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 15:41 -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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ttgsea.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ttgsea_1.13.0.tar.gz |
| StartedAt: 2024-06-10 11:42:56 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 11:52:53 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 597.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ttgsea.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ttgsea.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ttgsea_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ttgsea.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 17.39 3.09 59.80
predict_model 16.34 1.08 56.13
bi_gru 4.90 3.22 43.94
text_token 2.30 0.18 47.78
token_vector 2.03 0.29 47.97
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ttgsea ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2024-06-10 11:52:23.621366: 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: SSE SSE2 SSE3 SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
1/45 [..............................] - ETA: 3:03 - loss: 1.4805 - pearson_correlation: 0.0063
4/45 [=>............................] - ETA: 0s - loss: 1.6423 - pearson_correlation: 0.0056
8/45 [====>.........................] - ETA: 0s - loss: 1.6390 - pearson_correlation: 0.0600
11/45 [======>.......................] - ETA: 0s - loss: 1.6239 - pearson_correlation: 0.0875
14/45 [========>.....................] - ETA: 0s - loss: 1.6159 - pearson_correlation: 0.0979
17/45 [==========>...................] - ETA: 0s - loss: 1.5763 - pearson_correlation: 0.1125
20/45 [============>.................] - ETA: 0s - loss: 1.6020 - pearson_correlation: 0.1166
22/45 [=============>................] - ETA: 0s - loss: 1.5912 - pearson_correlation: 0.1250
25/45 [===============>..............] - ETA: 0s - loss: 1.6128 - pearson_correlation: 0.1415
28/45 [=================>............] - ETA: 0s - loss: 1.6060 - pearson_correlation: 0.1279
30/45 [===================>..........] - ETA: 0s - loss: 1.6039 - pearson_correlation: 0.1345
33/45 [=====================>........] - ETA: 0s - loss: 1.5855 - pearson_correlation: 0.1348
36/45 [=======================>......] - ETA: 0s - loss: 1.5830 - pearson_correlation: 0.1365
39/45 [=========================>....] - ETA: 0s - loss: 1.5677 - pearson_correlation: 0.1473
42/45 [===========================>..] - ETA: 0s - loss: 1.5643 - pearson_correlation: 0.1606
44/45 [============================>.] - ETA: 0s - loss: 1.5619 - pearson_correlation: 0.1550
45/45 [==============================] - 5s 25ms/step - loss: 1.5613 - pearson_correlation: 0.1598
1/4 [======>.......................] - ETA: 1s
4/4 [==============================] - 0s 5ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 31ms/step
1/32 [..............................] - ETA: 0s
11/32 [=========>....................] - ETA: 0s
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32/32 [==============================] - ETA: 0s
32/32 [==============================] - 0s 6ms/step
1/32 [..............................] - ETA: 0s
11/32 [=========>....................] - ETA: 0s
22/32 [===================>..........] - ETA: 0s
32/32 [==============================] - 0s 6ms/step
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 36ms/step
1/32 [..............................] - ETA: 0s
11/32 [=========>....................] - ETA: 0s
22/32 [===================>..........] - ETA: 0s
32/32 [==============================] - 0s 6ms/step
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32/32 [==============================] - 0s 7ms/step
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30/32 [===========================>..] - ETA: 0s
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22/32 [===================>..........] - ETA: 0s
32/32 [==============================] - 0s 6ms/step
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
28.17 13.81 60.56
ttgsea.Rcheck/ttgsea-Ex.timings
| name | user | system | elapsed | |
| bi_gru | 4.90 | 3.22 | 43.94 | |
| bi_lstm | 0.22 | 0.00 | 0.22 | |
| fit_model | 17.39 | 3.09 | 59.80 | |
| metric_pearson_correlation | 0.01 | 0.00 | 0.03 | |
| plot_model | 0.46 | 0.13 | 1.14 | |
| predict_model | 16.34 | 1.08 | 56.13 | |
| sampling_generator | 0 | 0 | 0 | |
| text_token | 2.30 | 0.18 | 47.78 | |
| token_vector | 2.03 | 0.29 | 47.97 | |