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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 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 1.17.16  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-10-09 13:45 -0400 (Thu, 09 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 12.7.1 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    OK  


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: 2025-10-10 05:34:41 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 05:57:47 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 1386.6 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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                  231.319  1.663 233.742
awblinmod                  58.109  1.926  60.139
read_rnaseq_counts         39.717  1.415  41.331
read_diann_proteingroups   37.077  0.299  37.101
LINMOD                     34.006  0.530  34.620
plot_exprs                 29.797  0.882  30.759
plot_exprs_per_coef        28.860  0.164  29.101
default_formula            25.174  0.674  25.754
read_somascan              19.387  0.044  19.493
analyze                    19.185  0.168  19.406
read_metabolon             19.026  0.064  19.137
plot_volcano               18.931  0.080  19.045
plot_summary               18.786  0.160  18.993
fit_survival               15.430  0.084  15.568
explore-transforms         14.302  0.040  14.382
plot_densities             14.192  0.103  14.329
fcluster                   13.561  0.072  13.662
ftype                      11.809  0.116  11.913
plot_detections            10.277  0.024  10.327
biplot_covariates           9.841  0.100   9.966
plot_xy_density             8.833  0.008   8.859
read_fragpipe               8.695  0.020   8.576
rm_diann_contaminants       8.203  0.184   8.290
plot_subgroup_points        8.232  0.075   8.324
log2transform               7.354  0.016   7.393
subtract_baseline           6.973  0.023   7.012
code                        6.966  0.028   7.011
plot_violins                6.862  0.032   6.908
reset_fit                   6.571  0.103   6.689
extract_contrast_features   6.243  0.032   6.285
sbind                       5.963  0.008   5.989
modelvar                    5.603  0.128   5.740
biplot                      5.403  0.076   5.490
biplot_corrections          4.971  0.024   5.005
annotate_uniprot_rest       0.936  0.060   6.417
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-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-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


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")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 158 ]
> 
> proc.time()
   user  system elapsed 
182.218   2.118 183.724 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS000
LINMOD34.006 0.53034.620
LINMODENGINES000
MAXQUANT_PATTERNS0.0000.0000.001
TAXON_TO_ORGNAME000
TESTS000
X1.6810.0201.704
abstract_fit1.4130.0511.466
add_adjusted_pvalues0.6990.0160.720
add_assay_means0.4560.0000.457
add_facetvars1.9280.0321.963
add_opentargets_by_uniprot0.5040.0120.521
add_psp0.6490.0080.661
add_smiles0.5880.0160.603
all_non_numeric0.8100.0000.812
analysis0.5860.0120.599
analyze19.185 0.16819.406
annotate_maxquant1.2010.0281.236
annotate_uniprot_rest0.9360.0606.417
assert_is_valid_sumexp0.6860.0120.698
awblinmod58.109 1.92660.139
biplot5.4030.0765.490
biplot_corrections4.9710.0245.005
biplot_covariates9.8410.1009.966
block2limma0.0020.0000.002
block2lm0.0040.0000.004
block2lme0.0030.0000.002
block2lmer0.0040.0000.005
block_has_two_levels0.8800.0030.882
center2.6360.0202.665
code6.9660.0287.011
collapsed_entrezg_to_symbol1.2170.0521.272
contrast_subgroup_cols0.7650.0080.772
contrastdt0.7990.0000.801
count_in0.0010.0000.002
counts0.4730.0080.483
counts2cpm0.4040.0000.404
counts2tpm0.3920.0000.393
cpm0.4570.0000.459
create_design0.9300.0120.941
default_formula25.174 0.67425.754
default_geom0.6400.0080.646
default_sfile0.0020.0000.002
demultiplex0.020.000.02
densities0.3020.0000.303
dequantify0.0030.0000.003
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.4990.0040.506
dot-merge0.0270.0000.027
dot-read_maxquant_proteingroups0.1260.0000.127
download_data000
download_gtf000
download_mcclain210.0010.0000.001
dt2mat0.0040.0000.004
enrichment1.6050.0001.611
entrezg_to_symbol0.1700.0040.174
explore-transforms14.302 0.04014.382
extract_contrast_features6.2430.0326.285
extract_rectangle0.1470.0000.148
factor.vars0.2540.0000.254
factorize1.1650.0041.172
fcluster13.561 0.07213.662
fcor2.0680.0802.154
fdata0.7260.0120.740
fdr2p1.3130.0041.318
filter_exprs_replicated_in_some_subgroup1.3710.0231.392
filter_features0.7210.0120.732
filter_medoid0.8020.0120.818
filter_samples0.7420.0040.744
fit_survival15.430 0.08415.568
fits0.4150.0000.416
fix_xlgenes0.0010.0000.002
flevels0.5240.0040.530
fnames0.6510.0000.653
formula2str000
ftype11.809 0.11611.913
fvalues0.5160.0000.518
fvars0.4990.0000.501
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.002
guess_fitsep0.6660.0000.667
guess_maxquant_quantity0.0060.0000.007
guess_sep0.6130.0120.624
has_multiple_levels0.0750.0000.075
hdlproteins0.0500.0040.065
impute4.6860.0084.706
invert_subgroups0.8330.0000.836
is_character_matrix0.1960.0000.197
is_collapsed_subset0.0010.0000.000
is_compounddiscoverer_output0.0570.0040.103
is_correlation_matrix0.0010.0000.001
is_diann_report0.0860.0000.064
is_fastadt0.0860.0000.086
is_file000
is_fraction0.0020.0000.002
is_fragpipe_tsv0.0920.0040.070
is_imputed1.0060.0001.008
is_maxquant_phosphosites0.0650.0000.053
is_maxquant_proteingroups0.0610.0000.049
is_positive_number0.0020.0000.002
is_scalar_subset0.4060.0000.407
is_sig1.9250.0001.929
is_valid_formula0.0640.0000.063
keep_estimable_features1.0840.0081.091
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.5370.0000.539
log2cpm0.4560.0040.462
log2diffs0.4550.0080.464
log2proteins0.4490.0000.450
log2sites0.5410.0080.550
log2tpm0.450.000.45
log2transform7.3540.0167.393
logical2factor0.0020.0000.002
make_alpha_palette0.6740.0320.704
make_colors0.0110.0000.012
make_volcano_dt1.2110.0121.227
map_fvalues0.4960.0000.498
matrix2sumexp1.3870.0081.396
mclust_breaks0.7010.0240.726
merge_sample_file0.6400.0040.646
merge_sdata0.8000.0150.815
message_df0.0030.0010.003
model_coefs0.9800.0110.991
modelvar5.6030.1285.740
object10.6760.0000.677
order_on_p1.8360.0081.846
overall_parameters0.0380.0000.038
pca4.4840.0044.499
pg_to_canonical0.0080.0000.009
plot_coef_densities1.9060.0401.949
plot_contrast_venn3.1380.0283.166
plot_contrastogram3.7420.0283.790
plot_data2.2240.0122.240
plot_densities14.192 0.10314.329
plot_design1.1820.0041.189
plot_detections10.277 0.02410.327
plot_exprs29.797 0.88230.759
plot_exprs_per_coef28.860 0.16429.101
plot_fit_summary2.9960.0083.006
plot_heatmap2.6660.0162.687
plot_matrix0.6580.0120.669
plot_subgroup_points8.2320.0758.324
plot_summary18.786 0.16018.993
plot_venn0.0190.0000.018
plot_venn_heatmap0.0300.0000.029
plot_violins6.8620.0326.908
plot_volcano18.931 0.08019.045
plot_xy_density8.8330.0088.859
preprocess_rnaseq_counts0.4260.0160.443
pull_columns0.0030.0000.003
pvalues_estimable0.0480.0040.052
read_affymetrix000
read_diann_proteingroups37.077 0.29937.101
read_fragpipe8.6950.0208.576
read_maxquant_phosphosites2.0980.0162.120
read_maxquant_proteingroups1.6990.0001.704
read_metabolon19.026 0.06419.137
read_msigdt0.0010.0000.002
read_olink1.7630.0081.757
read_rectangles0.2260.0120.238
read_rnaseq_counts39.717 1.41541.331
read_salmon0.0010.0000.000
read_somascan19.387 0.04419.493
read_uniprotdt0.4440.0160.462
reset_fit6.5710.1036.689
rm_diann_contaminants8.2030.1848.290
rm_missing_in_some_samples0.6360.0200.655
rm_unmatched_samples0.9260.0000.929
sbind5.9630.0085.989
scaledlibsizes0.5110.0000.513
scoremat1.1480.0161.166
slevels0.6180.0080.629
snames0.5390.0040.545
split_extract_fixed0.6670.0200.687
split_samples1.6930.0121.707
stepauc0.5290.0000.531
stri_any_regex0.0010.0000.001
stri_detect_fixed_in_collapsed0.4440.0070.453
subgroup_matrix0.6950.0090.702
subtract_baseline6.9730.0237.012
sumexp_to_longdt2.6260.0252.651
sumexp_to_tsv0.6460.0030.652
sumexplist_to_longdt2.1270.0122.146
summarize_fit2.3620.0042.368
survobj0.2020.0000.202
svalues0.5400.0040.551
svars0.5430.0000.545
systematic_nas0.8310.0000.833
tag_features1.2530.0161.273
tag_hdlproteins0.8040.0200.826
taxon2org0.0010.0000.001
tpm0.4550.0000.457
uncollapse0.0360.0080.044
values0.5780.0040.583
varlevels_dont_clash0.0310.0000.031
venn_detects0.8140.0000.817
weights0.4690.0000.471
write_xl231.319 1.663233.742
zero_to_na0.0020.0000.002