Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-06-02 11:02:11 -0400 (Fri, 02 Jun 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.0 RC (2023-04-13 r84266) -- "Already Tomorrow" | 4269 |
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 |
To the developers/maintainers of the DeepBlueR package: Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 511/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DeepBlueR 1.26.0 (landing page) Felipe Albrecht
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | ERROR | ||||||||
Package: DeepBlueR |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeepBlueR_1.26.0.tar.gz |
StartedAt: 2023-05-30 11:10:07 -0400 (Tue, 30 May 2023) |
EndedAt: 2023-05-30 11:17:51 -0400 (Tue, 30 May 2023) |
EllapsedTime: 463.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DeepBlueR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeepBlueR_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DeepBlueR.Rcheck’ * using R version 4.3.0 RC (2023-04-13 r84266) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DeepBlueR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DeepBlueR’ version ‘1.26.0’ * 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 ‘DeepBlueR’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: v0.99.0 Initial Bioconductor submission Cannot process chunk/lines: v1.0.0 Bioconductor 3.4 release Cannot process chunk/lines: v1.2.0 Bioconductor 3.5 release Cannot process chunk/lines: v1.4.0 Bioconductor 3.6 release Cannot process chunk/lines: v1.4.1 Bugfixes following changes in the DeepBlue API * 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 startup messages can be suppressed ... 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 ... OK * checking Rd files ... NOTE prepare_Rd: deepblue_enrich_regions_fast.Rd:35-38: Dropping empty section \examples * 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 deepblue_liftover 0.476 0.081 9.47 * 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 ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DeepBlueR.Rcheck/00check.log’ for details.
DeepBlueR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DeepBlueR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘DeepBlueR’ ... ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading Called method: deepblue_list_column_types Reported status was: okay Called method: deepblue_info Reported status was: okay ** 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 (DeepBlueR)
DeepBlueR.Rcheck/DeepBlueR-Ex.timings
name | user | system | elapsed | |
deepblue_aggregate | 0.068 | 0.010 | 0.817 | |
deepblue_batch_export_results | 0.358 | 0.053 | 3.094 | |
deepblue_binning | 0.043 | 0.005 | 0.537 | |
deepblue_cache_status | 0.002 | 0.002 | 0.006 | |
deepblue_cancel_request | 0.016 | 0.002 | 0.258 | |
deepblue_chromosomes | 0.053 | 0.005 | 0.319 | |
deepblue_clear_cache | 0.001 | 0.001 | 0.003 | |
deepblue_collection_experiments_count | 0.084 | 0.004 | 0.643 | |
deepblue_commands | 0.109 | 0.012 | 0.750 | |
deepblue_count_gene_ontology_terms | 0.097 | 0.006 | 0.501 | |
deepblue_count_regions | 0.032 | 0.005 | 0.551 | |
deepblue_coverage | 0.036 | 0.006 | 0.536 | |
deepblue_delete_request_from_cache | 0.002 | 0.002 | 0.009 | |
deepblue_diff | 0.130 | 0.045 | 0.735 | |
deepblue_distinct_column_values | 0.035 | 0.006 | 0.545 | |
deepblue_download_request_data | 0.229 | 0.031 | 1.721 | |
deepblue_echo | 0.013 | 0.002 | 0.257 | |
deepblue_enrich_regions_go_terms | 0.052 | 0.005 | 0.787 | |
deepblue_enrich_regions_overlap | 0.483 | 0.019 | 3.610 | |
deepblue_export_bed | 0.856 | 0.040 | 3.125 | |
deepblue_export_meta_data | 0.279 | 0.006 | 0.776 | |
deepblue_export_tab | 0.119 | 0.011 | 1.135 | |
deepblue_extend | 0.039 | 0.003 | 0.530 | |
deepblue_extract_ids | 0.000 | 0.000 | 0.003 | |
deepblue_extract_names | 0.001 | 0.000 | 0.001 | |
deepblue_faceting_experiments | 0.026 | 0.002 | 0.552 | |
deepblue_filter_regions | 0.021 | 0.002 | 0.268 | |
deepblue_find_motif | 0.024 | 0.002 | 0.271 | |
deepblue_flank | 0.040 | 0.003 | 0.546 | |
deepblue_get_biosource_children | 0.016 | 0.002 | 0.273 | |
deepblue_get_biosource_parents | 0.015 | 0.002 | 0.260 | |
deepblue_get_biosource_related | 0.017 | 0.003 | 0.274 | |
deepblue_get_biosource_synonyms | 0.016 | 0.002 | 0.258 | |
deepblue_get_experiments_by_query | 0.014 | 0.002 | 0.437 | |
deepblue_get_regions | 0.032 | 0.004 | 0.536 | |
deepblue_get_request_data | 0.058 | 0.006 | 1.015 | |
deepblue_info | 0.033 | 0.006 | 0.295 | |
deepblue_input_regions | 0.017 | 0.002 | 0.274 | |
deepblue_intersection | 0.056 | 0.006 | 0.794 | |
deepblue_is_biosource | 0.014 | 0.003 | 0.256 | |
deepblue_liftover | 0.476 | 0.081 | 9.470 | |
deepblue_list_annotations | 0.020 | 0.002 | 0.272 | |
deepblue_list_biosources | 0.017 | 0.002 | 0.255 | |
deepblue_list_cached_requests | 0.002 | 0.002 | 0.004 | |
deepblue_list_column_types | 0.057 | 0.004 | 0.434 | |
deepblue_list_epigenetic_marks | 0.390 | 0.013 | 1.184 | |
deepblue_list_experiments | 0.135 | 0.010 | 0.695 | |
deepblue_list_expressions | 0.155 | 0.010 | 0.610 | |
deepblue_list_gene_models | 0.016 | 0.002 | 0.262 | |
deepblue_list_genes | 0.258 | 0.008 | 1.085 | |
deepblue_list_genomes | 0.016 | 0.002 | 0.257 | |
deepblue_list_in_use | 0.320 | 0.007 | 1.566 | |
deepblue_list_projects | 0.016 | 0.002 | 0.285 | |
deepblue_list_recent_experiments | 0.029 | 0.002 | 0.284 | |
deepblue_list_requests | 0.016 | 0.003 | 0.261 | |
deepblue_list_samples | 0.123 | 0.022 | 0.714 | |
deepblue_list_similar_biosources | 0.021 | 0.002 | 0.448 | |
deepblue_list_similar_epigenetic_marks | 0.061 | 0.005 | 0.360 | |
deepblue_list_similar_experiments | 0.016 | 0.002 | 0.843 | |
deepblue_list_similar_genomes | 0.015 | 0.002 | 0.257 | |
deepblue_list_similar_projects | 0.017 | 0.002 | 0.264 | |
deepblue_list_similar_techniques | 0.017 | 0.002 | 0.606 | |
deepblue_list_techniques | 0.026 | 0.003 | 0.275 | |
deepblue_merge_queries | 0.056 | 0.005 | 0.874 | |
deepblue_meta_data_to_table | 0.271 | 0.010 | 1.002 | |
deepblue_name_to_id | 0.051 | 0.005 | 0.784 | |
deepblue_overlap | 0.059 | 0.005 | 0.804 | |
deepblue_preview_experiment | 0.013 | 0.001 | 0.254 | |
deepblue_query_cache | 0.070 | 0.007 | 1.044 | |
deepblue_query_experiment_type | 0.045 | 0.004 | 0.548 | |
deepblue_reset_options | 0.000 | 0.001 | 0.003 | |
deepblue_score_matrix | 0.036 | 0.004 | 0.519 | |
deepblue_search | 0.038 | 0.004 | 0.615 | |
deepblue_select_annotations | 0.021 | 0.002 | 0.268 | |
deepblue_select_column | 0.341 | 0.011 | 1.128 | |
deepblue_select_experiments | 0.019 | 0.002 | 0.263 | |
deepblue_select_expressions | 0.022 | 0.002 | 0.276 | |
deepblue_select_genes | 0.023 | 0.002 | 0.270 | |
deepblue_select_regions | 0.024 | 0.002 | 0.272 | |
deepblue_tiling_regions | 0.017 | 0.002 | 0.255 | |