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This page was generated on 2025-10-18 12:07 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 118/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.16  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: ca513f9
git_last_commit_date: 2025-10-03 08:57:56 -0400 (Fri, 03 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for autonomics on taishan

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: 1.17.16
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_1.17.16.tar.gz
StartedAt: 2025-10-17 06:07:27 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 06:49:27 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 2520.0 seconds
RetCode: None
Status:   TIMEOUT  
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_1.17.16.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 ‘1.17.16’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
write_xl                  239.918  2.513 247.482
awblinmod                  60.075  0.744  61.730
read_rnaseq_counts         41.211  1.259  49.067
read_diann_proteingroups   39.055  0.423  43.688
LINMOD                     34.913  0.649  37.402
plot_exprs                 30.553  0.195  32.848
plot_exprs_per_coef        29.286  0.075  32.071
default_formula            26.174  0.319  27.104
read_metabolon             21.596  0.227  22.746
analyze                    20.536  0.176  20.856
read_somascan              20.392  0.240  22.130
plot_volcano               20.184  0.087  22.825
plot_summary               19.819  0.116  21.357
fit_survival               16.027  0.115  16.644
explore-transforms         15.096  0.004  15.611
plot_densities             14.477  0.039  16.923
fcluster                   13.775  0.036  13.908
ftype                      12.157  0.123  12.671
plot_detections            10.643  0.040  10.868
biplot_covariates          10.063  0.020  10.340
plot_xy_density             9.393  0.052  10.421
read_fragpipe               8.911  0.008   9.463
plot_subgroup_points        8.856  0.060  11.319
rm_diann_contaminants       8.527  0.056   8.760
subtract_baseline           7.655  0.063   8.118
plot_violins                7.352  0.040   8.949
extract_contrast_features   7.320  0.035   7.464
log2transform               7.235  0.032   7.395
reset_fit                   6.733  0.043   6.805
code                        6.763  0.012   6.815
sbind                       6.211  0.032   6.665
modelvar                    5.734  0.148   6.123
biplot                      5.401  0.060   5.475
impute                      5.075  0.000   5.375
biplot_corrections          5.027  0.016   5.125
pca                         4.874  0.095   5.450
plot_contrastogram          4.080  0.100   5.210
annotate_uniprot_rest       1.069  0.191   6.879
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.5.0/bin/BATCH: line 60: 1082670 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 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")
* 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 ...

Installation output

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 ‘1.17.16’
** 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)

Tests output

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)

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")

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.001
COMPOUNDDISCOVERER_PATTERNS000
LINMOD34.913 0.64937.402
LINMODENGINES000
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME0.0010.0000.000
TESTS000
X1.7320.0231.769
abstract_fit1.4520.0201.477
add_adjusted_pvalues0.8130.0361.115
add_assay_means0.5100.0040.516
add_facetvars2.1770.0202.203
add_opentargets_by_uniprot0.5460.0160.568
add_psp0.7390.0080.752
add_smiles0.7030.0160.720
all_non_numeric0.8620.0120.877
analysis0.6420.0080.652
analyze20.536 0.17620.856
annotate_maxquant1.2300.0241.421
annotate_uniprot_rest1.0690.1916.879
assert_is_valid_sumexp0.6990.0710.773
awblinmod60.075 0.74461.730
biplot5.4010.0605.475
biplot_corrections5.0270.0165.125
biplot_covariates10.063 0.02010.340
block2limma0.0020.0000.003
block2lm0.0040.0000.004
block2lme0.0030.0000.003
block2lmer0.0050.0000.005
block_has_two_levels0.9110.0080.924
center2.6020.0082.616
code6.7630.0126.815
collapsed_entrezg_to_symbol1.2160.0481.318
contrast_subgroup_cols0.8050.0160.823
contrastdt0.8200.0040.826
count_in0.0010.0000.002
counts0.5370.0080.557
counts2cpm0.4340.0000.437
counts2tpm0.4110.0000.412
cpm0.4700.0000.471
create_design1.0050.0001.010
default_formula26.174 0.31927.104
default_geom0.7220.0120.742
default_sfile0.0020.0000.002
demultiplex0.0200.0000.021
densities0.3180.0000.320
dequantify0.0030.0000.003
dequantify_compounddiscoverer0.0020.0000.002
dot-coxph0.5150.0280.552
dot-merge0.0280.0000.027
dot-read_maxquant_proteingroups0.1360.0030.140
download_data0.0010.0000.001
download_gtf000
download_mcclain21000
dt2mat0.0050.0000.005
enrichment1.7340.0011.754
entrezg_to_symbol0.1810.0000.181
explore-transforms15.096 0.00415.611
extract_contrast_features7.3200.0357.464
extract_rectangle0.1490.0120.162
factor.vars0.2750.0000.276
factorize1.2430.0081.378
fcluster13.775 0.03613.908
fcor2.1350.0322.172
fdata0.7080.0000.710
fdr2p1.4370.0041.493
filter_exprs_replicated_in_some_subgroup1.3780.0121.394
filter_features0.6970.0080.717
filter_medoid0.8770.0000.880
filter_samples0.8550.0081.335
fit_survival16.027 0.11516.644
fits0.4390.0000.442
fix_xlgenes0.0020.0000.002
flevels0.5360.0040.542
fnames0.6610.0000.666
formula2str0.0010.0000.000
ftype12.157 0.12312.671
fvalues0.5200.0000.521
fvars0.5290.0000.574
genome_to_orgdb0.0010.0000.001
group_by_level0.0020.0000.002
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.7350.0000.756
guess_maxquant_quantity0.0070.0000.007
guess_sep0.6760.0000.679
has_multiple_levels0.0830.0000.083
hdlproteins0.0590.0010.177
impute5.0750.0005.375
invert_subgroups0.9960.0041.015
is_character_matrix0.2360.0000.237
is_collapsed_subset000
is_compounddiscoverer_output0.0780.0030.287
is_correlation_matrix0.0020.0000.002
is_diann_report0.0930.0000.158
is_fastadt0.0940.0000.191
is_file0.0000.0000.001
is_fraction0.0020.0000.002
is_fragpipe_tsv0.1040.0010.160
is_imputed1.0910.0001.288
is_maxquant_phosphosites0.0710.0000.065
is_maxquant_proteingroups0.0530.0040.057
is_positive_number0.0020.0000.002
is_scalar_subset0.4350.0000.521
is_sig2.1520.0072.243
is_valid_formula0.0720.0000.072
keep_estimable_features1.1460.0161.194
label2index0.0000.0000.001
list2mat0.0010.0000.001
log2counts0.5480.0040.571
log2cpm0.4660.0000.620
log2diffs0.4780.0040.547
log2proteins0.4590.0040.464
log2sites0.6060.0001.009
log2tpm0.4780.0000.660
log2transform7.2350.0327.395
logical2factor0.0020.0000.001
make_alpha_palette0.6800.0200.705
make_colors0.0070.0040.011
make_volcano_dt1.2500.0081.307
map_fvalues0.5440.0000.545
matrix2sumexp1.4890.0081.553
mclust_breaks0.6960.0190.719
merge_sample_file0.6420.0040.648
merge_sdata0.8480.0080.858
message_df0.0030.0000.003
model_coefs1.0510.0041.070
modelvar5.7340.1486.123
object10.6710.0001.019
order_on_p1.9810.0082.284
overall_parameters0.0420.0000.076
pca4.8740.0955.450
pg_to_canonical0.0080.0000.009
plot_coef_densities1.9120.0241.956
plot_contrast_venn3.4760.0123.626
plot_contrastogram4.080.105.21
plot_data2.3960.0042.965
plot_densities14.477 0.03916.923
plot_design1.1460.0081.157
plot_detections10.643 0.04010.868
plot_exprs30.553 0.19532.848
plot_exprs_per_coef29.286 0.07532.071
plot_fit_summary3.1330.0243.211
plot_heatmap2.6580.0002.769
plot_matrix0.6570.0160.674
plot_subgroup_points 8.856 0.06011.319
plot_summary19.819 0.11621.357
plot_venn0.0180.0000.018
plot_venn_heatmap0.0300.0000.031
plot_violins7.3520.0408.949
plot_volcano20.184 0.08722.825
plot_xy_density 9.393 0.05210.421
preprocess_rnaseq_counts0.4560.0040.462
pull_columns0.0030.0000.003
pvalues_estimable0.0550.0000.056
read_affymetrix000
read_diann_proteingroups39.055 0.42343.688
read_fragpipe8.9110.0089.463
read_maxquant_phosphosites2.1410.0242.190
read_maxquant_proteingroups1.7760.0071.994
read_metabolon21.596 0.22722.746
read_msigdt0.0010.0000.002
read_olink1.9330.0272.071
read_rectangles0.2450.0000.247
read_rnaseq_counts41.211 1.25949.067
read_salmon000
read_somascan20.392 0.24022.130
read_uniprotdt0.4510.0000.452
reset_fit6.7330.0436.805
rm_diann_contaminants8.5270.0568.760
rm_missing_in_some_samples0.7260.0160.743
rm_unmatched_samples1.0440.0041.106
sbind6.2110.0326.665
scaledlibsizes0.5290.0000.567
scoremat1.2160.0201.275
slevels0.6430.0000.680
snames0.5830.0040.745
split_extract_fixed0.7860.0440.832
split_samples1.8430.0641.911
stepauc0.5330.0000.536
stri_any_regex0.0000.0010.001
stri_detect_fixed_in_collapsed0.4830.0030.487
subgroup_matrix0.7670.0200.790
subtract_baseline7.6550.0638.118
sumexp_to_longdt2.7130.0122.811
sumexp_to_tsv0.6880.0040.779
sumexplist_to_longdt2.1640.0482.674
summarize_fit2.4120.0482.485
survobj0.2080.0000.209
svalues0.5590.0040.564
svars0.5700.0040.635
systematic_nas0.8030.0070.814
tag_features1.2380.0161.337
tag_hdlproteins0.7560.0200.783
taxon2org0.0020.0000.001
tpm0.4730.0000.474
uncollapse0.0420.0000.049
values0.5730.0000.750
varlevels_dont_clash0.0280.0000.028
venn_detects0.8180.0080.935
weights0.4760.0080.557
write_xl239.918 2.513247.482
zero_to_na0.0020.0000.002