Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:05:48 -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 nebbiolo2


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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ttgsea_1.2.1.tar.gz
StartedAt: 2022-01-23 10:05:38 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 10:07:50 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 132.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ttgsea.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ttgsea_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ttgsea.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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 24.605  3.817  13.055
fit_model     22.734  2.175  14.103
text_token    11.769  1.393   6.984
token_vector  10.666  0.491   6.663
* 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ttgsea
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-pc-linux-gnu (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 10:07:35.801011: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2022-01-23 10:07:35.801058: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
2022-01-23 10:07:38.554763: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
2022-01-23 10:07:38.556016: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
2022-01-23 10:07:38.608445: E tensorflow/stream_executor/cuda/cuda_driver.cc:328] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2022-01-23 10:07:38.608487: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (nebbiolo2): /proc/driver/nvidia/version does not exist
2022-01-23 10:07:38.608911: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2022-01-23 10:07:38.613229: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
2022-01-23 10:07:38.952474: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
2022-01-23 10:07:38.953497: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2200000000 Hz

 1/45 [..............................] - ETA: 2:16 - loss: 2.0044 - pearson_correlation: 0.2570
 3/45 [=>............................] - ETA: 1s - loss: 1.8447 - pearson_correlation: 0.1826  
 5/45 [==>...........................] - ETA: 1s - loss: 1.7752 - pearson_correlation: 0.1706
 8/45 [====>.........................] - ETA: 1s - loss: 1.7351 - pearson_correlation: 0.1492
11/45 [======>.......................] - ETA: 0s - loss: 1.7124 - pearson_correlation: 0.1349
14/45 [========>.....................] - ETA: 0s - loss: 1.6961 - pearson_correlation: 0.1194
17/45 [==========>...................] - ETA: 0s - loss: 1.6800 - pearson_correlation: 0.1127
19/45 [===========>..................] - ETA: 0s - loss: 1.6718 - pearson_correlation: 0.1118
22/45 [=============>................] - ETA: 0s - loss: 1.6598 - pearson_correlation: 0.1113
25/45 [===============>..............] - ETA: 0s - loss: 1.6479 - pearson_correlation: 0.1122
28/45 [=================>............] - ETA: 0s - loss: 1.6379 - pearson_correlation: 0.1149
30/45 [===================>..........] - ETA: 0s - loss: 1.6319 - pearson_correlation: 0.1170
33/45 [=====================>........] - ETA: 0s - loss: 1.6240 - pearson_correlation: 0.1201
36/45 [=======================>......] - ETA: 0s - loss: 1.6178 - pearson_correlation: 0.1222
38/45 [========================>.....] - ETA: 0s - loss: 1.6142 - pearson_correlation: 0.1234
41/45 [==========================>...] - ETA: 0s - loss: 1.6096 - pearson_correlation: 0.1245
44/45 [============================>.] - ETA: 0s - loss: 1.6062 - pearson_correlation: 0.1250
45/45 [==============================] - 4s 25ms/step - loss: 1.6041 - pearson_correlation: 0.1251
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 25.317   4.987  16.923 

Example timings

ttgsea.Rcheck/ttgsea-Ex.timings

nameusersystemelapsed
bi_gru2.9050.6213.213
bi_lstm0.2420.0090.251
fit_model22.734 2.17514.103
metric_pearson_correlation0.0270.0000.027
plot_model0.1890.0170.197
predict_model24.605 3.81713.055
sampling_generator0.0180.0000.018
text_token11.769 1.393 6.984
token_vector10.666 0.491 6.663