Aditya Bhagwat
| Snapshot Date: 2025-11-14 13:45 -0500 (Fri, 14 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/autonomics |
| git_branch: RELEASE_3_22 |
| git_last_commit: c22fce2 |
| git_last_commit_date: 2025-10-29 11:06:51 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-15 11:58 -0500 (Sat, 15 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | ||||
| Package 119/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| autonomics 1.18.0 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the autonomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/autonomics.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: autonomics |
| Version: 1.18.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.18.0.tar.gz |
| StartedAt: 2025-11-14 06:50:41 -0000 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 07:22:16 -0000 (Fri, 14 Nov 2025) |
| EllapsedTime: 1894.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: autonomics.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘autonomics’ 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 ... OK
* checking code 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 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
‘[magrittr:compound]{%<>%}’ ‘[magrittr:pipe]{%>%}’
‘[magrittr:aliases]{extract}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... ERROR
Running examples in ‘autonomics-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: .read_rnaseq_bams
> ### Title: Read rnaseq counts/bams
> ### Aliases: .read_rnaseq_bams .read_rnaseq_counts read_rnaseq_bams
> ### read_rnaseq_counts
>
> ### ** Examples
>
> # read_rnaseq_bams
> if (installed('Rsubread')){
+ dir <- download_data('billing16.bam.zip')
+ object <- read_rnaseq_bams(dir, paired = TRUE, genome = 'hg38')
+ object <- read_rnaseq_bams(dir, paired = TRUE, genome = 'hg38', plot = TRUE)
+ }
Downloading billing16.bam.zip
trying URL 'https://bitbucket.org/graumannlabtools/autonomics/downloads/billing16.bam.zip'
Content type 'application/x-zip-compressed' length 33512489 bytes (32.0 MB)
==================================================
downloaded 32.0 MB
unzip
NCBI RefSeq annotation for hg38 (build 38.2) is used.
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.24.0
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 11 BAM files ||
|| ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| star_Aligned.sortedByCoord.out_subset.bam ||
|| ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : inbuilt (hg38) ||
|| Dir for temp files : . ||
|| Threads : 32 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file hg38_RefSeq_exon.txt ... ||
|| Features : 261752 ||
|| Meta-features : 28395 ||
|| Chromosomes/contigs : 55 ||
|| ||
|| Process BAM file star_Aligned.sortedByCoord.out_subset.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 20477 ||
|| Successfully assigned alignments : 4537 (22.2%) ||
|| Running time : 0.03 minutes ||
|| ||
|| Process BAM file star_Aligned.sortedByCoord.out_subset.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 72708 ||
|| Successfully assigned alignments : 28675 (39.4%) ||
|| Running time : 0.01 minutes ||
|| ||
|| Process BAM file star_Aligned.sortedByCoord.out_subset.bam... ||
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
awblinmod 58.813 0.404 59.575
read_diann_proteingroups 58.646 0.570 59.623
LINMOD 34.288 0.391 34.818
plot_exprs 29.761 0.207 30.039
plot_exprs_per_coef 27.549 0.060 27.674
default_formula 24.690 0.384 25.268
analyze 19.509 0.115 20.042
read_metabolon 18.603 0.071 18.735
plot_summary 18.590 0.084 19.094
plot_volcano 18.215 0.123 18.554
explore-transforms 15.130 0.115 15.417
fit_survival 14.929 0.092 15.084
plot_densities 14.663 0.056 15.080
fcluster 12.582 0.028 13.534
ftype 11.182 0.159 11.362
plot_detections 10.497 0.028 10.553
biplot_covariates 10.080 0.036 10.143
read_fragpipe 8.484 0.031 8.494
plot_xy_density 8.397 0.056 8.480
plot_subgroup_points 8.030 0.048 8.094
plot_violins 7.552 0.084 7.702
code 7.303 0.016 7.377
log2transform 6.766 0.066 6.951
extract_contrast_features 6.545 0.012 6.604
biplot 5.228 0.027 5.466
pca 4.851 0.134 5.334
impute 4.800 0.024 5.017
plot_contrastogram 4.045 0.076 11.046
is_compounddiscoverer_output 0.106 0.051 10.348
annotate_uniprot_rest 0.106 0.011 7.286
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R-4.5.0/bin/BATCH: line 60: 1852855 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(autonomics)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘autonomics’ ... ** this is package ‘autonomics’ version ‘1.18.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to 'seq_along' Note: wrong number of arguments to 'sqrt' ** 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 (autonomics)
autonomics.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(autonomics)
autonomics.Rcheck/autonomics-Ex.timings
| name | user | system | elapsed | |
| AUTONOMICS_DATASETS | 0.001 | 0.000 | 0.001 | |
| COMPOUNDDISCOVERER_PATTERNS | 0.001 | 0.000 | 0.000 | |
| LINMOD | 34.288 | 0.391 | 34.818 | |
| LINMODENGINES | 0 | 0 | 0 | |
| MAXQUANT_PATTERNS | 0 | 0 | 0 | |
| TAXON_TO_ORGNAME | 0.001 | 0.000 | 0.001 | |
| TESTS | 0 | 0 | 0 | |
| X | 1.764 | 0.040 | 1.811 | |
| abstract_fit | 1.466 | 0.019 | 1.524 | |
| add_adjusted_pvalues | 0.715 | 0.028 | 0.752 | |
| add_assay_means | 0.513 | 0.044 | 0.559 | |
| add_facetvars | 1.984 | 0.012 | 2.001 | |
| add_opentargets_by_uniprot | 0.543 | 0.004 | 0.553 | |
| add_psp | 0.660 | 0.024 | 0.688 | |
| add_smiles | 0.631 | 0.016 | 0.646 | |
| all_non_numeric | 0.821 | 0.000 | 0.824 | |
| analysis | 0.533 | 0.004 | 0.539 | |
| analyze | 19.509 | 0.115 | 20.042 | |
| annotate_maxquant | 1.375 | 0.028 | 1.409 | |
| annotate_uniprot_rest | 0.106 | 0.011 | 7.286 | |
| assert_is_valid_sumexp | 0.774 | 0.008 | 0.805 | |
| awblinmod | 58.813 | 0.404 | 59.575 | |
| biplot | 5.228 | 0.027 | 5.466 | |
| biplot_corrections | 4.917 | 0.044 | 4.976 | |
| biplot_covariates | 10.080 | 0.036 | 10.143 | |
| block2limma | 0.003 | 0.000 | 0.003 | |
| block2lm | 0.004 | 0.000 | 0.004 | |
| block2lme | 0.000 | 0.002 | 0.002 | |
| block2lmer | 0.005 | 0.000 | 0.005 | |
| block_has_two_levels | 0.853 | 0.020 | 0.878 | |
| center | 2.878 | 0.012 | 2.904 | |
| code | 7.303 | 0.016 | 7.377 | |
| collapsed_entrezg_to_symbol | 1.119 | 0.048 | 1.170 | |
| contrast_subgroup_cols | 0.924 | 0.012 | 1.027 | |
| contrastdt | 0.814 | 0.008 | 0.825 | |
| count_in | 0.002 | 0.000 | 0.002 | |
| counts | 0.526 | 0.004 | 0.706 | |
| counts2cpm | 0.445 | 0.000 | 0.446 | |
| counts2tpm | 0.455 | 0.000 | 0.457 | |
| cpm | 0.468 | 0.000 | 0.470 | |
| create_design | 1.049 | 0.011 | 1.064 | |
| default_formula | 24.690 | 0.384 | 25.268 | |
| default_geom | 0.635 | 0.004 | 0.760 | |
| default_sfile | 0.002 | 0.000 | 0.002 | |
| demultiplex | 0.020 | 0.000 | 0.019 | |
| densities | 0.296 | 0.000 | 0.297 | |
| dequantify | 0.003 | 0.000 | 0.003 | |
| dequantify_compounddiscoverer | 0.002 | 0.000 | 0.001 | |
| dot-coxph | 0.516 | 0.012 | 0.592 | |
| dot-merge | 0.028 | 0.000 | 0.056 | |
| dot-read_maxquant_proteingroups | 0.128 | 0.004 | 0.264 | |
| download_data | 0.001 | 0.000 | 0.000 | |
| download_gtf | 0 | 0 | 0 | |
| download_mcclain21 | 0.000 | 0.000 | 0.001 | |
| dt2mat | 0.004 | 0.000 | 0.004 | |
| enrichment | 1.672 | 0.008 | 1.906 | |
| entrezg_to_symbol | 0.174 | 0.000 | 0.174 | |
| explore-transforms | 15.130 | 0.115 | 15.417 | |
| extract_contrast_features | 6.545 | 0.012 | 6.604 | |
| extract_rectangle | 0.144 | 0.004 | 0.149 | |
| factor.vars | 0.257 | 0.000 | 0.257 | |
| factorize | 1.089 | 0.000 | 1.197 | |
| fcluster | 12.582 | 0.028 | 13.534 | |
| fcor | 1.998 | 0.016 | 2.034 | |
| fdata | 0.732 | 0.004 | 0.737 | |
| fdr2p | 1.198 | 0.012 | 1.214 | |
| filter_exprs_replicated_in_some_subgroup | 1.302 | 0.008 | 1.313 | |
| filter_features | 0.686 | 0.012 | 0.703 | |
| filter_medoid | 0.820 | 0.012 | 0.834 | |
| filter_samples | 0.662 | 0.016 | 0.680 | |
| fit_survival | 14.929 | 0.092 | 15.084 | |
| fits | 0.414 | 0.000 | 0.415 | |
| fix_xlgenes | 0.001 | 0.000 | 0.002 | |
| flevels | 0.501 | 0.012 | 0.516 | |
| fnames | 0.561 | 0.020 | 0.582 | |
| formula2str | 0 | 0 | 0 | |
| ftype | 11.182 | 0.159 | 11.362 | |
| fvalues | 0.517 | 0.004 | 0.522 | |
| fvars | 0.497 | 0.004 | 0.503 | |
| genome_to_orgdb | 0.001 | 0.000 | 0.000 | |
| group_by_level | 0.001 | 0.000 | 0.001 | |
| guess_compounddiscoverer_quantity | 0.002 | 0.000 | 0.001 | |
| guess_fitsep | 0.598 | 0.004 | 0.604 | |
| guess_maxquant_quantity | 0.004 | 0.003 | 0.006 | |
| guess_sep | 0.705 | 0.008 | 0.715 | |
| has_multiple_levels | 0.072 | 0.000 | 0.072 | |
| hdlproteins | 0.045 | 0.012 | 0.170 | |
| impute | 4.800 | 0.024 | 5.017 | |
| invert_subgroups | 0.919 | 0.008 | 0.931 | |
| is_character_matrix | 0.197 | 0.003 | 0.203 | |
| is_collapsed_subset | 0.000 | 0.000 | 0.001 | |
| is_compounddiscoverer_output | 0.106 | 0.051 | 10.348 | |
| is_correlation_matrix | 0.002 | 0.000 | 0.001 | |
| is_diann_report | 0.173 | 0.008 | 0.182 | |
| is_fastadt | 0.083 | 0.000 | 0.084 | |
| is_file | 0.000 | 0.000 | 0.001 | |
| is_fraction | 0.002 | 0.000 | 0.002 | |
| is_fragpipe_tsv | 0.123 | 0.004 | 0.129 | |
| is_imputed | 0.946 | 0.003 | 0.957 | |
| is_maxquant_phosphosites | 0.101 | 0.001 | 0.091 | |
| is_maxquant_proteingroups | 0.077 | 0.015 | 0.096 | |
| is_positive_number | 0.002 | 0.000 | 0.003 | |
| is_scalar_subset | 0.418 | 0.015 | 0.453 | |
| is_sig | 1.890 | 0.042 | 1.998 | |
| is_valid_formula | 0.061 | 0.004 | 0.069 | |
| keep_estimable_features | 1.042 | 0.054 | 1.142 | |
| label2index | 0.001 | 0.000 | 0.001 | |
| list2mat | 0.001 | 0.000 | 0.001 | |
| log2counts | 0.434 | 0.003 | 0.457 | |
| log2cpm | 0.439 | 0.012 | 0.474 | |
| log2diffs | 0.481 | 0.019 | 0.526 | |
| log2proteins | 0.422 | 0.004 | 0.443 | |
| log2sites | 0.416 | 0.012 | 0.448 | |
| log2tpm | 0.441 | 0.008 | 0.473 | |
| log2transform | 6.766 | 0.066 | 6.951 | |
| logical2factor | 0.002 | 0.000 | 0.002 | |
| make_alpha_palette | 0.727 | 0.028 | 0.977 | |
| make_colors | 0.008 | 0.004 | 0.023 | |
| make_volcano_dt | 1.185 | 0.007 | 1.300 | |
| map_fvalues | 0.511 | 0.000 | 0.512 | |
| matrix2sumexp | 1.416 | 0.016 | 1.436 | |
| mclust_breaks | 0.702 | 0.028 | 0.732 | |
| merge_sample_file | 0.652 | 0.004 | 0.657 | |
| merge_sdata | 0.812 | 0.016 | 0.829 | |
| message_df | 0.003 | 0.000 | 0.003 | |
| model_coefs | 1.008 | 0.008 | 1.019 | |
| modelvar | 4.817 | 0.095 | 4.975 | |
| object1 | 0.690 | 0.011 | 0.739 | |
| order_on_p | 1.967 | 0.043 | 2.103 | |
| overall_parameters | 0.040 | 0.000 | 0.043 | |
| pca | 4.851 | 0.134 | 5.334 | |
| pg_to_canonical | 0.009 | 0.000 | 0.010 | |
| plot_coef_densities | 1.953 | 0.043 | 2.094 | |
| plot_contrast_venn | 3.436 | 0.016 | 3.463 | |
| plot_contrastogram | 4.045 | 0.076 | 11.046 | |
| plot_data | 2.517 | 0.008 | 2.600 | |
| plot_densities | 14.663 | 0.056 | 15.080 | |
| plot_design | 1.001 | 0.008 | 1.012 | |
| plot_detections | 10.497 | 0.028 | 10.553 | |
| plot_exprs | 29.761 | 0.207 | 30.039 | |
| plot_exprs_per_coef | 27.549 | 0.060 | 27.674 | |
| plot_fit_summary | 3.017 | 0.004 | 3.177 | |
| plot_heatmap | 2.724 | 0.000 | 2.734 | |
| plot_matrix | 0.745 | 0.020 | 0.766 | |
| plot_subgroup_points | 8.030 | 0.048 | 8.094 | |
| plot_summary | 18.590 | 0.084 | 19.094 | |
| plot_venn | 0.018 | 0.000 | 0.018 | |
| plot_venn_heatmap | 0.028 | 0.000 | 0.029 | |
| plot_violins | 7.552 | 0.084 | 7.702 | |
| plot_volcano | 18.215 | 0.123 | 18.554 | |
| plot_xy_density | 8.397 | 0.056 | 8.480 | |
| preprocess_rnaseq_counts | 0.454 | 0.020 | 0.475 | |
| pull_columns | 0.003 | 0.000 | 0.003 | |
| pvalues_estimable | 0.050 | 0.000 | 0.051 | |
| read_affymetrix | 0 | 0 | 0 | |
| read_diann_proteingroups | 58.646 | 0.570 | 59.623 | |
| read_fragpipe | 8.484 | 0.031 | 8.494 | |
| read_maxquant_phosphosites | 1.995 | 0.020 | 2.031 | |
| read_maxquant_proteingroups | 1.572 | 0.008 | 1.584 | |
| read_metabolon | 18.603 | 0.071 | 18.735 | |
| read_msigdt | 0.001 | 0.000 | 0.001 | |
| read_olink | 1.923 | 0.016 | 1.963 | |
| read_rectangles | 0.244 | 0.012 | 0.257 | |