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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 117/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.16.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_21
git_last_commit: a47f4df
git_last_commit_date: 2025-04-15 12:21:58 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for autonomics on kunpeng2

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.

raw results


Summary

Package: autonomics
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2025-10-14 06:20:09 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 06:39:53 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 1183.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: autonomics.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
read_rnaseq_counts       51.093  1.333  59.358
fit_linmod               47.704  0.143  48.306
plot_exprs_per_coef      36.951  0.067  39.297
plot_exprs               36.232  0.128  36.727
default_formula          25.493  0.453  27.382
analyze                  23.973  0.387  24.723
read_metabolon           22.463  0.163  23.061
read_somascan            22.271  0.102  23.894
plot_summary             21.837  0.128  23.437
plot_volcano             20.081  0.116  21.060
plot_densities           14.180  0.052  14.271
fcluster                 13.475  0.035  14.351
ftype                    12.073  0.092  12.788
plot_sample_nas          10.828  0.143  11.596
biplot_covariates         9.822  0.100  10.151
extract_coef_features     9.842  0.015  10.674
read_fragpipe             8.752  0.056   9.020
plot_subgroup_points      8.420  0.028   8.984
log2transform             7.750  0.067   7.984
code                      7.507  0.150   7.887
fit_survival              7.645  0.004   7.952
reset_fit                 7.155  0.027   7.463
plot_violins              6.749  0.107   7.736
biplot                    6.502  0.216   6.735
subtract_baseline         6.669  0.040   6.921
biplot_corrections        6.172  0.135   6.329
plot_joint_density        5.846  0.028   5.990
plot_survival             5.467  0.020   5.989
impute                    5.066  0.020   5.100
modelvar                  4.957  0.072   5.039
read_diann_proteingroups  4.946  0.031   5.216
annotate_uniprot_rest     0.118  0.028   7.410
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] nonexistent
  attr(,"class")
  [1] "vector_with_cause" "logical"          
  Backtrace:
      ▆
   1. ├─autonomics::.read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") at test-8_fit.R:76:9
   2. │ └─object %<>% ...
   3. └─autonomics::merge_sample_file(...)
   4.   └─autonomics:::assert_all_are_existing_files(sfile)
   5.     └─autonomics:::assert_engine(...)
   6.       └─autonomics:::give_feedback(handler_type, msg, predicate_name)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 157 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘autonomics’ ...
** this is package ‘autonomics’ version ‘1.16.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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)

Tests output

autonomics.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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)

Attaching package: 'autonomics'

The following objects are masked from 'package:stats':

    biplot, loadings

The following object is masked from 'package:base':

    beta

> 
> test_check("autonomics")
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 157 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-8_fit.R:76:9'):  fit: mcclain21  ───────────────────────────────
<assertionError/assertionCondition/simpleError/error/condition>
Error in `merge_sample_file(., sfile = sfile, by.x = "sample_id", by.y = by.y)`: is_existing_file : Some or all of the files specified by sfile do not exist.
/home/biocbuild/.cache/R/autonomics/datasets/mcclain21/GSE161731_counts_key.csv.gz 
                                                                             FALSE 
attr(,"cause")
[1] nonexistent
attr(,"class")
[1] "vector_with_cause" "logical"          
Backtrace:
    ▆
 1. ├─autonomics::.read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") at test-8_fit.R:76:9
 2. │ └─object %<>% ...
 3. └─autonomics::merge_sample_file(...)
 4.   └─autonomics:::assert_all_are_existing_files(sfile)
 5.     └─autonomics:::assert_engine(...)
 6.       └─autonomics:::give_feedback(handler_type, msg, predicate_name)

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 157 ]
Error: Test failures
Execution halted

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
FITSEP000
LINMODENGINES000
MAXQUANT_PATTERNS000
SURVIVALENGINES000
TAXON_TO_ORGNAME000
TESTS0.0000.0000.001
X2.0120.1512.170
abstract_fit2.5130.0962.617
add_adjusted_pvalues0.7930.0160.814
add_assay_means0.4910.0200.512
add_facetvars2.2280.0522.286
add_opentargets_by_uniprot0.5200.0150.541
add_psp0.6860.0080.699
add_smiles0.6620.0120.676
analysis0.5360.0200.557
analyze23.973 0.38724.723
annotate_maxquant1.2130.0441.301
annotate_uniprot_rest0.1180.0287.410
assert_is_valid_sumexp0.7430.0600.804
bin0.5700.0280.600
biplot6.5020.2166.735
biplot_corrections6.1720.1356.329
biplot_covariates 9.822 0.10010.151
block2lme0.0040.0000.004
center2.5730.0083.044
code7.5070.1507.887
coefs1.0600.0241.210
collapsed_entrezg_to_symbol0.0010.0000.000
contrast_subgroup_cols0.7260.0080.735
count_in0.0010.0000.001
counts0.4480.0040.459
counts2cpm0.3950.0000.396
counts2tpm0.3870.0000.388
cpm0.4470.0000.748
create_design0.9040.0120.971
default_formula25.493 0.45327.382
default_geom0.7120.0030.717
default_sfile0.0020.0000.002
demultiplex0.020.000.02
dequantify0.0000.0030.003
dequantify_compounddiscoverer0.0010.0000.002
dot-coxph0.5560.0050.718
dot-merge0.0210.0040.024
dot-read_maxquant_proteingroups0.1340.0030.138
download_data0.0010.0000.000
download_gtf000
download_mcclain210.0000.0010.006
dt2mat0.0040.0000.004
enrichment2.6130.0002.759
entrezg_to_symbol000
extract_coef_features 9.842 0.01510.674
extract_rectangle0.1520.0050.158
fcluster13.475 0.03514.351
fcor2.0900.0082.112
fdata0.8520.0000.858
fdr2p1.3500.0561.450
filter_exprs_replicated_in_some_subgroup1.3190.0041.619
filter_features0.6850.0080.695
filter_medoid0.9600.0040.997
filter_samples0.7270.0030.821
fit_linmod47.704 0.14348.306
fit_survival7.6450.0047.952
fitcoefs1.2110.0521.268
fits1.0300.0081.040
fix_xlgenes0.0020.0000.002
flevels0.5890.0040.594
fnames0.620.000.72
formula2str000
ftype12.073 0.09212.788
fvalues0.5500.0000.551
fvars0.5870.0000.588
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0020.0000.001
guess_fitsep0.6430.0040.921
guess_maxquant_quantity0.0070.0000.007
guess_sep0.6950.0000.696
has_multiple_levels0.0720.0000.072
hdlproteins0.0610.0120.085
impute5.0660.0205.100
invert_subgroups0.9030.0080.912
is_collapsed_subset0.0010.0000.001
is_correlation_matrix0.0020.0000.001
is_diann_report0.2110.0120.336
is_fastadt0.0820.0000.099
is_file0.0010.0000.000
is_fraction0.0020.0000.002
is_imputed0.9850.0000.989
is_positive_number0.0020.0000.002
is_scalar_subset0.4590.0000.460
is_sig2.3650.0002.374
is_valid_formula0.0570.0000.057
keep_connected_blocks0.6950.0000.700
keep_connected_features0.9440.0190.967
keep_replicated_features1.1000.0201.125
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.4180.0040.423
log2cpm0.4020.0000.402
log2diffs0.4550.0080.464
log2proteins0.4060.0000.407
log2sites0.4540.0080.469
log2tpm0.4060.0000.407
log2transform7.7500.0677.984
logical2factor0.0010.0000.002
make_alpha_palette0.6600.0040.666
make_colors0.0110.0000.011
make_volcano_dt1.1880.0041.205
map_fvalues0.5610.0040.566
matrix2sumexp1.3870.0001.473
merge_sample_file0.5740.0040.580
merge_sdata0.7200.0190.742
message_df0.0020.0000.002
model_coefs0.9910.0040.997
modelvar4.9570.0725.039
order_on_p1.6060.0201.631
pca4.7980.0124.997
pg_to_canonical0.0070.0000.008
plot_coef_densities1.8620.0081.873
plot_contrast_venn3.3770.0403.425
plot_contrastogram3.9480.0204.080
plot_data2.2230.0082.531
plot_densities14.180 0.05214.271
plot_design1.0400.0151.057
plot_exprs36.232 0.12836.727
plot_exprs_per_coef36.951 0.06739.297
plot_fit_summary3.2600.0723.439
plot_heatmap3.3530.0203.403
plot_joint_density5.8460.0285.990
plot_matrix0.7250.0360.799
plot_sample_nas10.828 0.14311.596
plot_subgroup_points8.4200.0288.984
plot_summary21.837 0.12823.437
plot_survival5.4670.0205.989
plot_venn0.0050.0000.006
plot_venn_heatmap0.0310.0000.031
plot_violins6.7490.1077.736
plot_volcano20.081 0.11621.060
preprocess_rnaseq_counts0.4230.0000.438
pull_columns0.0030.0000.003
read_affymetrix000
read_diann_proteingroups4.9460.0315.216
read_fragpipe8.7520.0569.020
read_maxquant_phosphosites2.0110.0122.123
read_maxquant_proteingroups1.6780.0441.789
read_metabolon22.463 0.16323.061
read_msigdt0.0010.0000.001
read_olink1.8930.0522.111
read_rectangles0.2280.0000.233
read_rnaseq_counts51.093 1.33359.358
read_salmon000
read_somascan22.271 0.10223.894
read_uniprotdt0.3790.0080.393
reset_fit7.1550.0277.463
rm_diann_contaminants1.5210.0081.691
rm_missing_in_some_samples0.7690.0110.870
rm_unmatched_samples0.7920.0000.884
scaledlibsizes0.3800.0040.385
scoremat1.3560.0081.618
slevels0.5240.0080.532
snames0.5710.0240.607
split_extract_fixed0.6420.0320.676
split_samples1.5800.0281.613
stri_any_regex000
stri_detect_fixed_in_collapsed0.4170.0040.422
subgroup_matrix0.6860.0120.699
subtract_baseline6.6690.0406.921
sumexp_to_longdt2.5150.0192.587
sumexp_to_tsv0.6780.0040.685
sumexplist_to_longdt2.0470.0002.088
summarize_fit2.3080.0052.705
svalues0.5340.0000.552
svars0.4970.0120.511
systematic_nas0.8030.0000.870
tag_features1.3010.0551.451
tag_hdlproteins0.7740.0270.830
taxon2org0.0000.0010.002
tpm0.4240.0090.439
uncollapse0.0380.0000.038
values0.5520.0030.556
varlevels_dont_clash0.0290.0000.029
venn_detects0.8070.0040.812
weights0.4250.0000.425
write_xl0.9470.0080.957
zero_to_na0.0020.0000.002