Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:08:57 -0500 (Wed, 26 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: 2022-01-25 01:55:07 -0500 (Tue, 25 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: 2022-01-25 19:19:51 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 19:23:21 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 209.7 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 37.198  7.006  24.208
fit_model     35.835  5.269  25.462
text_token    19.744  2.581  11.813
token_vector  18.277  0.693  11.260
bi_gru         6.251  0.920   7.126
* 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")
2022-01-25 19:22:57.850926: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7fe2484d8670 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2022-01-25 19:22:57.850998: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): Host, Default Version

 1/45 [..............................] - ETA: 0s - loss: 1.8284 - pearson_correlation: 0.0510
 2/45 [>.............................] - ETA: 1s - loss: 1.7317 - pearson_correlation: 0.0875
 3/45 [=>............................] - ETA: 1s - loss: 1.7232 - pearson_correlation: 0.1343
 4/45 [=>............................] - ETA: 1s - loss: 1.7403 - pearson_correlation: 0.1589
 6/45 [===>..........................] - ETA: 1s - loss: 1.7360 - pearson_correlation: 0.1542
 8/45 [====>.........................] - ETA: 1s - loss: 1.6924 - pearson_correlation: 0.1899
10/45 [=====>........................] - ETA: 1s - loss: 1.7187 - pearson_correlation: 0.2134
12/45 [=======>......................] - ETA: 1s - loss: 1.6668 - pearson_correlation: 0.2242
14/45 [========>.....................] - ETA: 1s - loss: 1.6525 - pearson_correlation: 0.2462
16/45 [=========>....................] - ETA: 1s - loss: 1.6130 - pearson_correlation: 0.1941
18/45 [===========>..................] - ETA: 1s - loss: 1.5983 - pearson_correlation: 0.1984
20/45 [============>.................] - ETA: 1s - loss: 1.5934 - pearson_correlation: 0.1710
22/45 [=============>................] - ETA: 1s - loss: 1.5797 - pearson_correlation: 0.1717
24/45 [===============>..............] - ETA: 0s - loss: 1.5728 - pearson_correlation: 0.1902
26/45 [================>.............] - ETA: 0s - loss: 1.5601 - pearson_correlation: 0.1808
28/45 [=================>............] - ETA: 0s - loss: 1.5667 - pearson_correlation: 0.1794
30/45 [===================>..........] - ETA: 0s - loss: 1.5786 - pearson_correlation: 0.1857
32/45 [====================>.........] - ETA: 0s - loss: 1.5810 - pearson_correlation: 0.1864
34/45 [=====================>........] - ETA: 0s - loss: 1.5796 - pearson_correlation: 0.1706
36/45 [=======================>......] - ETA: 0s - loss: 1.5732 - pearson_correlation: 0.1658
38/45 [========================>.....] - ETA: 0s - loss: 1.5727 - pearson_correlation: 0.1589
40/45 [=========================>....] - ETA: 0s - loss: 1.5778 - pearson_correlation: 0.1679
42/45 [===========================>..] - ETA: 0s - loss: 1.5612 - pearson_correlation: 0.1642
44/45 [============================>.] - ETA: 0s - loss: 1.5603 - pearson_correlation: 0.1624
45/45 [==============================] - 2s 43ms/step - loss: 1.5598 - pearson_correlation: 0.1646
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 37.970   8.401  31.242 

Example timings

ttgsea.Rcheck/ttgsea-Ex.timings

nameusersystemelapsed
bi_gru6.2510.9207.126
bi_lstm0.3780.0080.383
fit_model35.835 5.26925.462
metric_pearson_correlation0.0760.0040.080
plot_model0.3730.0300.403
predict_model37.198 7.00624.208
sampling_generator0.0300.0000.031
text_token19.744 2.58111.813
token_vector18.277 0.69311.260