| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:23 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
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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 507/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DeepBlueR 1.25.1 (landing page) Felipe Albrecht
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: DeepBlueR |
| Version: 1.25.1 |
| 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_1.25.1.tar.gz |
| StartedAt: 2023-04-11 19:45:28 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 20:01:02 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 934.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DeepBlueR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.25.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DeepBlueR.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* 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 ‘1.25.1’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
deepblue_enrich_regions_overlap 0.47 0.033 10.325
* 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 | 0.069 | 0.012 | 0.928 | |
| deepblue_batch_export_results | 0.375 | 0.228 | 3.561 | |
| deepblue_binning | 0.037 | 0.008 | 0.632 | |
| deepblue_cache_status | 0.002 | 0.000 | 0.003 | |
| deepblue_cancel_request | 0.008 | 0.004 | 0.322 | |
| deepblue_chromosomes | 0.045 | 0.000 | 0.342 | |
| deepblue_clear_cache | 0.002 | 0.000 | 0.002 | |
| deepblue_collection_experiments_count | 0.086 | 0.000 | 0.658 | |
| deepblue_commands | 0.140 | 0.008 | 1.421 | |
| deepblue_count_gene_ontology_terms | 0.083 | 0.000 | 0.385 | |
| deepblue_count_regions | 0.033 | 0.000 | 0.607 | |
| deepblue_coverage | 0.045 | 0.004 | 0.619 | |
| deepblue_delete_request_from_cache | 0.005 | 0.000 | 0.006 | |
| deepblue_diff | 0.126 | 0.032 | 0.759 | |
| deepblue_distinct_column_values | 0.043 | 0.004 | 0.644 | |
| deepblue_download_request_data | 0.250 | 0.115 | 1.800 | |
| deepblue_echo | 0.010 | 0.004 | 0.305 | |
| deepblue_enrich_regions_go_terms | 0.061 | 0.001 | 0.929 | |
| deepblue_enrich_regions_overlap | 0.470 | 0.033 | 10.325 | |
| deepblue_export_bed | 1.144 | 0.221 | 3.327 | |
| deepblue_export_meta_data | 0.211 | 0.007 | 0.627 | |
| deepblue_export_tab | 0.143 | 0.015 | 1.262 | |
| deepblue_extend | 0.029 | 0.009 | 0.613 | |
| deepblue_extract_ids | 0.001 | 0.000 | 0.000 | |
| deepblue_extract_names | 0.000 | 0.000 | 0.001 | |
| deepblue_faceting_experiments | 0.032 | 0.004 | 0.793 | |
| deepblue_filter_regions | 0.025 | 0.004 | 0.333 | |
| deepblue_find_motif | 0.022 | 0.003 | 0.454 | |
| deepblue_flank | 0.043 | 0.000 | 0.607 | |
| deepblue_get_biosource_children | 0.025 | 0.000 | 0.319 | |
| deepblue_get_biosource_parents | 0.025 | 0.000 | 0.319 | |
| deepblue_get_biosource_related | 0.027 | 0.000 | 0.296 | |
| deepblue_get_biosource_synonyms | 0.019 | 0.004 | 0.317 | |
| deepblue_get_experiments_by_query | 0.018 | 0.000 | 0.312 | |
| deepblue_get_regions | 0.051 | 0.008 | 0.647 | |
| deepblue_get_request_data | 0.055 | 0.004 | 1.248 | |
| deepblue_info | 0.019 | 0.011 | 0.324 | |
| deepblue_input_regions | 0.011 | 0.004 | 0.323 | |
| deepblue_intersection | 0.057 | 0.011 | 0.913 | |
| deepblue_is_biosource | 0.015 | 0.008 | 0.314 | |
| deepblue_liftover | 0.379 | 0.064 | 2.822 | |
| deepblue_list_annotations | 0.015 | 0.004 | 0.311 | |
| deepblue_list_biosources | 0.014 | 0.000 | 0.303 | |
| deepblue_list_cached_requests | 0.002 | 0.000 | 0.002 | |
| deepblue_list_column_types | 0.033 | 0.012 | 0.452 | |
| deepblue_list_epigenetic_marks | 0.312 | 0.011 | 1.530 | |
| deepblue_list_experiments | 0.109 | 0.008 | 0.663 | |
| deepblue_list_expressions | 0.127 | 0.024 | 0.679 | |
| deepblue_list_gene_models | 0.013 | 0.000 | 0.304 | |
| deepblue_list_genes | 0.186 | 0.009 | 1.961 | |
| deepblue_list_genomes | 0.015 | 0.000 | 0.342 | |
| deepblue_list_in_use | 0.241 | 0.031 | 1.867 | |
| deepblue_list_projects | 0.010 | 0.005 | 0.406 | |
| deepblue_list_recent_experiments | 0.027 | 0.000 | 0.276 | |
| deepblue_list_requests | 0.016 | 0.003 | 0.342 | |
| deepblue_list_samples | 0.198 | 0.024 | 1.127 | |
| deepblue_list_similar_biosources | 0.021 | 0.000 | 0.435 | |
| deepblue_list_similar_epigenetic_marks | 0.031 | 0.004 | 0.347 | |
| deepblue_list_similar_experiments | 0.018 | 0.005 | 0.853 | |
| deepblue_list_similar_genomes | 0.021 | 0.000 | 0.271 | |
| deepblue_list_similar_projects | 0.012 | 0.004 | 0.264 | |
| deepblue_list_similar_techniques | 0.023 | 0.000 | 0.317 | |
| deepblue_list_techniques | 0.024 | 0.003 | 0.319 | |
| deepblue_merge_queries | 0.049 | 0.004 | 0.889 | |
| deepblue_meta_data_to_table | 0.228 | 0.024 | 1.045 | |
| deepblue_name_to_id | 0.047 | 0.000 | 0.917 | |
| deepblue_overlap | 0.082 | 0.012 | 0.937 | |
| deepblue_preview_experiment | 0.015 | 0.000 | 0.311 | |
| deepblue_query_cache | 0.108 | 0.011 | 1.267 | |
| deepblue_query_experiment_type | 0.102 | 0.007 | 0.714 | |
| deepblue_reset_options | 0.001 | 0.000 | 0.001 | |
| deepblue_score_matrix | 0.054 | 0.011 | 0.649 | |
| deepblue_search | 0.033 | 0.007 | 0.659 | |
| deepblue_select_annotations | 0.019 | 0.008 | 0.319 | |
| deepblue_select_column | 0.307 | 0.040 | 1.801 | |
| deepblue_select_experiments | 0.019 | 0.000 | 0.271 | |
| deepblue_select_expressions | 0.024 | 0.004 | 0.166 | |
| deepblue_select_genes | 0.029 | 0.004 | 0.339 | |
| deepblue_select_regions | 0.017 | 0.016 | 0.328 | |
| deepblue_tiling_regions | 0.015 | 0.004 | 0.309 | |