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This page was generated on 2023-02-27 02:34:32 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 486/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DeepBlueR 1.25.1 (landing page) Felipe Albrecht
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| 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/library --timings DeepBlueR_1.25.1.tar.gz |
| StartedAt: 2023-02-24 09:55:19 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 10:06:12 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 653.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: DeepBlueR.Rcheck |
| Warnings: NA |
##############################################################################
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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/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 Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 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 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 0.527 7.086 24.284
deepblue_list_experiments 0.170 2.915 11.876
deepblue_select_column 0.414 1.263 5.656
deepblue_enrich_regions_overlap 0.651 0.048 8.435
deepblue_batch_export_results 0.318 0.048 7.921
deepblue_export_bed 0.209 0.012 5.593
* 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 ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘DeepBlueR.Rmd’ using rmarkdown
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820591&key=anonymous_key'
Content type 'application/x-bzip2' length 45606 bytes (44 KB)
==================================================
downloaded 44 KB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r3726035&key=anonymous_key'
Content type 'application/x-bzip2' length 1394381 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820593&key=anonymous_key'
Content type 'application/x-bzip2' length 2618 bytes
==================================================
downloaded 2618 bytes
trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r820594&key=anonymous_key'
Content type 'application/x-bzip2' length 8189 bytes
==================================================
downloaded 8189 bytes
Killed
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 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/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 | 0.066 | 0.004 | 2.122 | |
| deepblue_batch_export_results | 0.318 | 0.048 | 7.921 | |
| deepblue_binning | 0.072 | 0.008 | 1.476 | |
| deepblue_cache_status | 0.003 | 0.000 | 0.002 | |
| deepblue_cancel_request | 0.015 | 0.000 | 0.758 | |
| deepblue_chromosomes | 0.062 | 0.000 | 0.752 | |
| deepblue_clear_cache | 0.000 | 0.001 | 0.001 | |
| deepblue_collection_experiments_count | 0.101 | 0.006 | 1.316 | |
| deepblue_commands | 0.122 | 0.000 | 3.728 | |
| deepblue_count_gene_ontology_terms | 0.111 | 0.000 | 1.532 | |
| deepblue_count_regions | 0.032 | 0.000 | 2.483 | |
| deepblue_coverage | 0.030 | 0.003 | 1.449 | |
| deepblue_delete_request_from_cache | 0.003 | 0.000 | 0.002 | |
| deepblue_diff | 0.126 | 0.012 | 1.525 | |
| deepblue_distinct_column_values | 0.037 | 0.000 | 2.351 | |
| deepblue_download_request_data | 0.163 | 0.024 | 4.209 | |
| deepblue_echo | 0.009 | 0.004 | 0.721 | |
| deepblue_enrich_regions_go_terms | 0.050 | 0.012 | 3.230 | |
| deepblue_enrich_regions_overlap | 0.651 | 0.048 | 8.435 | |
| deepblue_export_bed | 0.209 | 0.012 | 5.593 | |
| deepblue_export_meta_data | 0.331 | 0.000 | 1.329 | |
| deepblue_export_tab | 0.125 | 0.008 | 2.910 | |
| deepblue_extend | 0.045 | 0.003 | 1.453 | |
| deepblue_extract_ids | 0.001 | 0.001 | 0.001 | |
| deepblue_extract_names | 0.000 | 0.000 | 0.002 | |
| deepblue_faceting_experiments | 0.028 | 0.004 | 1.252 | |
| deepblue_filter_regions | 0.017 | 0.008 | 0.712 | |
| deepblue_find_motif | 0.031 | 0.000 | 0.696 | |
| deepblue_flank | 0.039 | 0.007 | 1.425 | |
| deepblue_get_biosource_children | 0.014 | 0.004 | 0.728 | |
| deepblue_get_biosource_parents | 0.016 | 0.000 | 0.725 | |
| deepblue_get_biosource_related | 0.020 | 0.000 | 0.742 | |
| deepblue_get_biosource_synonyms | 0.017 | 0.000 | 0.705 | |
| deepblue_get_experiments_by_query | 0.015 | 0.000 | 0.710 | |
| deepblue_get_regions | 0.037 | 0.000 | 1.484 | |
| deepblue_get_request_data | 0.090 | 0.016 | 2.856 | |
| deepblue_info | 0.031 | 0.008 | 0.746 | |
| deepblue_input_regions | 0.014 | 0.024 | 1.104 | |
| deepblue_intersection | 0.058 | 0.008 | 2.210 | |
| deepblue_is_biosource | 0.011 | 0.008 | 0.746 | |
| deepblue_liftover | 0.527 | 7.086 | 24.284 | |
| deepblue_list_annotations | 0.027 | 0.000 | 0.729 | |
| deepblue_list_biosources | 0.019 | 0.000 | 0.725 | |
| deepblue_list_cached_requests | 0.000 | 0.003 | 0.007 | |
| deepblue_list_column_types | 0.060 | 0.009 | 1.095 | |
| deepblue_list_epigenetic_marks | 0.483 | 0.043 | 2.890 | |
| deepblue_list_experiments | 0.170 | 2.915 | 11.876 | |
| deepblue_list_expressions | 0.132 | 0.017 | 1.188 | |
| deepblue_list_gene_models | 0.011 | 0.004 | 0.705 | |
| deepblue_list_genes | 0.332 | 0.036 | 4.144 | |
| deepblue_list_genomes | 0.017 | 0.000 | 0.736 | |
| deepblue_list_in_use | 0.411 | 0.015 | 3.615 | |
| deepblue_list_projects | 0.014 | 0.002 | 0.725 | |
| deepblue_list_recent_experiments | 0.029 | 0.000 | 0.698 | |
| deepblue_list_requests | 0.018 | 0.000 | 0.708 | |
| deepblue_list_samples | 0.141 | 0.009 | 3.277 | |
| deepblue_list_similar_biosources | 0.024 | 0.000 | 0.918 | |
| deepblue_list_similar_epigenetic_marks | 0.022 | 0.000 | 0.744 | |
| deepblue_list_similar_experiments | 0.016 | 0.000 | 1.265 | |
| deepblue_list_similar_genomes | 0.015 | 0.000 | 0.692 | |
| deepblue_list_similar_projects | 0.016 | 0.000 | 0.676 | |
| deepblue_list_similar_techniques | 0.016 | 0.000 | 0.685 | |
| deepblue_list_techniques | 0.022 | 0.005 | 0.728 | |
| deepblue_merge_queries | 0.055 | 0.000 | 2.153 | |
| deepblue_meta_data_to_table | 0.416 | 0.019 | 2.204 | |
| deepblue_name_to_id | 0.038 | 0.015 | 3.000 | |
| deepblue_overlap | 0.058 | 0.016 | 2.148 | |
| deepblue_preview_experiment | 0.025 | 1.416 | 4.823 | |
| deepblue_query_cache | 0.079 | 0.007 | 2.867 | |
| deepblue_query_experiment_type | 0.050 | 0.000 | 1.477 | |
| deepblue_reset_options | 0.001 | 0.000 | 0.000 | |
| deepblue_score_matrix | 0.039 | 0.008 | 1.479 | |
| deepblue_search | 0.048 | 0.006 | 1.054 | |
| deepblue_select_annotations | 0.025 | 0.007 | 0.784 | |
| deepblue_select_column | 0.414 | 1.263 | 5.656 | |
| deepblue_select_experiments | 0.018 | 0.004 | 0.739 | |
| deepblue_select_expressions | 0.028 | 0.000 | 0.728 | |
| deepblue_select_genes | 0.026 | 0.000 | 0.694 | |
| deepblue_select_regions | 0.025 | 0.004 | 0.718 | |
| deepblue_tiling_regions | 0.013 | 0.006 | 0.727 | |