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 11:05:19 -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: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DeepBlueR_1.26.0.tar.gz |
| StartedAt: 2023-05-29 20:27:20 -0400 (Mon, 29 May 2023) |
| EndedAt: 2023-05-29 20:42:24 -0400 (Mon, 29 May 2023) |
| EllapsedTime: 904.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DeepBlueR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DeepBlueR_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DeepBlueR.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84269)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘DeepBlueR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.
DeepBlueR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DeepBlueR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 | 0.049 | 0.008 | 0.855 | |
| deepblue_batch_export_results | 0.380 | 0.056 | 3.319 | |
| deepblue_binning | 0.034 | 0.000 | 0.618 | |
| deepblue_cache_status | 0.002 | 0.000 | 0.002 | |
| deepblue_cancel_request | 0.014 | 0.000 | 0.305 | |
| deepblue_chromosomes | 0.048 | 0.000 | 0.340 | |
| deepblue_clear_cache | 0.001 | 0.000 | 0.002 | |
| deepblue_collection_experiments_count | 0.089 | 0.000 | 0.840 | |
| deepblue_commands | 0.075 | 0.039 | 1.602 | |
| deepblue_count_gene_ontology_terms | 0.073 | 0.005 | 0.601 | |
| deepblue_count_regions | 0.032 | 0.000 | 0.600 | |
| deepblue_coverage | 0.027 | 0.000 | 0.590 | |
| deepblue_delete_request_from_cache | 0.002 | 0.000 | 0.002 | |
| deepblue_diff | 0.209 | 0.007 | 0.816 | |
| deepblue_distinct_column_values | 0.029 | 0.001 | 0.610 | |
| deepblue_download_request_data | 0.135 | 0.012 | 1.537 | |
| deepblue_echo | 0.011 | 0.004 | 0.307 | |
| deepblue_enrich_regions_go_terms | 0.046 | 0.000 | 0.904 | |
| deepblue_enrich_regions_overlap | 0.426 | 0.048 | 4.783 | |
| deepblue_export_bed | 0.249 | 0.071 | 2.271 | |
| deepblue_export_meta_data | 0.214 | 0.032 | 0.672 | |
| deepblue_export_tab | 0.155 | 0.016 | 1.265 | |
| deepblue_extend | 0.038 | 0.019 | 0.622 | |
| deepblue_extract_ids | 0.001 | 0.000 | 0.001 | |
| deepblue_extract_names | 0.001 | 0.000 | 0.001 | |
| deepblue_faceting_experiments | 0.031 | 0.004 | 0.767 | |
| deepblue_filter_regions | 0.030 | 0.008 | 0.290 | |
| deepblue_find_motif | 0.045 | 0.000 | 0.338 | |
| deepblue_flank | 0.084 | 0.008 | 0.657 | |
| deepblue_get_biosource_children | 0.030 | 0.004 | 0.327 | |
| deepblue_get_biosource_parents | 0.021 | 0.003 | 0.316 | |
| deepblue_get_biosource_related | 0.033 | 0.004 | 0.340 | |
| deepblue_get_biosource_synonyms | 0.036 | 0.000 | 0.330 | |
| deepblue_get_experiments_by_query | 0.022 | 0.004 | 0.319 | |
| deepblue_get_regions | 0.052 | 0.006 | 0.626 | |
| deepblue_get_request_data | 0.068 | 0.011 | 1.347 | |
| deepblue_info | 0.025 | 0.007 | 0.323 | |
| deepblue_input_regions | 0.022 | 0.003 | 0.334 | |
| deepblue_intersection | 0.055 | 0.012 | 0.903 | |
| deepblue_is_biosource | 0.079 | 0.076 | 0.444 | |
| deepblue_liftover | 0.376 | 0.029 | 2.764 | |
| deepblue_list_annotations | 0.022 | 0.000 | 0.314 | |
| deepblue_list_biosources | 0.013 | 0.000 | 0.301 | |
| deepblue_list_cached_requests | 0.000 | 0.003 | 0.004 | |
| deepblue_list_column_types | 0.066 | 0.008 | 0.476 | |
| deepblue_list_epigenetic_marks | 0.253 | 0.036 | 1.593 | |
| deepblue_list_experiments | 0.103 | 0.000 | 0.654 | |
| deepblue_list_expressions | 0.121 | 0.076 | 0.676 | |
| deepblue_list_gene_models | 0.008 | 0.004 | 0.302 | |
| deepblue_list_genes | 0.193 | 0.001 | 1.941 | |
| deepblue_list_genomes | 0.015 | 0.000 | 0.316 | |
| deepblue_list_in_use | 0.262 | 0.011 | 1.964 | |
| deepblue_list_projects | 0.009 | 0.004 | 0.312 | |
| deepblue_list_recent_experiments | 0.022 | 0.000 | 0.277 | |
| deepblue_list_requests | 0.013 | 0.000 | 0.318 | |
| deepblue_list_samples | 0.139 | 0.016 | 1.147 | |
| deepblue_list_similar_biosources | 0.016 | 0.004 | 0.368 | |
| deepblue_list_similar_epigenetic_marks | 0.029 | 0.000 | 0.329 | |
| deepblue_list_similar_experiments | 0.075 | 0.088 | 1.024 | |
| deepblue_list_similar_genomes | 0.025 | 0.003 | 0.277 | |
| deepblue_list_similar_projects | 0.023 | 0.000 | 0.316 | |
| deepblue_list_similar_techniques | 0.015 | 0.001 | 0.306 | |
| deepblue_list_techniques | 0.044 | 0.000 | 0.335 | |
| deepblue_merge_queries | 0.062 | 0.003 | 0.857 | |
| deepblue_meta_data_to_table | 0.322 | 0.016 | 1.017 | |
| deepblue_name_to_id | 0.053 | 0.012 | 0.919 | |
| deepblue_overlap | 0.077 | 0.004 | 0.915 | |
| deepblue_preview_experiment | 0.012 | 0.000 | 0.310 | |
| deepblue_query_cache | 0.074 | 0.004 | 1.183 | |
| deepblue_query_experiment_type | 0.056 | 0.000 | 0.657 | |
| deepblue_reset_options | 0 | 0 | 0 | |
| deepblue_score_matrix | 0.040 | 0.004 | 0.640 | |
| deepblue_search | 0.069 | 0.004 | 0.678 | |
| deepblue_select_annotations | 0.025 | 0.000 | 0.274 | |
| deepblue_select_column | 1.035 | 0.209 | 2.571 | |
| deepblue_select_experiments | 0.014 | 0.000 | 0.317 | |
| deepblue_select_expressions | 0.025 | 0.003 | 0.319 | |
| deepblue_select_genes | 0.032 | 0.000 | 0.321 | |
| deepblue_select_regions | 0.041 | 0.000 | 0.334 | |
| deepblue_tiling_regions | 0.02 | 0.00 | 0.27 | |