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This page was generated on 2022-01-24 13:04:59 -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 nebbiolo2


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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DeepPINCS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DeepPINCS_1.2.1.tar.gz
StartedAt: 2022-01-23 07:15:36 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 07:18:30 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 174.4 seconds
RetCode: 0
Status:   OK  
CheckDir: DeepPINCS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DeepPINCS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DeepPINCS_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/DeepPINCS.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 ‘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 for sufficient/correct file permissions ... 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 13.656    1.7  12.877
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/DeepPINCS.Rcheck/00check.log’
for details.



Installation output

DeepPINCS.Rcheck/00install.out

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


* installing to library ‘/home/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
** 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)

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-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(DeepPINCS)
Loading required package: keras
> 
> test_check("DeepPINCS")
2022-01-23 07:17:21.505752: 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 07:17:21.505797: 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 07:17:33.155490: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
2022-01-23 07:17:33.157393: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
2022-01-23 07:17:33.206051: 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 07:17:33.206102: 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 07:17:33.206623: 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 07:17:33.209943: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
2022-01-23 07:17:34.261712: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
2022-01-23 07:17:34.282259: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2200000000 Hz

1/7 [===>..........................] - ETA: 5s - loss: 0.7151 - accuracy: 0.3125
7/7 [==============================] - 2s 118ms/step - loss: 0.6994 - accuracy: 0.4564 - val_loss: 0.6926 - val_accuracy: 0.4800

1/7 [===>..........................] - ETA: 5s - loss: 0.6941 - accuracy: 0.5000
7/7 [==============================] - 1s 53ms/step - loss: 0.6908 - accuracy: 0.5222 - val_loss: 0.6938 - val_accuracy: 0.4800

1/7 [===>..........................] - ETA: 6s - loss: 0.7000 - accuracy: 0.3750
7/7 [==============================] - 1s 53ms/step - loss: 0.6891 - accuracy: 0.5591 - val_loss: 0.6883 - val_accuracy: 0.5000
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 76.742   2.642  71.055 

Example timings

DeepPINCS.Rcheck/DeepPINCS-Ex.timings

nameusersystemelapsed
cpi_model13.656 1.70012.877
encoder_in_out0.2120.0000.216
get_canonical_smiles0.0200.0010.019
get_fingerprint0.9450.0600.302
get_graph_structure_node_feature0.0880.0000.045
get_seq_encode_pad0.0340.0040.037
metric_concordance_index2.3450.1182.052
metric_f1_score2.6050.1551.718
multiple_sampling_generator0.0150.0030.018
seq_check0.0110.0000.011
seq_preprocessing0.0200.0040.021