Dongmin Jung
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ttgsea |
| git_branch: RELEASE_3_13 |
| git_last_commit: 9a72aa9 |
| git_last_commit_date: 2021-05-19 12:58:36 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:57 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the ttgsea package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1973/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ttgsea 1.0.0 (landing page) Dongmin Jung
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ttgsea |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ttgsea_1.0.0.tar.gz |
| StartedAt: 2021-10-15 01:00:29 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:03:28 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 179.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ttgsea.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ttgsea_1.0.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ttgsea.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.0.0’
* 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 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
predict_model 32.942 9.001 20.517
fit_model 33.032 7.418 22.100
token_vector 12.815 0.839 6.842
text_token 12.566 0.515 6.481
bi_gru 6.163 0.981 7.290
* 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: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ttgsea ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
2021-10-15 01:03:05.743309: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7fd51e724c70 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2021-10-15 01:03:05.743363: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
1/45 [..............................] - ETA: 0s - loss: 1.8396 - pearson_correlation: -0.1671
2/45 [>.............................] - ETA: 1s - loss: 1.5448 - pearson_correlation: -0.0444
3/45 [=>............................] - ETA: 1s - loss: 1.6076 - pearson_correlation: -0.1222
4/45 [=>............................] - ETA: 2s - loss: 1.6501 - pearson_correlation: -0.0878
5/45 [==>...........................] - ETA: 2s - loss: 1.6323 - pearson_correlation: -0.0174
6/45 [===>..........................] - ETA: 2s - loss: 1.5794 - pearson_correlation: 0.0520
7/45 [===>..........................] - ETA: 2s - loss: 1.5982 - pearson_correlation: 0.0732
8/45 [====>.........................] - ETA: 2s - loss: 1.5932 - pearson_correlation: 0.1149
9/45 [=====>........................] - ETA: 2s - loss: 1.5561 - pearson_correlation: 0.0722
10/45 [=====>........................] - ETA: 2s - loss: 1.5732 - pearson_correlation: 0.0922
11/45 [======>.......................] - ETA: 2s - loss: 1.5657 - pearson_correlation: 0.0952
12/45 [=======>......................] - ETA: 2s - loss: 1.5964 - pearson_correlation: 0.1034
13/45 [=======>......................] - ETA: 2s - loss: 1.6039 - pearson_correlation: 0.0915
14/45 [========>.....................] - ETA: 1s - loss: 1.6102 - pearson_correlation: 0.1005
15/45 [=========>....................] - ETA: 1s - loss: 1.5897 - pearson_correlation: 0.0848
16/45 [=========>....................] - ETA: 1s - loss: 1.6002 - pearson_correlation: 0.0846
17/45 [==========>...................] - ETA: 1s - loss: 1.6058 - pearson_correlation: 0.0938
18/45 [===========>..................] - ETA: 1s - loss: 1.6050 - pearson_correlation: 0.0935
19/45 [===========>..................] - ETA: 1s - loss: 1.6041 - pearson_correlation: 0.1032
20/45 [============>.................] - ETA: 1s - loss: 1.6055 - pearson_correlation: 0.0859
21/45 [=============>................] - ETA: 1s - loss: 1.6102 - pearson_correlation: 0.0828
22/45 [=============>................] - ETA: 1s - loss: 1.6201 - pearson_correlation: 0.0882
23/45 [==============>...............] - ETA: 1s - loss: 1.6116 - pearson_correlation: 0.0929
24/45 [===============>..............] - ETA: 1s - loss: 1.6003 - pearson_correlation: 0.1043
25/45 [===============>..............] - ETA: 1s - loss: 1.6165 - pearson_correlation: 0.1121
26/45 [================>.............] - ETA: 1s - loss: 1.6135 - pearson_correlation: 0.1045
27/45 [=================>............] - ETA: 1s - loss: 1.6121 - pearson_correlation: 0.1108
28/45 [=================>............] - ETA: 1s - loss: 1.6053 - pearson_correlation: 0.1222
29/45 [==================>...........] - ETA: 1s - loss: 1.6041 - pearson_correlation: 0.1309
30/45 [===================>..........] - ETA: 0s - loss: 1.6027 - pearson_correlation: 0.1337
31/45 [===================>..........] - ETA: 0s - loss: 1.5960 - pearson_correlation: 0.1281
32/45 [====================>.........] - ETA: 0s - loss: 1.5910 - pearson_correlation: 0.1248
33/45 [=====================>........] - ETA: 0s - loss: 1.5899 - pearson_correlation: 0.1145
34/45 [=====================>........] - ETA: 0s - loss: 1.5907 - pearson_correlation: 0.1138
35/45 [======================>.......] - ETA: 0s - loss: 1.5923 - pearson_correlation: 0.1099
36/45 [=======================>......] - ETA: 0s - loss: 1.5879 - pearson_correlation: 0.1117
37/45 [=======================>......] - ETA: 0s - loss: 1.5870 - pearson_correlation: 0.1096
38/45 [========================>.....] - ETA: 0s - loss: 1.5922 - pearson_correlation: 0.1117
39/45 [=========================>....] - ETA: 0s - loss: 1.5953 - pearson_correlation: 0.1123
40/45 [=========================>....] - ETA: 0s - loss: 1.5929 - pearson_correlation: 0.1092
42/45 [===========================>..] - ETA: 0s - loss: 1.5791 - pearson_correlation: 0.1064
43/45 [===========================>..] - ETA: 0s - loss: 1.5760 - pearson_correlation: 0.1087
45/45 [==============================] - ETA: 0s - loss: 1.5683 - pearson_correlation: 0.1209
45/45 [==============================] - 3s 62ms/step - loss: 1.5683 - pearson_correlation: 0.1209
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
37.898 12.182 29.498
ttgsea.Rcheck/ttgsea-Ex.timings
| name | user | system | elapsed | |
| bi_gru | 6.163 | 0.981 | 7.290 | |
| bi_lstm | 0.469 | 0.016 | 0.483 | |
| fit_model | 33.032 | 7.418 | 22.100 | |
| metric_pearson_correlation | 0.036 | 0.001 | 0.038 | |
| plot_model | 0.343 | 0.031 | 0.372 | |
| predict_model | 32.942 | 9.001 | 20.517 | |
| sampling_generator | 0.026 | 0.001 | 0.026 | |
| text_token | 12.566 | 0.515 | 6.481 | |
| token_vector | 12.815 | 0.839 | 6.842 | |