Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1581/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
psygenet2r 1.37.0 (landing page) Alba Gutierrez-Sacristan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the psygenet2r package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psygenet2r.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: psygenet2r |
Version: 1.37.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:psygenet2r.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings psygenet2r_1.37.0.tar.gz |
StartedAt: 2024-06-10 07:35:40 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 07:43:54 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 494.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: psygenet2r.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:psygenet2r.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings psygenet2r_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'psygenet2r/DESCRIPTION' ... OK * this is package 'psygenet2r' version '1.37.0' * checking package namespace information ... NOTE Found export directives that require package 'methods': 'exportClasses' 'exportMethods' Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains 'methods'. * 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 whether package 'psygenet2r' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: 'GO.db' All declared Imports should be used. package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .category_plot: no visible binding for global variable 'category' .category_plot: no visible binding for global variable 'value' .category_plot: no visible binding for global variable 'variable' .gene_plot: no visible binding for global variable 'gene' .gene_plot: no visible binding for global variable 'value' .gene_plot: no visible binding for global variable 'variable' .index_plot: no visible binding for global variable 'Category' .index_plot: no visible binding for global variable 'value' .index_plot: no visible binding for global variable 'variable' .pie_plot: no visible global function definition for 'pie' ListPsyGeNETIds: no visible global function definition for 'read.csv' disGenetCurated: no visible global function definition for 'read.csv' enrichedPD : <anonymous>: no visible global function definition for 'phyper' getUMLs: no visible global function definition for 'read.csv' jaccardEstimation: no visible binding for global variable 'universe' multipleInput: no visible global function definition for 'new' pantherGraphic: no visible binding for global variable 'Var1' pantherGraphic: no visible binding for global variable 'perc' pantherGraphic: no visible binding for global variable 'diseases' plot_pmids_barplot: no visible binding for global variable 'c2.DiseaseName' plot_pmids_barplot: no visible binding for global variable 'c0.Number_of_Abstracts' plot_pmids_barplot: no visible binding for global variable 'c1.Gene_Symbol' plot_psy_heatmap: no visible binding for global variable 'c2.PsychiatricDisorder' plot_psy_heatmap: no visible binding for global variable 'c1.Gene_Symbol' plot_psy_heatmap: no visible binding for global variable 'value' plot_psy_heatmapDisease: no visible binding for global variable 'c2.DiseaseName' plot_psy_heatmapDisease: no visible binding for global variable 'c1.Gene_Symbol' plot_psy_heatmapDisease: no visible binding for global variable 'c0.Score' plot_psy_heatmapGenes: no visible binding for global variable 'c1.Gene_Symbol' plot_psy_heatmapGenes: no visible binding for global variable 'c2.DiseaseName' plot_psy_heatmapGenes: no visible binding for global variable 'c0.Score' psyGenDisId: no visible global function definition for 'read.csv' psyPanther: no visible global function definition for 'read.csv' psygenetAll: no visible global function definition for 'read.csv' psygenetDisease: no visible global function definition for 'read.csv' psygenetDisease: no visible global function definition for 'new' psygenetDiseaseSentences: no visible global function definition for 'read.csv' psygenetDiseaseSentences: no visible global function definition for 'new' psygenetGene: no visible global function definition for 'read.csv' psygenetGene: no visible global function definition for 'new' psygenetGeneSentences: no visible global function definition for 'read.csv' psygenetGeneSentences: no visible global function definition for 'new' singleInput: no visible global function definition for 'combn' singleInput: no visible global function definition for 'new' singleInput.genes: no visible global function definition for 'new' topAnatEnrichment: no visible binding for global variable 'database' topAnatEnrichment: no visible global function definition for 'read.delim' plot,JaccardIndexPsy-ANY: no visible binding for global variable 'Disease1' plot,JaccardIndexPsy-ANY: no visible binding for global variable 'Disease2' plot,JaccardIndexPsy-ANY: no visible binding for global variable 'JaccardIndex' plot,JaccardIndexPsy-ANY: no visible binding for global variable 'value' plot,JaccardIndexPsy-ANY: no visible binding for global variable 'variable' Undefined global functions or variables: Category Disease1 Disease2 JaccardIndex Var1 c0.Number_of_Abstracts c0.Score c1.Gene_Symbol c2.DiseaseName c2.PsychiatricDisorder category combn database diseases gene new perc phyper pie read.csv read.delim universe value variable Consider adding importFrom("graphics", "pie") importFrom("methods", "new") importFrom("stats", "phyper") importFrom("utils", "combn", "read.csv", "read.delim") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 psygenetGeneSentences 0.28 0.02 20.26 enrichedPD-methods 0.10 0.00 5.14 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck/00check.log' for details.
psygenet2r.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL psygenet2r ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'psygenet2r' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (psygenet2r)
psygenet2r.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(psygenet2r) > > test_check("psygenet2r") [ FAIL 0 | WARN 0 | SKIP 4 | PASS 18 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • empty test (4): 'test_basic_disease.R:20:1', 'test_basic_disease.R:25:1', 'test_basic_gene.R:18:1', 'test_basic_gene.R:22:1' [ FAIL 0 | WARN 0 | SKIP 4 | PASS 18 ] > > proc.time() user system elapsed 6.09 9.65 66.87
psygenet2r.Rcheck/psygenet2r-Ex.timings
name | user | system | elapsed | |
JaccardIndexPsy-class | 0.13 | 0.02 | 3.64 | |
enrichedPD-methods | 0.10 | 0.00 | 5.14 | |
extract | 0.00 | 0.00 | 0.03 | |
extractSentences | 0.00 | 0.02 | 0.01 | |
getUMLs-methods | 0.03 | 0.00 | 3.13 | |
jaccardEstimation-methods | 0.07 | 0.01 | 3.17 | |
ndisease | 0 | 0 | 0 | |
ngene | 0 | 0 | 0 | |
pantherGraphic-methods | 0.25 | 0.01 | 4.54 | |
plot-DataGeNET.Psy-ANY-method | 0.06 | 0.03 | 0.16 | |
plot-JaccardIndexPsy-ANY-method | 0 | 0 | 0 | |
psygenetDisease-methods | 0.06 | 0.00 | 3.83 | |
psygenetDiseaseSentences | 0.05 | 0.00 | 2.39 | |
psygenetGene-methods | 0.04 | 0.00 | 2.72 | |
psygenetGeneSentences | 0.28 | 0.02 | 20.26 | |
qr | 0 | 0 | 0 | |
topAnatEnrichment-methods | 0 | 0 | 0 | |
universe | 0 | 0 | 0 | |