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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2207/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ttgsea 1.14.0  (landing page)
Dongmin Jung
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ttgsea
git_branch: RELEASE_3_20
git_last_commit: 1eda37a
git_last_commit_date: 2024-10-29 10:54:10 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ttgsea on merida1

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.

raw results


Summary

Package: ttgsea
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2024-12-20 11:07:16 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 11:12:15 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 298.6 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ttgsea.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.14.0’
* 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 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     39.468  3.630  32.011
predict_model 38.618  3.816  30.378
bi_gru        17.191  2.535  23.813
token_vector  15.835  1.110  12.270
text_token    15.661  0.936  12.146
* 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


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/4.4-x86_64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: 6:39 - loss: 1.5532 - pearson_correlation: 0.1869
 2/45 [>.............................] - ETA: 2s - loss: 1.5100 - pearson_correlation: 0.0766  
 4/45 [=>............................] - ETA: 1s - loss: 1.5660 - pearson_correlation: 0.0340
 6/45 [===>..........................] - ETA: 1s - loss: 1.4885 - pearson_correlation: 0.0714
 8/45 [====>.........................] - ETA: 1s - loss: 1.4920 - pearson_correlation: 0.1081
10/45 [=====>........................] - ETA: 1s - loss: 1.4859 - pearson_correlation: 0.1224
12/45 [=======>......................] - ETA: 1s - loss: 1.4919 - pearson_correlation: 0.0582
14/45 [========>.....................] - ETA: 1s - loss: 1.5029 - pearson_correlation: 0.0368
16/45 [=========>....................] - ETA: 1s - loss: 1.4922 - pearson_correlation: 0.0344
18/45 [===========>..................] - ETA: 1s - loss: 1.5106 - pearson_correlation: 0.0353
20/45 [============>.................] - ETA: 0s - loss: 1.5438 - pearson_correlation: 0.0491
22/45 [=============>................] - ETA: 0s - loss: 1.5371 - pearson_correlation: 0.0647
24/45 [===============>..............] - ETA: 0s - loss: 1.5381 - pearson_correlation: 0.0608
26/45 [================>.............] - ETA: 0s - loss: 1.5442 - pearson_correlation: 0.0614
28/45 [=================>............] - ETA: 0s - loss: 1.5495 - pearson_correlation: 0.0692
30/45 [===================>..........] - ETA: 0s - loss: 1.5531 - pearson_correlation: 0.0765
32/45 [====================>.........] - ETA: 0s - loss: 1.5621 - pearson_correlation: 0.0781
34/45 [=====================>........] - ETA: 0s - loss: 1.5648 - pearson_correlation: 0.0837
36/45 [=======================>......] - ETA: 0s - loss: 1.5508 - pearson_correlation: 0.0696
38/45 [========================>.....] - ETA: 0s - loss: 1.5568 - pearson_correlation: 0.0817
40/45 [=========================>....] - ETA: 0s - loss: 1.5541 - pearson_correlation: 0.0927
42/45 [===========================>..] - ETA: 0s - loss: 1.5644 - pearson_correlation: 0.0942
44/45 [============================>.] - ETA: 0s - loss: 1.5561 - pearson_correlation: 0.1019
45/45 [==============================] - 11s 34ms/step - loss: 1.5554 - pearson_correlation: 0.0994

1/4 [======>.......................] - ETA: 2s
4/4 [==============================] - 1s 10ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 49ms/step

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32/32 [==============================] - 0s 11ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 57ms/step

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 1/32 [..............................] - ETA: 1s
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 1/32 [..............................] - ETA: 2s
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32/32 [==============================] - 0s 12ms/step
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 55.941   6.728  51.889 

Example timings

ttgsea.Rcheck/ttgsea-Ex.timings

nameusersystemelapsed
bi_gru17.191 2.53523.813
bi_lstm0.5420.0320.589
fit_model39.468 3.63032.011
metric_pearson_correlation0.0230.0030.029
plot_model0.4390.0470.519
predict_model38.618 3.81630.378
sampling_generator0.0010.0000.001
text_token15.661 0.93612.146
token_vector15.835 1.11012.270