Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:08:33 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

CHECK results for ttgsea on machv2


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.

raw results

Package 2014/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ttgsea 1.2.1  (landing page)
Dongmin Jung
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/ttgsea
git_branch: RELEASE_3_14
git_last_commit: bdfd91e
git_last_commit_date: 2021-12-14 18:58:49 -0500 (Tue, 14 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ttgsea
Version: 1.2.1
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_1.2.1.tar.gz
StartedAt: 2022-01-23 19:21:46 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 19:25:19 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 212.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ttgsea.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ttgsea.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.2.1’
* 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 38.041  7.347  24.837
fit_model     37.072  5.701  26.437
text_token    19.827  2.630  11.872
token_vector  18.271  0.730  11.328
bi_gru         6.257  0.916   7.106
* 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


Installation output

ttgsea.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ttgsea
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output

ttgsea.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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")
2022-01-23 19:24:55.758777: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7fe8d2c5ad50 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2022-01-23 19:24:55.758870: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): Host, Default Version

 1/45 [..............................] - ETA: 0s - loss: 2.3270 - pearson_correlation: 0.0800
 2/45 [>.............................] - ETA: 1s - loss: 2.0089 - pearson_correlation: 0.1391
 3/45 [=>............................] - ETA: 1s - loss: 1.9073 - pearson_correlation: 0.0538
 4/45 [=>............................] - ETA: 1s - loss: 1.7609 - pearson_correlation: 0.0792
 5/45 [==>...........................] - ETA: 1s - loss: 1.7287 - pearson_correlation: 0.0986
 6/45 [===>..........................] - ETA: 1s - loss: 1.6679 - pearson_correlation: 0.1183
 7/45 [===>..........................] - ETA: 1s - loss: 1.5996 - pearson_correlation: 0.1138
 8/45 [====>.........................] - ETA: 1s - loss: 1.6268 - pearson_correlation: 0.1526
10/45 [=====>........................] - ETA: 1s - loss: 1.5721 - pearson_correlation: 0.1294
11/45 [======>.......................] - ETA: 1s - loss: 1.5847 - pearson_correlation: 0.1446
13/45 [=======>......................] - ETA: 1s - loss: 1.5955 - pearson_correlation: 0.1509
15/45 [=========>....................] - ETA: 1s - loss: 1.5657 - pearson_correlation: 0.1743
17/45 [==========>...................] - ETA: 1s - loss: 1.5703 - pearson_correlation: 0.1921
19/45 [===========>..................] - ETA: 1s - loss: 1.5753 - pearson_correlation: 0.1690
21/45 [=============>................] - ETA: 1s - loss: 1.5688 - pearson_correlation: 0.1811
23/45 [==============>...............] - ETA: 1s - loss: 1.5700 - pearson_correlation: 0.1689
25/45 [===============>..............] - ETA: 0s - loss: 1.5802 - pearson_correlation: 0.1526
27/45 [=================>............] - ETA: 0s - loss: 1.5699 - pearson_correlation: 0.1547
29/45 [==================>...........] - ETA: 0s - loss: 1.5727 - pearson_correlation: 0.1545
31/45 [===================>..........] - ETA: 0s - loss: 1.5658 - pearson_correlation: 0.1580
33/45 [=====================>........] - ETA: 0s - loss: 1.5648 - pearson_correlation: 0.1627
35/45 [======================>.......] - ETA: 0s - loss: 1.5750 - pearson_correlation: 0.1573
37/45 [=======================>......] - ETA: 0s - loss: 1.5778 - pearson_correlation: 0.1646
39/45 [=========================>....] - ETA: 0s - loss: 1.5702 - pearson_correlation: 0.1543
41/45 [==========================>...] - ETA: 0s - loss: 1.5730 - pearson_correlation: 0.1470
43/45 [===========================>..] - ETA: 0s - loss: 1.5717 - pearson_correlation: 0.1526
44/45 [============================>.] - ETA: 0s - loss: 1.5689 - pearson_correlation: 0.1481
45/45 [==============================] - 2s 45ms/step - loss: 1.5690 - pearson_correlation: 0.1501
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 39.404   8.196  32.644 

Example timings

ttgsea.Rcheck/ttgsea-Ex.timings

nameusersystemelapsed
bi_gru6.2570.9167.106
bi_lstm0.4520.0080.484
fit_model37.072 5.70126.437
metric_pearson_correlation0.0780.0030.081
plot_model0.4190.0290.449
predict_model38.041 7.34724.837
sampling_generator0.0420.0010.042
text_token19.827 2.63011.872
token_vector18.271 0.73011.328