Felipe Albrecht
| Snapshot Date: 2023-05-29 14:00:15 -0400 (Mon, 29 May 2023) |
| git_url: https://git.bioconductor.org/packages/DeepBlueR |
| git_branch: RELEASE_3_17 |
| git_last_commit: 422a55a |
| git_last_commit_date: 2023-04-25 10:48:12 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-05-30 11:06:04 -0400 (Tue, 30 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" | 4617 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" | 4368 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow" | 4326 |
| 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: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DeepBlueR.git to reflect on this report. See Troubleshooting Build Report for more information. - 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
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: DeepBlueR |
| Version: 1.26.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeepBlueR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DeepBlueR_1.26.0.tar.gz |
| StartedAt: 2023-05-30 01:10:07 -0400 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 01:14:49 -0400 (Tue, 30 May 2023) |
| EllapsedTime: 282.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DeepBlueR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DeepBlueR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DeepBlueR_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/DeepBlueR.Rcheck'
* using R version 4.3.0 RC (2023-04-13 r84269 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 1.17 0.02 5.05
* 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
'F:/biocbuild/bbs-3.17-bioc/meat/DeepBlueR.Rcheck/00check.log'
for details.
DeepBlueR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL DeepBlueR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 | 0.08 | 0.00 | 0.68 | |
| deepblue_batch_export_results | 0.42 | 0.26 | 3.50 | |
| deepblue_binning | 0.06 | 0.00 | 0.45 | |
| deepblue_cache_status | 0 | 0 | 0 | |
| deepblue_cancel_request | 0.02 | 0.00 | 0.22 | |
| deepblue_chromosomes | 0.09 | 0.00 | 0.30 | |
| deepblue_clear_cache | 0 | 0 | 0 | |
| deepblue_collection_experiments_count | 0.08 | 0.00 | 0.55 | |
| deepblue_commands | 0.11 | 0.00 | 0.59 | |
| deepblue_count_gene_ontology_terms | 0.08 | 0.00 | 0.38 | |
| deepblue_count_regions | 0.03 | 0.02 | 0.43 | |
| deepblue_coverage | 0.03 | 0.00 | 0.44 | |
| deepblue_delete_request_from_cache | 0 | 0 | 0 | |
| deepblue_diff | 0.23 | 0.04 | 1.00 | |
| deepblue_distinct_column_values | 0.03 | 0.00 | 0.44 | |
| deepblue_download_request_data | 0.25 | 0.19 | 2.23 | |
| deepblue_echo | 0.04 | 0.00 | 0.22 | |
| deepblue_enrich_regions_go_terms | 0.04 | 0.00 | 0.64 | |
| deepblue_enrich_regions_overlap | 0.48 | 0.02 | 3.11 | |
| deepblue_export_bed | 0.25 | 0.04 | 1.76 | |
| deepblue_export_meta_data | 0.35 | 0.02 | 0.66 | |
| deepblue_export_tab | 0.11 | 0.01 | 0.94 | |
| deepblue_extend | 0.04 | 0.00 | 0.43 | |
| deepblue_extract_ids | 0 | 0 | 0 | |
| deepblue_extract_names | 0 | 0 | 0 | |
| deepblue_faceting_experiments | 0.02 | 0.00 | 0.44 | |
| deepblue_filter_regions | 0.01 | 0.00 | 0.22 | |
| deepblue_find_motif | 0.02 | 0.00 | 0.22 | |
| deepblue_flank | 0.03 | 0.00 | 0.44 | |
| deepblue_get_biosource_children | 0.03 | 0.00 | 0.23 | |
| deepblue_get_biosource_parents | 0.0 | 0.0 | 0.2 | |
| deepblue_get_biosource_related | 0.02 | 0.00 | 0.24 | |
| deepblue_get_biosource_synonyms | 0.01 | 0.00 | 0.22 | |
| deepblue_get_experiments_by_query | 0.03 | 0.00 | 0.22 | |
| deepblue_get_regions | 0.05 | 0.00 | 0.42 | |
| deepblue_get_request_data | 0.07 | 0.00 | 0.86 | |
| deepblue_info | 0.05 | 0.00 | 0.24 | |
| deepblue_input_regions | 0.02 | 0.00 | 0.22 | |
| deepblue_intersection | 0.04 | 0.00 | 0.65 | |
| deepblue_is_biosource | 0.04 | 0.00 | 0.22 | |
| deepblue_liftover | 1.17 | 0.02 | 5.05 | |
| deepblue_list_annotations | 0.03 | 0.00 | 0.22 | |
| deepblue_list_biosources | 0.01 | 0.00 | 0.22 | |
| deepblue_list_cached_requests | 0.00 | 0.00 | 0.01 | |
| deepblue_list_column_types | 0.03 | 0.00 | 0.33 | |
| deepblue_list_epigenetic_marks | 0.31 | 0.00 | 0.80 | |
| deepblue_list_experiments | 0.14 | 0.02 | 0.56 | |
| deepblue_list_expressions | 0.18 | 0.01 | 0.48 | |
| deepblue_list_gene_models | 0.03 | 0.00 | 0.22 | |
| deepblue_list_genes | 0.15 | 0.02 | 0.77 | |
| deepblue_list_genomes | 0.02 | 0.00 | 0.22 | |
| deepblue_list_in_use | 0.28 | 0.01 | 1.25 | |
| deepblue_list_projects | 0.02 | 0.00 | 0.21 | |
| deepblue_list_recent_experiments | 0.04 | 0.00 | 0.24 | |
| deepblue_list_requests | 0.03 | 0.00 | 0.23 | |
| deepblue_list_samples | 0.10 | 0.02 | 0.53 | |
| deepblue_list_similar_biosources | 0.01 | 0.00 | 0.39 | |
| deepblue_list_similar_epigenetic_marks | 0.03 | 0.00 | 0.24 | |
| deepblue_list_similar_experiments | 0.04 | 0.00 | 0.78 | |
| deepblue_list_similar_genomes | 0.03 | 0.00 | 0.22 | |
| deepblue_list_similar_projects | 0.03 | 0.00 | 0.21 | |
| deepblue_list_similar_techniques | 0.00 | 0.00 | 0.21 | |
| deepblue_list_techniques | 0.03 | 0.00 | 0.22 | |
| deepblue_merge_queries | 0.06 | 0.00 | 0.67 | |
| deepblue_meta_data_to_table | 0.25 | 0.02 | 0.76 | |
| deepblue_name_to_id | 0.03 | 0.00 | 0.63 | |
| deepblue_overlap | 0.08 | 0.00 | 0.67 | |
| deepblue_preview_experiment | 0.02 | 0.00 | 0.23 | |
| deepblue_query_cache | 0.11 | 0.02 | 0.88 | |
| deepblue_query_experiment_type | 0.03 | 0.00 | 0.55 | |
| deepblue_reset_options | 0 | 0 | 0 | |
| deepblue_score_matrix | 0.03 | 0.00 | 0.45 | |
| deepblue_search | 0.05 | 0.00 | 0.57 | |
| deepblue_select_annotations | 0.01 | 0.00 | 0.22 | |
| deepblue_select_column | 0.45 | 0.00 | 0.97 | |
| deepblue_select_experiments | 0.02 | 0.00 | 0.22 | |
| deepblue_select_expressions | 0.05 | 0.00 | 0.23 | |
| deepblue_select_genes | 0.03 | 0.00 | 0.31 | |
| deepblue_select_regions | 0.01 | 0.00 | 0.22 | |
| deepblue_tiling_regions | 0.04 | 0.00 | 0.22 | |