| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-31 05:44:33 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 503/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DeepBlueR 1.27.0 (landing page) Felipe Albrecht
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: DeepBlueR |
| Version: 1.27.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings DeepBlueR_1.27.0.tar.gz |
| StartedAt: 2023-05-30 05:13:06 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 05:38:50 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 1544.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DeepBlueR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:DeepBlueR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings DeepBlueR_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DeepBlueR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-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 ‘1.27.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
deepblue_batch_export_results 1.291 0.198 8.660
deepblue_enrich_regions_overlap 0.557 0.092 8.826
deepblue_liftover 0.453 0.056 6.414
deepblue_list_genes 0.275 0.023 9.826
deepblue_export_bed 0.226 0.063 6.359
* 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-3.18-bioc/meat/DeepBlueR.Rcheck/00check.log’
for details.
DeepBlueR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL DeepBlueR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 | 0.074 | 0.012 | 2.140 | |
| deepblue_batch_export_results | 1.291 | 0.198 | 8.660 | |
| deepblue_binning | 0.041 | 0.000 | 1.427 | |
| deepblue_cache_status | 0.002 | 0.000 | 0.003 | |
| deepblue_cancel_request | 0.013 | 0.000 | 0.709 | |
| deepblue_chromosomes | 0.053 | 0.003 | 0.745 | |
| deepblue_clear_cache | 0.001 | 0.001 | 0.001 | |
| deepblue_collection_experiments_count | 0.104 | 0.004 | 1.315 | |
| deepblue_commands | 0.115 | 0.012 | 1.877 | |
| deepblue_count_gene_ontology_terms | 0.112 | 0.008 | 1.160 | |
| deepblue_count_regions | 0.036 | 0.000 | 1.369 | |
| deepblue_coverage | 0.029 | 0.008 | 1.404 | |
| deepblue_delete_request_from_cache | 0.003 | 0.000 | 0.003 | |
| deepblue_diff | 0.121 | 0.020 | 1.470 | |
| deepblue_distinct_column_values | 0.025 | 0.012 | 1.362 | |
| deepblue_download_request_data | 0.165 | 0.035 | 4.119 | |
| deepblue_echo | 0.013 | 0.001 | 0.662 | |
| deepblue_enrich_regions_go_terms | 0.055 | 0.008 | 2.032 | |
| deepblue_enrich_regions_overlap | 0.557 | 0.092 | 8.826 | |
| deepblue_export_bed | 0.226 | 0.063 | 6.359 | |
| deepblue_export_meta_data | 0.307 | 0.017 | 1.329 | |
| deepblue_export_tab | 0.125 | 0.016 | 2.879 | |
| deepblue_extend | 0.047 | 0.000 | 1.410 | |
| deepblue_extract_ids | 0.000 | 0.001 | 0.001 | |
| deepblue_extract_names | 0.000 | 0.001 | 0.000 | |
| deepblue_faceting_experiments | 0.030 | 0.002 | 1.144 | |
| deepblue_filter_regions | 0.021 | 0.004 | 0.686 | |
| deepblue_find_motif | 0.026 | 0.000 | 0.703 | |
| deepblue_flank | 0.045 | 0.000 | 1.374 | |
| deepblue_get_biosource_children | 0.016 | 0.004 | 0.691 | |
| deepblue_get_biosource_parents | 0.012 | 0.004 | 0.716 | |
| deepblue_get_biosource_related | 0.018 | 0.000 | 0.693 | |
| deepblue_get_biosource_synonyms | 0.016 | 0.000 | 0.688 | |
| deepblue_get_experiments_by_query | 0.011 | 0.004 | 0.702 | |
| deepblue_get_regions | 0.034 | 0.004 | 1.422 | |
| deepblue_get_request_data | 0.047 | 0.020 | 2.754 | |
| deepblue_info | 0.038 | 0.000 | 0.715 | |
| deepblue_input_regions | 0.018 | 0.000 | 0.715 | |
| deepblue_intersection | 0.054 | 0.009 | 2.086 | |
| deepblue_is_biosource | 0.015 | 0.000 | 0.671 | |
| deepblue_liftover | 0.453 | 0.056 | 6.414 | |
| deepblue_list_annotations | 0.021 | 0.003 | 0.684 | |
| deepblue_list_biosources | 0.014 | 0.004 | 0.701 | |
| deepblue_list_cached_requests | 0.002 | 0.000 | 0.002 | |
| deepblue_list_column_types | 0.067 | 0.000 | 1.103 | |
| deepblue_list_epigenetic_marks | 0.478 | 0.036 | 4.938 | |
| deepblue_list_experiments | 0.155 | 0.020 | 1.542 | |
| deepblue_list_expressions | 0.135 | 0.015 | 1.165 | |
| deepblue_list_gene_models | 0.008 | 0.008 | 0.688 | |
| deepblue_list_genes | 0.275 | 0.023 | 9.826 | |
| deepblue_list_genomes | 0.014 | 0.005 | 0.688 | |
| deepblue_list_in_use | 0.474 | 0.116 | 4.012 | |
| deepblue_list_projects | 0.019 | 0.000 | 0.692 | |
| deepblue_list_recent_experiments | 0.031 | 0.000 | 0.711 | |
| deepblue_list_requests | 0.015 | 0.004 | 0.689 | |
| deepblue_list_samples | 0.141 | 0.015 | 1.868 | |
| deepblue_list_similar_biosources | 0.024 | 0.000 | 0.886 | |
| deepblue_list_similar_epigenetic_marks | 0.023 | 0.004 | 0.709 | |
| deepblue_list_similar_experiments | 0.018 | 0.000 | 1.255 | |
| deepblue_list_similar_genomes | 0.018 | 0.000 | 0.706 | |
| deepblue_list_similar_projects | 0.013 | 0.004 | 0.695 | |
| deepblue_list_similar_techniques | 0.017 | 0.000 | 0.707 | |
| deepblue_list_techniques | 0.027 | 0.000 | 0.705 | |
| deepblue_merge_queries | 0.056 | 0.005 | 2.059 | |
| deepblue_meta_data_to_table | 0.318 | 0.039 | 2.009 | |
| deepblue_name_to_id | 0.050 | 0.005 | 2.066 | |
| deepblue_overlap | 0.067 | 0.004 | 2.109 | |
| deepblue_preview_experiment | 0.016 | 0.000 | 0.676 | |
| deepblue_query_cache | 0.075 | 0.012 | 2.835 | |
| deepblue_query_experiment_type | 0.048 | 0.004 | 1.407 | |
| deepblue_reset_options | 0 | 0 | 0 | |
| deepblue_score_matrix | 0.047 | 0.000 | 1.416 | |
| deepblue_search | 0.051 | 0.000 | 1.049 | |
| deepblue_select_annotations | 0.023 | 0.003 | 0.717 | |
| deepblue_select_column | 0.402 | 0.152 | 3.288 | |
| deepblue_select_experiments | 0.014 | 0.016 | 0.695 | |
| deepblue_select_expressions | 0.031 | 0.004 | 0.709 | |
| deepblue_select_genes | 0.022 | 0.016 | 0.726 | |
| deepblue_select_regions | 0.027 | 0.012 | 0.685 | |
| deepblue_tiling_regions | 0.021 | 0.004 | 0.726 | |