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This page was generated on 2025-10-18 12:03 -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 nebbiolo2

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.

raw results


Summary

Package: autonomics
Version: 1.17.16
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings autonomics_1.17.16.tar.gz
StartedAt: 2025-10-17 21:07:03 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 21:26:15 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 1152.0 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings autonomics_1.17.16.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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                 159.232  1.856 161.071
read_diann_proteingroups  95.104  0.943  91.542
awblinmod                 40.011  0.236  38.529
read_rnaseq_counts        29.013  2.633  31.463
LINMOD                    23.477  0.398  23.125
rm_diann_contaminants     21.955  0.899  21.372
plot_exprs                19.137  0.068  19.088
plot_exprs_per_coef       18.481  0.037  18.389
default_formula           17.473  0.356  17.409
read_somascan             13.124  0.403  13.433
plot_volcano              13.161  0.052  13.161
analyze                   12.850  0.090  12.826
plot_summary              12.300  0.067  12.285
read_metabolon            11.912  0.004  11.812
fit_survival              10.037  0.075  10.115
explore-transforms         9.288  0.024   9.313
plot_densities             9.110  0.057   9.093
fcluster                   8.770  0.074   8.754
ftype                      7.900  0.081   7.538
plot_detections            6.887  0.061   6.901
biplot_covariates          6.458  0.029   6.449
plot_xy_density            6.052  0.007   6.059
read_fragpipe              5.763  0.012   5.474
plot_subgroup_points       5.488  0.061   5.470
subtract_baseline          5.108  0.025   5.043
* 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 re-building of vignette outputs ... OK
* 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

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
137.495   4.162 139.405 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS000
LINMOD23.477 0.39823.125
LINMODENGINES000
MAXQUANT_PATTERNS0.0010.0000.000
TAXON_TO_ORGNAME0.0000.0010.000
TESTS000
X1.1900.0131.182
abstract_fit1.0270.0101.002
add_adjusted_pvalues0.5080.0060.516
add_assay_means0.3240.0150.339
add_facetvars1.3420.0551.375
add_opentargets_by_uniprot0.3490.0080.358
add_psp0.4600.0100.471
add_smiles0.4290.0090.417
all_non_numeric0.5430.0010.544
analysis0.4380.0090.447
analyze12.850 0.09012.826
annotate_maxquant0.8540.0220.876
annotate_uniprot_rest1.2230.1013.723
assert_is_valid_sumexp0.5370.0100.510
awblinmod40.011 0.23638.529
biplot3.5810.0153.557
biplot_corrections3.3820.0243.377
biplot_covariates6.4580.0296.449
block2limma0.0010.0000.001
block2lm0.0020.0000.002
block2lme0.0020.0000.001
block2lmer0.0030.0000.003
block_has_two_levels0.6210.0080.592
center1.7770.0041.777
code4.5250.0724.575
collapsed_entrezg_to_symbol0.8630.0450.909
contrast_subgroup_cols0.5750.0060.545
contrastdt0.5480.0010.549
count_in0.0010.0000.001
counts0.3370.0010.338
counts2cpm0.2940.0000.293
counts2tpm0.2820.0010.282
cpm0.3100.0000.309
create_design0.6770.0060.645
default_formula17.473 0.35617.409
default_geom0.4700.0060.445
default_sfile0.0010.0000.001
demultiplex0.0130.0000.013
densities0.2010.0010.203
dequantify0.0020.0000.002
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.3460.0090.355
dot-merge0.0180.0010.019
dot-read_maxquant_proteingroups0.1090.0020.111
download_data0.0000.0000.001
download_gtf000
download_mcclain210.0010.0000.001
dt2mat0.0030.0000.003
enrichment1.1010.0011.102
entrezg_to_symbol0.1190.0030.121
explore-transforms9.2880.0249.313
extract_contrast_features4.2790.0684.310
extract_rectangle0.1040.0050.109
factor.vars0.1640.0010.165
factorize0.7750.0020.777
fcluster8.7700.0748.754
fcor1.3640.0101.375
fdata0.4720.0000.471
fdr2p0.8810.0070.866
filter_exprs_replicated_in_some_subgroup0.9490.0030.897
filter_features0.4880.0070.474
filter_medoid0.5220.0010.523
filter_samples0.5210.0040.505
fit_survival10.037 0.07510.115
fits0.2760.0010.278
fix_xlgenes0.0010.0000.002
flevels0.3630.0030.366
fnames0.4330.0050.438
formula2str000
ftype7.9000.0817.538
fvalues0.3590.0040.364
fvars0.3550.0020.357
genome_to_orgdb000
group_by_level000
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4510.0020.453
guess_maxquant_quantity0.0050.0000.005
guess_sep0.4370.0110.428
has_multiple_levels0.0500.0000.051
hdlproteins0.0370.0040.043
impute3.1600.0063.166
invert_subgroups0.6150.0020.617
is_character_matrix0.1340.0000.134
is_collapsed_subset0.0010.0000.001
is_compounddiscoverer_output0.0830.0280.181
is_correlation_matrix0.0030.0000.001
is_diann_report0.1670.0070.110
is_fastadt0.0620.0010.059
is_file0.0000.0000.001
is_fraction0.0020.0000.001
is_fragpipe_tsv0.0880.0050.065
is_imputed0.6860.0000.682
is_maxquant_phosphosites0.0810.0030.062
is_maxquant_proteingroups0.0840.0000.059
is_positive_number0.0020.0000.002
is_scalar_subset0.2810.0030.284
is_sig1.3140.0021.316
is_valid_formula0.040.000.04
keep_estimable_features0.7290.0090.691
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.3320.0000.332
log2cpm0.2810.0010.282
log2diffs0.2930.0010.294
log2proteins0.2890.0010.290
log2sites0.3390.0010.340
log2tpm0.2930.0020.295
log2transform4.7700.0064.777
logical2factor0.0020.0000.002
make_alpha_palette0.4820.0090.469
make_colors0.0090.0010.009
make_volcano_dt0.8250.0180.843
map_fvalues0.3520.0000.352
matrix2sumexp0.9720.0090.959
mclust_breaks0.4870.0100.497
merge_sample_file0.4410.0020.443
merge_sdata0.6000.0070.570
message_df0.0030.0000.002
model_coefs0.6940.0040.660
modelvar4.0440.0924.082
object10.4410.0000.441
order_on_p1.1930.0071.178
overall_parameters0.0250.0000.025
pca2.8850.0292.893
pg_to_canonical0.0050.0000.005
plot_coef_densities1.1990.0051.182
plot_contrast_venn2.1060.0142.044
plot_contrastogram2.6330.0102.575
plot_data1.5390.0071.525
plot_densities9.1100.0579.093
plot_design0.6460.0010.647
plot_detections6.8870.0616.901
plot_exprs19.137 0.06819.088
plot_exprs_per_coef18.481 0.03718.389
plot_fit_summary2.0920.0081.989
plot_heatmap1.7730.0041.777
plot_matrix0.4770.0050.445
plot_subgroup_points5.4880.0615.470
plot_summary12.300 0.06712.285
plot_venn0.0160.0000.016
plot_venn_heatmap0.0190.0020.021
plot_violins4.5730.0264.578
plot_volcano13.161 0.05213.161
plot_xy_density6.0520.0076.059
preprocess_rnaseq_counts0.3180.0010.319
pull_columns0.0020.0000.002
pvalues_estimable0.0310.0030.034
read_affymetrix000
read_diann_proteingroups95.104 0.94391.542
read_fragpipe5.7630.0125.474
read_maxquant_phosphosites2.4330.0032.436
read_maxquant_proteingroups1.1240.0051.129
read_metabolon11.912 0.00411.812
read_msigdt0.0000.0010.000
read_olink1.3420.0081.257
read_rectangles0.1680.0010.169
read_rnaseq_counts29.013 2.63331.463
read_salmon000
read_somascan13.124 0.40313.433
read_uniprotdt0.2770.0080.285
reset_fit4.7260.1324.739
rm_diann_contaminants21.955 0.89921.372
rm_missing_in_some_samples0.5110.0080.491
rm_unmatched_samples0.6740.0090.683
sbind4.2440.0274.272
scaledlibsizes0.320.000.32
scoremat0.8870.0050.859
slevels0.3950.0020.397
snames0.3800.0050.385
split_extract_fixed0.5810.0060.549
split_samples1.2600.0051.225
stepauc0.3240.0000.324
stri_any_regex000
stri_detect_fixed_in_collapsed0.3410.0010.342
subgroup_matrix0.6010.0130.572
subtract_baseline5.1080.0255.043
sumexp_to_longdt1.9680.0291.900
sumexp_to_tsv0.4660.0010.468
sumexplist_to_longdt1.5100.0541.564
summarize_fit1.8500.0181.742
survobj0.1360.0000.137
svalues0.3810.0010.382
svars0.4700.0440.514
systematic_nas0.5530.0130.566
tag_features1.2290.0191.249
tag_hdlproteins0.5360.0060.541
taxon2org0.0010.0000.001
tpm0.3110.0010.312
uncollapse0.0290.0000.029
values0.5200.0350.555
varlevels_dont_clash0.0250.0010.026
venn_detects0.5380.0060.544
weights0.3180.0040.321
write_xl159.232 1.856161.071
zero_to_na0.0000.0010.002