Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:07:10 -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 tokay2


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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ttgsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ttgsea_1.2.1.tar.gz
StartedAt: 2022-01-24 03:59:08 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 04:03:23 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 255.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ttgsea.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ttgsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ttgsea_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ttgsea.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
text_token 3.78   0.27   19.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
predict_model 27.49   1.08   26.08
fit_model     24.56   0.77   28.25
bi_gru         3.66   0.76    5.10
text_token     2.82   0.14   17.97
token_vector   2.70   0.06   17.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ttgsea_1.2.1.tar.gz && rm -rf ttgsea.buildbin-libdir && mkdir ttgsea.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ttgsea.buildbin-libdir ttgsea_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ttgsea_1.2.1.zip && rm ttgsea_1.2.1.tar.gz ttgsea_1.2.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  140k  100  140k    0     0   748k      0 --:--:-- --:--:-- --:--:--  753k

install for i386

* installing *source* package 'ttgsea' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ttgsea'
    finding HTML links ... done
    bi_gru                                  html  
    bi_lstm                                 html  
    fit_model                               html  
    metric_pearson_correlation              html  
    plot_model                              html  
    predict_model                           html  
    sampling_generator                      html  
    text_token                              html  
    token_vector                            html  
** 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

install for x64

* installing *source* package 'ttgsea' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ttgsea' as ttgsea_1.2.1.zip
* DONE (ttgsea)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ttgsea' successfully unpacked and MD5 sums checked

Tests output

ttgsea.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
[ FAIL 0 | WARN 0 | SKIP 13 | PASS 0 ]

== Skipped tests ===============================================================
* Python is not available on this system (13)

[ FAIL 0 | WARN 0 | SKIP 13 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   4.32    0.50   12.09 

ttgsea.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
2022-01-24 04:03:04.904483: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2
Train on 1420 samples

  32/1420 [..............................] - ETA: 2:23 - loss: 1.6877 - pearson_correlation: 0.1831
 128/1420 [=>............................] - ETA: 34s - loss: 1.5867 - pearson_correlation: 0.0228 
 224/1420 [===>..........................] - ETA: 18s - loss: 1.5711 - pearson_correlation: 0.1110
 320/1420 [=====>........................] - ETA: 12s - loss: 1.5345 - pearson_correlation: 0.1726
 384/1420 [=======>......................] - ETA: 9s - loss: 1.5679 - pearson_correlation: 0.1933 
 448/1420 [========>.....................] - ETA: 7s - loss: 1.6067 - pearson_correlation: 0.1861
 544/1420 [==========>...................] - ETA: 6s - loss: 1.6006 - pearson_correlation: 0.1723
 608/1420 [===========>..................] - ETA: 5s - loss: 1.6214 - pearson_correlation: 0.1837
 672/1420 [=============>................] - ETA: 4s - loss: 1.6102 - pearson_correlation: 0.1834
 736/1420 [==============>...............] - ETA: 3s - loss: 1.5970 - pearson_correlation: 0.1838
 800/1420 [===============>..............] - ETA: 3s - loss: 1.5905 - pearson_correlation: 0.1834
 864/1420 [=================>............] - ETA: 2s - loss: 1.5650 - pearson_correlation: 0.1669
 928/1420 [==================>...........] - ETA: 2s - loss: 1.5511 - pearson_correlation: 0.1597
 992/1420 [===================>..........] - ETA: 1s - loss: 1.5469 - pearson_correlation: 0.1631
1056/1420 [=====================>........] - ETA: 1s - loss: 1.5571 - pearson_correlation: 0.1694
1120/1420 [======================>.......] - ETA: 1s - loss: 1.5663 - pearson_correlation: 0.1679
1184/1420 [========================>.....] - ETA: 0s - loss: 1.5617 - pearson_correlation: 0.1657
1248/1420 [=========================>....] - ETA: 0s - loss: 1.5721 - pearson_correlation: 0.1798
1312/1420 [==========================>...] - ETA: 0s - loss: 1.5648 - pearson_correlation: 0.1785
1376/1420 [============================>.] - ETA: 0s - loss: 1.5686 - pearson_correlation: 0.1767
1420/1420 [==============================] - 5s 3ms/sample - loss: 1.5599 - pearson_correlation: 0.1799
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  31.39    1.48   27.09 

Example timings

ttgsea.Rcheck/examples_i386/ttgsea-Ex.timings

nameusersystemelapsed
bi_gru0.060.080.14
bi_lstm0.020.010.03
fit_model0.030.000.03
metric_pearson_correlation0.030.000.03
plot_model0.040.000.03
predict_model0.030.000.03
sampling_generator000
text_token 3.78 0.2719.44
token_vector0.030.010.05

ttgsea.Rcheck/examples_x64/ttgsea-Ex.timings

nameusersystemelapsed
bi_gru3.660.765.10
bi_lstm0.430.000.42
fit_model24.56 0.7728.25
metric_pearson_correlation0.030.000.03
plot_model0.30.00.3
predict_model27.49 1.0826.08
sampling_generator0.050.000.05
text_token 2.82 0.1417.97
token_vector 2.70 0.0617.48