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This page was generated on 2021-10-15 15:06:02 -0400 (Fri, 15 Oct 2021).
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. |
Package 462/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DeepPINCS 1.0.2 (landing page) Dongmin Jung
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: DeepPINCS |
Version: 1.0.2 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeepPINCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DeepPINCS_1.0.2.tar.gz |
StartedAt: 2021-10-14 22:01:12 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:04:51 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 218.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DeepPINCS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeepPINCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DeepPINCS_1.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DeepPINCS.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 'DeepPINCS/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DeepPINCS' version '1.0.2' * 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 15.02 1.23 19.12 * 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-3.13-bioc/meat/DeepPINCS.Rcheck/00check.log' for details.
DeepPINCS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch DeepPINCS ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.13-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
DeepPINCS.Rcheck/tests/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(DeepPINCS) Loading required package: keras Loading required package: tensorflow > > test_check("DeepPINCS") 2021-10-14 22:03:43.649587: 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: 6s - loss: 0.6868 - accuracy: 0.5000 100/100 [==============================] - 2s 17ms/sample - loss: 0.6804 - accuracy: 0.5100 - val_loss: 0.6938 - val_accuracy: 0.4800 Train on 100 samples, validate on 100 samples 16/100 [===>..........................] - ETA: 5s - loss: 0.7471 - accuracy: 0.3125 100/100 [==============================] - 1s 13ms/sample - loss: 0.7001 - accuracy: 0.4800 - val_loss: 0.6867 - val_accuracy: 0.6700 Train on 100 samples, validate on 100 samples 16/100 [===>..........................] - ETA: 5s - loss: 0.6872 - accuracy: 0.8125 100/100 [==============================] - 1s 14ms/sample - loss: 0.6839 - accuracy: 0.5800 - val_loss: 0.6874 - val_accuracy: 0.4500 [ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ] > > proc.time() user system elapsed 81.07 2.10 77.37
DeepPINCS.Rcheck/DeepPINCS-Ex.timings
name | user | system | elapsed | |
cpi_model | 15.02 | 1.23 | 19.12 | |
encoder_in_out | 0.15 | 0.00 | 0.16 | |
get_canonical_smiles | 0.01 | 0.00 | 0.02 | |
get_fingerprint | 1.00 | 0.10 | 0.37 | |
get_graph_structure_node_feature | 0.11 | 0.00 | 0.11 | |
get_seq_encode_pad | 0.03 | 0.00 | 0.03 | |
metric_concordance_index | 2.83 | 0.06 | 3.08 | |
metric_f1_score | 3.91 | 0.11 | 2.75 | |
multiple_sampling_generator | 0.03 | 0.00 | 0.03 | |
seq_check | 0.02 | 0.00 | 0.01 | |
seq_preprocessing | 0.03 | 0.00 | 0.03 | |