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This page was generated on 2025-09-29 12:07 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4833
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4621
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4566
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 116/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.2  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: b9e7bf3
git_last_commit_date: 2025-09-25 03:15:20 -0400 (Thu, 25 Sep 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: 1.17.2
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_1.17.2.tar.gz
StartedAt: 2025-09-26 04:48:13 -0000 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 05:08:04 -0000 (Fri, 26 Sep 2025)
EllapsedTime: 1191.7 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_1.17.2.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 ‘1.17.2’
* 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
awblinmod                 61.011  0.391  61.520
read_rnaseq_counts        43.001  1.909  45.173
read_diann_proteingroups  36.574  0.407  36.764
LINMOD                    34.244  0.463  34.788
plot_exprs                31.910  0.236  32.250
plot_exprs_per_coef       28.877  0.091  29.066
default_formula           26.201  0.354  26.477
read_somascan             20.921  0.363  21.346
analyze                   20.770  0.212  21.032
read_metabolon            19.660  0.088  19.811
plot_volcano              19.484  0.071  19.618
plot_summary              19.402  0.080  19.539
fit_survival              15.721  0.091  15.871
plot_densities            15.439  0.080  15.565
explore-transforms        14.342  0.036  14.420
fcluster                  13.115  0.024  13.168
ftype                     12.179  0.076  12.256
plot_detections           11.370  0.040  11.447
rm_diann_contaminants     10.183  0.255  10.341
biplot_covariates         10.040  0.036  10.103
plot_xy_density            9.233  0.020   9.286
read_fragpipe              8.809  0.032   8.698
plot_subgroup_points       8.142  0.036   8.200
plot_violins               7.221  0.092   7.335
subtract_baseline          7.168  0.108   7.288
log2transform              7.085  0.012   7.120
reset_fit                  7.035  0.044   7.097
code                       6.684  0.016   6.716
extract_contrast_features  6.290  0.012   6.316
sbind                      6.049  0.028   6.092
biplot                     5.491  0.075   5.580
modelvar                   5.089  0.004   5.105
biplot_corrections         5.041  0.008   5.061
* 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 ‘1.17.2’
** 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 
192.757   2.546 194.758 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
LINMOD34.244 0.46334.788
LINMODENGINES0.0000.0000.001
MAXQUANT_PATTERNS000
TAXON_TO_ORGNAME0.0010.0000.000
TESTS000
X1.8020.0361.841
abstract_fit1.5080.0081.517
add_adjusted_pvalues0.7820.0440.833
add_assay_means0.5510.0040.556
add_facetvars2.0370.0082.048
add_opentargets_by_uniprot0.5910.0000.603
add_psp0.7490.0030.757
add_smiles0.6480.0080.655
all_non_numeric0.8550.0040.862
analysis0.5480.0040.553
analyze20.770 0.21221.032
annotate_maxquant1.2090.0201.236
annotate_uniprot_rest0.1140.0004.583
assert_is_valid_sumexp0.9370.0040.941
awblinmod61.011 0.39161.520
biplot5.4910.0755.580
biplot_corrections5.0410.0085.061
biplot_covariates10.040 0.03610.103
block2limma0.0020.0000.002
block2lm0.0030.0000.004
block2lme0.0030.0000.003
block2lmer0.0050.0000.005
block_has_two_levels0.9030.0120.913
center2.6460.0202.674
code6.6840.0166.716
collapsed_entrezg_to_symbol1.1940.0441.242
contrast_subgroup_cols0.8680.0080.875
contrastdt0.4710.0000.473
count_in0.0020.0000.002
counts0.4830.0040.490
counts2cpm0.5180.0000.519
counts2tpm0.4230.0000.425
cpm0.4960.0040.502
create_design0.9880.0321.020
default_formula26.201 0.35426.477
default_geom0.6350.0120.646
default_sfile0.0010.0000.001
demultiplex0.0190.0000.020
densities0.3340.0040.340
dequantify0.0030.0000.003
dequantify_compounddiscoverer0.0020.0000.002
dot-coxph0.4840.0120.498
dot-merge0.0290.0000.029
dot-read_maxquant_proteingroups0.1330.0040.138
download_data0.0000.0000.001
download_gtf000
download_mcclain21000
dt2mat0.0010.0020.005
enrichment1.5760.0161.599
entrezg_to_symbol0.1790.0000.179
explore-transforms14.342 0.03614.420
extract_contrast_features6.2900.0126.316
extract_rectangle0.1400.0080.147
factor.vars0.2640.0000.265
factorize1.0800.0041.089
fcluster13.115 0.02413.168
fcor2.0110.0202.035
fdata0.7260.0000.732
fdr2p1.2830.0161.299
filter_exprs_replicated_in_some_subgroup1.3790.0041.381
filter_features0.6990.0160.715
filter_medoid0.9030.0040.911
filter_samples0.6690.0160.684
fit_survival15.721 0.09115.871
fits0.4800.0040.486
fix_xlgenes0.0020.0000.003
flevels0.5420.0000.544
fnames0.6720.0000.674
formula2str0.0010.0000.001
ftype12.179 0.07612.256
fvalues0.5690.0000.571
fvars0.5190.0040.525
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.6220.0000.625
guess_maxquant_quantity0.0070.0000.007
guess_sep0.6950.0280.722
has_multiple_levels0.0780.0000.077
hdlproteins0.0490.0040.066
impute4.9440.0164.978
invert_subgroups1.0040.0041.011
is_character_matrix0.2430.0000.244
is_collapsed_subset0.0000.0000.001
is_correlation_matrix0.0020.0000.002
is_diann_report0.3110.0200.312
is_fastadt0.0940.0000.094
is_file000
is_fraction0.0020.0000.002
is_imputed1.0410.0001.044
is_positive_number0.0020.0000.002
is_scalar_subset0.5220.0040.527
is_sig2.0690.0082.083
is_valid_formula0.0710.0000.071
keep_estimable_features1.1150.0161.129
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.4600.0000.461
log2cpm0.5400.0000.542
log2diffs0.4470.0080.456
log2proteins0.4420.0000.443
log2sites0.4510.0000.453
log2tpm0.4870.0000.488
log2transform7.0850.0127.120
logical2factor0.0010.0000.002
make_alpha_palette0.7650.0120.776
make_colors0.0110.0000.011
make_volcano_dt1.1880.0041.196
map_fvalues0.5670.0000.568
matrix2sumexp1.5020.0081.512
mclust_breaks0.8060.0280.837
merge_sample_file0.7090.0110.724
merge_sdata0.7870.0120.799
message_df0.0030.0000.003
model_coefs1.0910.0121.103
modelvar5.0890.0045.105
object10.7510.0000.754
order_on_p2.0710.0442.122
overall_parameters0.0370.0040.041
pca4.9630.0245.000
pg_to_canonical0.010.000.01
plot_coef_densities2.0450.0082.059
plot_contrast_venn3.5040.0443.551
plot_contrastogram4.2890.0364.352
plot_data2.5310.0162.555
plot_densities15.439 0.08015.565
plot_design1.1200.0071.132
plot_detections11.370 0.04011.447
plot_exprs31.910 0.23632.250
plot_exprs_per_coef28.877 0.09129.066
plot_fit_summary3.1050.0113.121
plot_heatmap2.6230.0322.663
plot_matrix0.6960.0040.699
plot_subgroup_points8.1420.0368.200
plot_summary19.402 0.08019.539
plot_venn0.0190.0000.019
plot_venn_heatmap0.0310.0000.030
plot_violins7.2210.0927.335
plot_volcano19.484 0.07119.618
plot_xy_density9.2330.0209.286
preprocess_rnaseq_counts0.5090.0000.511
pull_columns0.0030.0000.003
pvalues_estimable0.0540.0000.054
read_affymetrix000
read_diann_proteingroups36.574 0.40736.764
read_fragpipe8.8090.0328.698
read_maxquant_phosphosites2.1780.0042.188
read_maxquant_proteingroups1.8020.0031.811
read_metabolon19.660 0.08819.811
read_msigdt0.0010.0000.002
read_olink1.9390.0241.953
read_rectangles0.2370.0040.242
read_rnaseq_counts43.001 1.90945.173
read_salmon000
read_somascan20.921 0.36321.346
read_uniprotdt0.3860.0200.408
reset_fit7.0350.0447.097
rm_diann_contaminants10.183 0.25510.341
rm_missing_in_some_samples0.7110.0160.727
rm_unmatched_samples0.9580.0160.977
sbind6.0490.0286.092
scaledlibsizes0.4550.0000.457
scoremat1.2230.0361.260
slevels0.5660.0040.572
snames0.6210.0040.627
split_extract_fixed0.7280.0240.751
split_samples1.7310.0311.766
stepauc0.4930.0280.522
stri_any_regex0.0000.0000.001
stri_detect_fixed_in_collapsed0.5240.0240.549
subgroup_matrix0.8170.0200.837
subtract_baseline7.1680.1087.288
sumexp_to_longdt2.6420.0322.673
sumexp_to_tsv0.7330.0280.763
sumexplist_to_longdt2.0850.0482.139
summarize_fit2.3930.0162.410
survobj0.2160.0000.217
svalues0.5890.0080.600
svars0.6520.0040.658
systematic_nas0.8070.0040.813
tag_features1.4750.0191.499
tag_hdlproteins0.7610.0120.775
taxon2org0.0020.0000.001
tpm0.4940.0000.495
uncollapse0.0450.0000.044
values0.7150.0160.732
varlevels_dont_clash0.0320.0040.036
venn_detects0.8070.0120.821
weights0.5420.0040.548
write_xl1.0920.0121.104
zero_to_na0.0020.0000.002