Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:06:08 -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 DeepPINCS on tokay2


To the developers/maintainers of the DeepPINCS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeepPINCS.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 470/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeepPINCS 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/DeepPINCS
git_branch: RELEASE_3_14
git_last_commit: 210a4cb
git_last_commit_date: 2021-12-14 19:41:15 -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: DeepPINCS
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeepPINCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DeepPINCS_1.2.1.tar.gz
StartedAt: 2022-01-23 17:57:35 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 18:00:52 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 197.1 seconds
RetCode: 0
Status:   OK  
CheckDir: DeepPINCS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeepPINCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DeepPINCS_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DeepPINCS.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 'DeepPINCS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeepPINCS' 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'DeepPINCS' 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 ... NOTE
fit_cpi: no visible binding for global variable 'compound'
fit_cpi: no visible binding for global variable 'compound_args'
fit_cpi: no visible binding for global variable 'protein'
fit_cpi: no visible binding for global variable 'protein_args'
fit_cpi: no visible binding for global variable 'max_atoms'
gcn_in_out : Layer : f: no visible binding for global variable 'object'
gcn_in_out : initialize: no visible global function definition for
  'super'
gcn_in_out : call: no visible binding for global variable 'self'
gcn_in_out : get_config: no visible binding for global variable 'self'
gcn_in_out: no visible binding for global variable 'temp_units'
multiple_sampling_generator : <anonymous>: no visible binding for
  global variable 'batch_start'
Undefined global functions or variables:
  batch_start compound compound_args max_atoms object protein
  protein_args self super temp_units
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
cpi_model 14.72   1.29   15.68
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/DeepPINCS.Rcheck/00check.log'
for details.



Installation output

DeepPINCS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch DeepPINCS
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
* installing *source* package 'DeepPINCS' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DeepPINCS'
    finding HTML links ... done
    SARS_CoV2_3CL_Protease                  html  
    antiviral_drug                          html  
    cpi_model                               html  
    encoder_in_out                          html  
    example_bioassay                        html  
    example_cci                             html  
    example_chem                            html  
    example_cpi                             html  
    example_pd                              html  
    example_ppi                             html  
    example_prot                            html  
    get_canonical_smiles                    html  
    get_fingerprint                         html  
    get_graph_structure_node_feature        html  
    get_seq_encode_pad                      html  
    metric_concordance_index                html  
    metric_f1_score                         html  
    multiple_sampling_generator             html  
    seq_check                               html  
    seq_preprocessing                       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
* DONE (DeepPINCS)
Making 'packages.html' ... done

Tests output

DeepPINCS.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-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(DeepPINCS)
Loading required package: keras
> 
> test_check("DeepPINCS")
2022-01-23 17:59:44.532784: 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 100 samples, validate on 100 samples

 16/100 [===>..........................] - ETA: 8s - loss: 0.7233 - accuracy: 0.3125
100/100 [==============================] - 2s 24ms/sample - loss: 0.6891 - accuracy: 0.5200 - val_loss: 0.6957 - val_accuracy: 0.4800
Train on 100 samples, validate on 100 samples

 16/100 [===>..........................] - ETA: 4s - loss: 0.7001 - accuracy: 0.4375
100/100 [==============================] - 1s 12ms/sample - loss: 0.6930 - accuracy: 0.5500 - val_loss: 0.6903 - val_accuracy: 0.5200
Train on 100 samples, validate on 100 samples

 16/100 [===>..........................] - ETA: 5s - loss: 0.6891 - accuracy: 0.3750
100/100 [==============================] - 1s 13ms/sample - loss: 0.6867 - accuracy: 0.5600 - val_loss: 0.6898 - val_accuracy: 0.5100
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  81.56    1.96   77.54 

Example timings

DeepPINCS.Rcheck/DeepPINCS-Ex.timings

nameusersystemelapsed
cpi_model14.72 1.2915.68
encoder_in_out0.160.000.15
get_canonical_smiles0.020.000.02
get_fingerprint0.800.060.36
get_graph_structure_node_feature0.060.000.07
get_seq_encode_pad0.040.000.03
metric_concordance_index2.740.033.42
metric_f1_score4.330.063.50
multiple_sampling_generator0.050.000.05
seq_check0.030.000.03
seq_preprocessing0.070.000.05