [=====>........................] - ETA: 1s - loss: 1.5665 - pearson_correlation: 0.0553
11/45 [======>.......................] - ETA: 1s - loss: 1.5513 - pearson_correlation: 0.0608
12/45 [=======>......................] - ETA: 1s - loss: 1.5762 - pearson_correlation: 0.1002
13/45 [=======>......................] - ETA: 1s - loss: 1.5665 - pearson_correlation: 0.0971
14/45 [========>.....................] - ETA: 1s - loss: 1.5642 - pearson_correlation: 0.0946
15/45 [=========>....................] - ETA: 1s - loss: 1.5834 - pearson_correlation: 0.0829
16/45 [=========>....................] - ETA: 1s - loss: 1.5656 - pearson_correlation: 0.0827
17/45 [==========>...................] - ETA: 1s - loss: 1.5529 - pearson_correlation: 0.0861
18/45 [===========>..................] - ETA: 1s - loss: 1.5466 - pearson_correlation: 0.0920
19/45 [===========>..................] - ETA: 1s - loss: 1.5425 - pearson_correlation: 0.0898
20/45 [============>.................] - ETA: 1s - loss: 1.5467 - pearson_correlation: 0.0926
21/45 [=============>................] - ETA: 1s - loss: 1.5344 - pearson_correlation: 0.1059
22/45 [=============>................] - ETA: 1s - loss: 1.5395 - pearson_correlation: 0.0924
23/45 [==============>...............] - ETA: 1s - loss: 1.5359 - pearson_correlation: 0.0981
24/45 [===============>..............] - ETA: 1s - loss: 1.5434 - pearson_correlation: 0.0882
25/45 [===============>..............] - ETA: 1s - loss: 1.5330 - pearson_correlation: 0.0941
26/45 [================>.............] - ETA: 1s - loss: 1.5241 - pearson_correlation: 0.0960
27/45 [=================>............] - ETA: 1s - loss: 1.5348 - pearson_correlation: 0.0982
28/45 [=================>............] - ETA: 1s - loss: 1.5329 - pearson_correlation: 0.1033
29/45 [==================>...........] - ETA: 1s - loss: 1.5513 - pearson_correlation: 0.1022
30/45 [===================>..........] - ETA: 0s - loss: 1.5581 - pearson_correlation: 0.0979
31/45 [===================>..........] - ETA: 0s - loss: 1.5601 - pearson_correlation: 0.0989
32/45 [====================>.........] - ETA: 0s - loss: 1.5672 - pearson_correlation: 0.0922
33/45 [=====================>........] - ETA: 0s - loss: 1.5672 - pearson_correlation: 0.0957
34/45 [=====================>........] - ETA: 0s - loss: 1.5695 - pearson_correlation: 0.0942
35/45 [======================>.......] - ETA: 0s - loss: 1.5688 - pearson_correlation: 0.0859
36/45 [=======================>......] - ETA: 0s - loss: 1.5671 - pearson_correlation: 0.0824
37/45 [=======================>......] - ETA: 0s - loss: 1.5679 - pearson_correlation: 0.0844
38/45 [========================>.....] - ETA: 0s - loss: 1.5598 - pearson_correlation: 0.0936
39/45 [=========================>....] - ETA: 0s - loss: 1.5523 - pearson_correlation: 0.0978
40/45 [=========================>....] - ETA: 0s - loss: 1.5519 - pearson_correlation: 0.0957
41/45 [==========================>...] - ETA: 0s - loss: 1.5542 - pearson_correlation: 0.0875
42/45 [===========================>..] - ETA: 0s - loss: 1.5622 - pearson_correlation: 0.0937
43/45 [===========================>..] - ETA: 0s - loss: 1.5604 - pearson_correlation: 0.0927
44/45 [============================>.] - ETA: 0s - loss: 1.5586 - pearson_correlation: 0.1016
45/45 [==============================] - ETA: 0s - loss: 1.5535 - pearson_correlation: 0.0980
45/45 [==============================] - 9s 65ms/step - loss: 1.5535 - pearson_correlation: 0.0980
1/4 [======>.......................] - ETA: 1s
4/4 [==============================] - 1s 9ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 34ms/step
1/32 [..............................] - ETA: 1s
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32/32 [==============================] - 0s 11ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 32ms/step
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32/32 [==============================] - 0s 13ms/step
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32/32 [==============================] - 0s 13ms/step
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
30.528 1.611 30.494
ttgsea.Rcheck/ttgsea-Ex.timings
| name | user | system | elapsed | |
| bi_gru | 5.876 | 0.743 | 10.521 | |
| bi_lstm | 0.395 | 0.012 | 0.407 | |
| fit_model | 24.181 | 1.139 | 20.816 | |
| metric_pearson_correlation | 0.016 | 0.000 | 0.016 | |
| plot_model | 0.321 | 0.012 | 0.343 | |
| predict_model | 23.716 | 0.942 | 19.781 | |
| sampling_generator | 0.001 | 0.000 | 0.000 | |
| text_token | 9.466 | 0.505 | 6.283 | |
| token_vector | 9.591 | 0.459 | 6.385 | |