Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:26 -0400 (Fri, 15 Oct 2021).

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.
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raw results

Package 1973/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ttgsea 1.0.0  (landing page)
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)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.0.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ttgsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ttgsea_1.0.0.tar.gz
StartedAt: 2021-10-15 07:01:49 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 07:06:02 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 252.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ttgsea.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ttgsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ttgsea_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ttgsea.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.0.0'
* 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 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    4   0.27   17.98
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
predict_model 33.89   1.14   26.97
fit_model     27.31   1.07   28.40
token_vector   2.68   0.11   16.17
text_token     2.59   0.07   16.66
* 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://155.52.207.165/BBS/3.13/bioc/src/contrib/ttgsea_1.0.0.tar.gz && rm -rf ttgsea.buildbin-libdir && mkdir ttgsea.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ttgsea.buildbin-libdir ttgsea_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ttgsea_1.0.0.zip && rm ttgsea_1.0.0.tar.gz ttgsea_1.0.0.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   613k      0 --:--:-- --:--:-- --:--:--  615k

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_1.0.0.zip
* DONE (ttgsea)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ttgsea' successfully unpacked and MD5 sums checked

Tests output

ttgsea.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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")
== Skipped tests ===============================================================
* Python is not available on this system (13)

[ FAIL 0 | WARN 0 | SKIP 13 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   6.70    0.46    7.15 

ttgsea.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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")
2021-10-15 07:05:32.006671: 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: 3:11 - loss: 1.8816 - pearson_correlation: -0.0398
  96/1420 [=>............................] - ETA: 1:02 - loss: 1.6625 - pearson_correlation: 0.0598 
 128/1420 [=>............................] - ETA: 46s - loss: 1.6288 - pearson_correlation: -0.0142
 192/1420 [===>..........................] - ETA: 29s - loss: 1.6205 - pearson_correlation: 0.0282 
 224/1420 [===>..........................] - ETA: 25s - loss: 1.6522 - pearson_correlation: 0.0165
 256/1420 [====>.........................] - ETA: 21s - loss: 1.5908 - pearson_correlation: -0.0079
 288/1420 [=====>........................] - ETA: 19s - loss: 1.5778 - pearson_correlation: 0.0098 
 320/1420 [=====>........................] - ETA: 16s - loss: 1.5805 - pearson_correlation: 0.0229
 352/1420 [======>.......................] - ETA: 15s - loss: 1.5612 - pearson_correlation: 0.0133
 384/1420 [=======>......................] - ETA: 13s - loss: 1.5868 - pearson_correlation: 0.0237
 416/1420 [=======>......................] - ETA: 12s - loss: 1.5744 - pearson_correlation: 0.0166
 448/1420 [========>.....................] - ETA: 11s - loss: 1.5620 - pearson_correlation: 0.0356
 480/1420 [=========>....................] - ETA: 10s - loss: 1.5568 - pearson_correlation: 0.0510
 512/1420 [=========>....................] - ETA: 9s - loss: 1.5516 - pearson_correlation: 0.0457 
 544/1420 [==========>...................] - ETA: 8s - loss: 1.5284 - pearson_correlation: 0.0527
 576/1420 [===========>..................] - ETA: 7s - loss: 1.5253 - pearson_correlation: 0.0653
 608/1420 [===========>..................] - ETA: 7s - loss: 1.5428 - pearson_correlation: 0.0733
 640/1420 [============>.................] - ETA: 6s - loss: 1.5453 - pearson_correlation: 0.0864
 672/1420 [=============>................] - ETA: 6s - loss: 1.5283 - pearson_correlation: 0.0760
 704/1420 [=============>................] - ETA: 5s - loss: 1.5373 - pearson_correlation: 0.0820
 736/1420 [==============>...............] - ETA: 5s - loss: 1.5389 - pearson_correlation: 0.0893
 768/1420 [===============>..............] - ETA: 4s - loss: 1.5436 - pearson_correlation: 0.0845
 800/1420 [===============>..............] - ETA: 4s - loss: 1.5527 - pearson_correlation: 0.1007
 832/1420 [================>.............] - ETA: 4s - loss: 1.5406 - pearson_correlation: 0.1014
 864/1420 [=================>............] - ETA: 3s - loss: 1.5535 - pearson_correlation: 0.1154
 896/1420 [=================>............] - ETA: 3s - loss: 1.5523 - pearson_correlation: 0.1191
 928/1420 [==================>...........] - ETA: 3s - loss: 1.5507 - pearson_correlation: 0.1134
 960/1420 [===================>..........] - ETA: 2s - loss: 1.5499 - pearson_correlation: 0.1043
 992/1420 [===================>..........] - ETA: 2s - loss: 1.5532 - pearson_correlation: 0.1124
1024/1420 [====================>.........] - ETA: 2s - loss: 1.5542 - pearson_correlation: 0.1121
1056/1420 [=====================>........] - ETA: 2s - loss: 1.5563 - pearson_correlation: 0.1136
1088/1420 [=====================>........] - ETA: 1s - loss: 1.5599 - pearson_correlation: 0.1175
1120/1420 [======================>.......] - ETA: 1s - loss: 1.5590 - pearson_correlation: 0.1220
1152/1420 [=======================>......] - ETA: 1s - loss: 1.5607 - pearson_correlation: 0.1344
1184/1420 [========================>.....] - ETA: 1s - loss: 1.5574 - pearson_correlation: 0.1370
1216/1420 [========================>.....] - ETA: 1s - loss: 1.5674 - pearson_correlation: 0.1420
1248/1420 [=========================>....] - ETA: 0s - loss: 1.5722 - pearson_correlation: 0.1395
1280/1420 [==========================>...] - ETA: 0s - loss: 1.5761 - pearson_correlation: 0.1397
1312/1420 [==========================>...] - ETA: 0s - loss: 1.5667 - pearson_correlation: 0.1348
1344/1420 [===========================>..] - ETA: 0s - loss: 1.5637 - pearson_correlation: 0.1366
1376/1420 [============================>.] - ETA: 0s - loss: 1.5638 - pearson_correlation: 0.1322
1408/1420 [============================>.] - ETA: 0s - loss: 1.5608 - pearson_correlation: 0.1269
1420/1420 [==============================] - 7s 5ms/sample - loss: 1.5630 - pearson_correlation: 0.1196
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  48.23    3.04   23.20 

Example timings

ttgsea.Rcheck/examples_i386/ttgsea-Ex.timings

nameusersystemelapsed
bi_gru0.100.110.22
bi_lstm0.050.000.04
fit_model0.020.020.03
metric_pearson_correlation0.030.000.03
plot_model0.020.000.03
predict_model0.030.000.03
sampling_generator000
text_token 4.00 0.2717.98
token_vector0.030.010.05

ttgsea.Rcheck/examples_x64/ttgsea-Ex.timings

nameusersystemelapsed
bi_gru3.120.744.50
bi_lstm0.770.040.61
fit_model27.31 1.0728.40
metric_pearson_correlation0.030.000.03
plot_model0.280.000.29
predict_model33.89 1.1426.97
sampling_generator0.050.000.05
text_token 2.59 0.0716.66
token_vector 2.68 0.1116.17