Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1749/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RiboCrypt 1.12.0 (landing page) Michal Swirski
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the RiboCrypt package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RiboCrypt.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: RiboCrypt |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RiboCrypt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RiboCrypt_1.12.0.tar.gz |
StartedAt: 2024-12-21 06:46:11 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 06:51:57 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 345.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RiboCrypt.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RiboCrypt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RiboCrypt_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RiboCrypt.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RiboCrypt/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RiboCrypt’ version ‘1.12.0’ * package encoding: UTF-8 * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RiboCrypt’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: images 2.2Mb rmd 4.3Mb * 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 Unexported objects imported by ':::' calls: ‘ORFik:::name_decider’ ‘ORFik:::remove.file_ext’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘distribution_plot’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE DEG_plot: no visible binding for global variable ‘rna’ DEG_plot: no visible binding for global variable ‘rfp’ DEG_plot: no visible binding for global variable ‘Regulation’ DEG_plot: no visible binding for global variable ‘contrast’ DEG_plot: no visible binding for global variable ‘meanCounts’ DEG_plot: no visible binding for global variable ‘LFC’ RiboCrypt_app: no visible global function definition for ‘is’ RiboCrypt_app : server: no visible binding for global variable ‘df’ RiboCrypt_app : server: no visible binding for global variable ‘experiments’ RiboCrypt_app : server: no visible binding for global variable ‘tx’ RiboCrypt_app : server: no visible binding for global variable ‘org’ RiboCrypt_app : server: no visible binding for global variable ‘gene_name_list’ RiboCrypt_app : server: no visible binding for global variable ‘df_with’ RiboCrypt_app_modular: no visible global function definition for ‘is’ RiboCrypt_app_modular : server: no visible binding for global variable ‘df’ RiboCrypt_app_modular : server: no visible binding for global variable ‘experiments’ RiboCrypt_app_modular : server: no visible binding for global variable ‘tx’ RiboCrypt_app_modular : server: no visible binding for global variable ‘org’ RiboCrypt_app_modular : server: no visible binding for global variable ‘gene_name_list’ RiboCrypt_app_modular : server: no visible binding for global variable ‘df_with’ browser_plot_assembler: no visible binding for global variable ‘profiles’ browser_plot_assembler: no visible binding for global variable ‘mainPlotControls’ browser_plot_assembler: no visible global function definition for ‘mainPlotControls’ click_plot_browser_new_controller: no visible binding for global variable ‘extend_trailers’ click_plot_codon: no visible binding for global variable ‘variable’ click_plot_codon: no visible binding for global variable ‘seqs’ click_plot_heatmap_main_controller: no visible global function definition for ‘shifts.load’ click_plot_heatmap_main_controller: no visible binding for global variable ‘fraction’ createSeqPanelPattern: no visible binding for global variable ‘frames’ distribution_plot: no visible binding for global variable ‘RPKM’ dt_fft: no visible global function definition for ‘spec.pgram’ dt_fft: no visible binding for global variable ‘fraction’ extend_all_to: no visible binding for global variable ‘tx_name’ fivePlots: no visible binding for global variable ‘seqType’ fivePlots: no visible global function definition for ‘readLengthMeta’ fivePlots: no visible binding for global variable ‘position’ fivePlots: no visible binding for global variable ‘index’ fivePlots: no visible binding for global variable ‘frames’ fivePlots: no visible binding for global variable ‘ratio’ fourPlots: no visible binding for global variable ‘seqType’ fourPlots: no visible binding for global variable ‘position’ fourPlots: no visible binding for global variable ‘index’ fourPlots: no visible binding for global variable ‘frames’ geneModelPanelPlot: no visible binding for global variable ‘layers’ geneModelPanelPlot: no visible binding for global variable ‘rect_starts’ geneModelPanelPlot: no visible binding for global variable ‘rect_ends’ geneModelPanelPlot: no visible binding for global variable ‘labels_locations’ geneModelPanelPlot: no visible binding for global variable ‘gene_names’ geneTrackLayer: no visible binding for global variable ‘subjectHits’ geneTrackLayer: no visible binding for global variable ‘queryHits’ getCoverageProfile: no visible global function definition for ‘is’ getIndexes: no visible global function definition for ‘nrun’ getMetaCoverage: no visible global function definition for ‘.’ getMetaCoverage: no visible binding for global variable ‘position’ getMetaCoverage: no visible binding for global variable ‘index’ getMetaCoverage: no visible binding for global variable ‘frames’ getPlotAnimate: no visible binding for global variable ‘position’ getPlotAnimate: no visible binding for global variable ‘frame’ getProfileAnimate: no visible global function definition for ‘is’ getRelativeFrames: no visible binding for global variable ‘cum_width’ getRelativeFrames: no visible binding for global variable ‘rel_frame’ getRiboProfile: no visible global function definition for ‘is’ getRiboProfile: no visible binding for global variable ‘frame’ getStartWindow: no visible binding for global variable ‘.’ getStopWindow: no visible binding for global variable ‘.’ get_gene_name_categories: no visible binding for global variable ‘merged_name’ heatmap_data: no visible binding for global variable ‘position’ heatmap_data: no visible binding for global variable ‘readlength’ heatmap_data: no visible binding for global variable ‘fraction’ load_custom_regions: no visible binding for global variable ‘.’ make_summary_track: no visible global function definition for ‘.’ make_summary_track: no visible binding for global variable ‘position’ make_summary_track: no visible binding for global variable ‘frame’ metaPlot: no visible binding for global variable ‘index’ metaPlot: no visible binding for global variable ‘frames’ multiOmicsPlot_internal: no visible global function definition for ‘is’ multiOmicsPlot_internal: no visible binding for global variable ‘ylabels_full_name’ multiOmicsPlot_internal: no visible binding for global variable ‘display_dist’ observed_cds_heatmap: no visible binding for global variable ‘gene_id’ observed_cds_heatmap: no visible binding for global variable ‘cds_len’ observed_cds_heatmap: no visible binding for global variable ‘utr5_len’ periodicity_plot: no visible binding for global variable ‘fraction’ periodicity_plot: no visible binding for global variable ‘frame’ periodicity_plot : <anonymous>: no visible binding for global variable ‘read_length’ periodicity_plot : <anonymous>: no visible binding for global variable ‘periods’ periodicity_plot : <anonymous>: no visible binding for global variable ‘amplitude’ plotSeqPanel: no visible binding for global variable ‘frames’ profilesFetcher: no visible global function definition for ‘is’ quality_server : <anonymous>: no visible binding for global variable ‘frame’ quality_server : <anonymous>: no visible binding for global variable ‘position’ quality_server : <anonymous>: no visible binding for global variable ‘fraction’ singlePlot_select_plot_type: no visible binding for global variable ‘position’ singlePlot_select_plot_type: no visible binding for global variable ‘frame’ singlePlotsFetcher: no visible global function definition for ‘is’ singlePlotsFetcher: no visible binding for global variable ‘BPPARAM’ sra_search_server : <anonymous>: no visible global function definition for ‘capture.output’ sra_search_server : <anonymous>: no visible binding for global variable ‘dt’ startCoverage: no visible binding for global variable ‘position’ stopCoverage: no visible binding for global variable ‘position’ threePlots: no visible binding for global variable ‘seqType’ threePlots: no visible binding for global variable ‘position’ threePlots: no visible binding for global variable ‘index’ tx_update_select: no visible binding for global variable ‘label’ unlistToExtremities: no visible global function definition for ‘.’ valuesToColors: no visible global function definition for ‘colorRampPalette’ Undefined global functions or variables: . BPPARAM LFC RPKM Regulation amplitude capture.output cds_len colorRampPalette contrast cum_width df df_with display_dist dt experiments extend_trailers fraction frame frames gene_id gene_name_list gene_names index is label labels_locations layers mainPlotControls meanCounts merged_name nrun org periods position profiles queryHits ratio readLengthMeta read_length readlength rect_ends rect_starts rel_frame rfp rna seqType seqs shifts.load spec.pgram subjectHits tx tx_name utr5_len variable ylabels_full_name Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "frame") importFrom("methods", "is") importFrom("stats", "df", "dt", "spec.pgram") importFrom("utils", "capture.output") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DEG_plot 17.431 0.382 17.834 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/RiboCrypt.Rcheck/00check.log’ for details.
RiboCrypt.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RiboCrypt ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘RiboCrypt’ ... ** 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 (RiboCrypt)
RiboCrypt.Rcheck/RiboCrypt-Ex.timings
name | user | system | elapsed | |
DEG_plot | 17.431 | 0.382 | 17.834 | |
RiboCrypt_app | 0 | 0 | 0 | |
multiOmicsPlot_ORFikExp | 2.999 | 0.058 | 3.058 | |
multiOmicsPlot_animate | 0.892 | 0.015 | 0.907 | |
multiOmicsPlot_list | 3.205 | 0.093 | 2.973 | |