Back to Build/check report for BioC 3.22 experimental data |
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This page was generated on 2025-07-24 15:41 -0400 (Thu, 24 Jul 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4792 |
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 |
Package 305/429 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
ProteinGymR 1.3.6 (landing page) Tram Nguyen
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the ProteinGymR package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: ProteinGymR |
Version: 1.3.6 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ProteinGymR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ProteinGymR_1.3.6.tar.gz |
StartedAt: 2025-07-24 12:52:43 -0400 (Thu, 24 Jul 2025) |
EndedAt: 2025-07-24 13:07:02 -0400 (Thu, 24 Jul 2025) |
EllapsedTime: 858.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ProteinGymR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ProteinGymR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ProteinGymR_1.3.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/ProteinGymR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘ProteinGymR/DESCRIPTION’ ... OK * this is package ‘ProteinGymR’ version ‘1.3.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘ProteinGymR’ 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 code 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 loading without being on the library search path ... 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 benchmark_models: no visible binding for global variable ‘.data’ color_line: no visible global function definition for ‘qnorm’ color_line: no visible global function definition for ‘ecdf’ color_line: no visible binding for global variable ‘aggregate_score’ color_line: no visible binding for global variable ‘quant_score’ color_line: no visible binding for global variable ‘quant_clamped’ color_line: no visible binding for global variable ‘color_index’ dms_corr_plot: no visible binding for global variable ‘uID’ dms_corr_plot: no visible binding for global variable ‘.data’ filter_by_pos: no visible binding for global variable ‘pos’ model_corr_plot: no visible binding for global variable ‘uID’ model_corr_plot: no visible binding for global variable ‘.data’ model_match_id: no visible binding for global variable ‘model_df1’ model_match_id: no visible binding for global variable ‘model_df2’ model_match_id: no visible binding for global variable ‘DMS_id.y’ model_match_id: no visible binding for global variable ‘DMS_id.x’ model_match_id: no visible binding for global variable ‘UniProt_id’ model_match_id: no visible binding for global variable ‘mutant’ pg_filter_am_table: no visible binding for global variable ‘.data’ pg_match_id: no visible binding for global variable ‘DMS_score.y’ pg_match_id: no visible binding for global variable ‘DMS_score.x’ pg_match_id: no visible binding for global variable ‘UniProt_id’ pg_match_id: no visible binding for global variable ‘mutant’ pg_match_id: no visible binding for global variable ‘DMS_score’ plot_dms_heatmap: no visible binding for global variable ‘.data’ plot_dms_heatmap: no visible binding for global variable ‘ref’ plot_structure: no visible binding for global variable ‘DMS_score’ plot_structure: no visible binding for global variable ‘.data’ plot_structure: no visible binding for global variable ‘aggregate_score’ plot_structure: no visible global function definition for ‘qnorm’ plot_structure: no visible global function definition for ‘ecdf’ plot_structure: no visible binding for global variable ‘quant_score’ plot_structure: no visible binding for global variable ‘quant_clamped’ plot_zeroshot_heatmap: no visible binding for global variable ‘.data’ Undefined global functions or variables: .data DMS_id.x DMS_id.y DMS_score DMS_score.x DMS_score.y UniProt_id aggregate_score color_index ecdf model_df1 model_df2 mutant pos qnorm quant_clamped quant_score ref uID Consider adding importFrom("stats", "ecdf", "qnorm") to your NAMESPACE file. * 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 plot_structure 79.902 8.164 90.124 model_corr_plot 76.138 6.407 84.711 supervised_scores 55.788 5.157 62.576 plot_zeroshot_heatmap 48.784 4.400 53.625 dms_corr_plot 49.145 3.935 54.821 plot_dms_heatmap 44.598 2.931 48.511 zeroshot_scores 23.077 2.059 25.881 ProteinGym_DMS 23.299 1.807 25.512 benchmark_models 5.017 0.919 6.365 am_scores 4.082 0.653 5.117 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.22-data-experiment/meat/ProteinGymR.Rcheck/00check.log’ for details.
ProteinGymR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ProteinGymR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ProteinGymR’ ... ** this is package ‘ProteinGymR’ version ‘1.3.6’ ** using staged installation ** R ** inst ** 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 (ProteinGymR)
ProteinGymR.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(ProteinGymR) > > test_check("ProteinGymR") see ?ProteinGymR and browseVignettes('ProteinGymR') for documentation loading from cache Using default AlphaMissense modelfrom `ProteinGymR::am_scores()`. see ?ProteinGymR and browseVignettes('ProteinGymR') for documentation loading from cache 1 invalid values were found (fake_id) and removed from the query. Field 'accession_id' with no valid entries has been removed from query. No fold_scheme specified, using contiguous scheme as default. Loading semi-supervised model scores with contiguous folding scheme see ?ProteinGymR and browseVignettes('ProteinGymR') for documentation loading from cache 'dms_table' not provided, using default table from `ProteinGymR::dms_substitutions()` see ?ProteinGymR and browseVignettes('ProteinGymR') for documentation loading from cache [1] "r = 0.66; Pval = 0" [ FAIL 0 | WARN 1 | SKIP 0 | PASS 20 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 20 ] > > proc.time() user system elapsed 52.540 2.875 59.364
ProteinGymR.Rcheck/ProteinGymR-Ex.timings
name | user | system | elapsed | |
ProteinGym_DMS | 23.299 | 1.807 | 25.512 | |
am_scores | 4.082 | 0.653 | 5.117 | |
benchmark_models | 5.017 | 0.919 | 6.365 | |
dms_corr_plot | 49.145 | 3.935 | 54.821 | |
model_corr_plot | 76.138 | 6.407 | 84.711 | |
plot_dms_heatmap | 44.598 | 2.931 | 48.511 | |
plot_structure | 79.902 | 8.164 | 90.124 | |
plot_zeroshot_heatmap | 48.784 | 4.400 | 53.625 | |
supervised_scores | 55.788 | 5.157 | 62.576 | |
zeroshot_scores | 23.077 | 2.059 | 25.881 | |