Back to Multiple platform build/check report for BioC 3.22:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-18 12:04 -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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.17.16.tar.gz
StartedAt: 2025-10-17 20:16:51 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 20:42:02 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 1511.0 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.17.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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                  173.515 11.247 254.738
read_diann_proteingroups  117.651  3.850 127.954
awblinmod                  48.420  0.295  49.007
read_rnaseq_counts         35.969  3.792  40.909
rm_diann_contaminants      26.818  0.529  27.660
LINMOD                     25.764  0.346  26.268
plot_exprs                 22.498  0.233  23.033
plot_exprs_per_coef        22.014  0.198  22.376
default_formula            19.758  0.630  20.568
read_somascan              16.105  0.148  16.420
plot_volcano               16.057  0.166  16.306
read_metabolon             15.582  0.190  15.967
analyze                    15.224  0.234  15.575
plot_summary               14.878  0.118  15.063
fit_survival               13.114  0.122  13.316
explore-transforms         12.992  0.124  13.211
fcluster                   11.952  0.098  12.142
plot_densities             10.391  0.418  12.357
ftype                       9.283  0.302   9.675
read_fragpipe               8.335  0.205   8.651
biplot_covariates           8.282  0.080   8.413
plot_xy_density             7.978  0.066   8.100
plot_detections             7.944  0.060   8.077
plot_subgroup_points        6.542  0.145   6.935
subtract_baseline           6.239  0.146   6.462
code                        5.740  0.092   5.971
plot_violins                5.609  0.117   5.769
reset_fit                   5.414  0.152   5.657
extract_contrast_features   5.341  0.101   5.485
log2transform               5.214  0.045   5.286
sbind                       5.010  0.102   5.244
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
139.173  19.606 272.143 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.001
COMPOUNDDISCOVERER_PATTERNS0.0000.0010.001
LINMOD25.764 0.34626.268
LINMODENGINES000
MAXQUANT_PATTERNS0.0000.0000.001
TAXON_TO_ORGNAME0.0000.0000.001
TESTS0.0000.0010.001
X1.3050.0471.359
abstract_fit1.1440.0511.203
add_adjusted_pvalues0.5650.0130.582
add_assay_means0.3510.0070.359
add_facetvars1.4490.0491.503
add_opentargets_by_uniprot0.4210.0070.432
add_psp0.5570.0140.574
add_smiles0.5250.0540.601
all_non_numeric0.7270.0050.736
analysis0.4200.0070.428
analyze15.224 0.23415.575
annotate_maxquant1.0270.1081.146
annotate_uniprot_rest0.0810.0122.073
assert_is_valid_sumexp0.7500.0490.810
awblinmod48.420 0.29549.007
biplot4.4430.0744.556
biplot_corrections4.2380.0634.338
biplot_covariates8.2820.0808.413
block2limma0.0020.0000.003
block2lm0.0030.0000.004
block2lme0.0030.0000.003
block2lmer0.0040.0010.005
block_has_two_levels0.7530.0460.804
center2.3020.0322.356
code5.7400.0925.971
collapsed_entrezg_to_symbol1.1040.0981.222
contrast_subgroup_cols0.7920.0570.861
contrastdt0.7310.0110.748
count_in0.0010.0010.002
counts0.3950.0050.405
counts2cpm0.4220.0060.430
counts2tpm0.3580.0050.381
cpm0.4480.0060.461
create_design0.8420.0510.900
default_formula19.758 0.63020.568
default_geom0.5210.0420.568
default_sfile0.0010.0000.002
demultiplex0.0150.0010.016
densities0.2600.0070.270
dequantify0.0030.0010.004
dequantify_compounddiscoverer0.0010.0000.002
dot-coxph0.4540.0570.533
dot-merge0.0260.0010.027
dot-read_maxquant_proteingroups0.1180.0060.124
download_data0.0000.0000.001
download_gtf000
download_mcclain210.0000.0010.001
dt2mat0.0030.0010.004
enrichment1.3830.0171.408
entrezg_to_symbol0.2050.0060.211
explore-transforms12.992 0.12413.211
extract_contrast_features5.3410.1015.485
extract_rectangle0.1530.0460.205
factor.vars0.1950.0010.196
factorize0.9540.0170.981
fcluster11.952 0.09812.142
fcor2.0000.0422.063
fdata0.6400.0170.662
fdr2p1.1090.0531.172
filter_exprs_replicated_in_some_subgroup1.0390.0501.100
filter_features0.6360.0410.682
filter_medoid0.6510.0050.659
filter_samples0.5860.0440.635
fit_survival13.114 0.12213.316
fits1.3920.0111.409
fix_xlgenes0.0020.0010.002
flevels0.4700.0070.479
fnames0.5760.0090.590
formula2str0.0010.0000.001
ftype9.2830.3029.675
fvalues0.4610.0070.470
fvars0.4500.0090.462
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0010.002
guess_compounddiscoverer_quantity0.0010.0010.002
guess_fitsep0.5070.0070.517
guess_maxquant_quantity0.0050.0020.007
guess_sep0.5740.0420.620
has_multiple_levels0.0620.0030.066
hdlproteins0.0490.0370.097
impute3.6810.0363.737
invert_subgroups0.7380.0080.749
is_character_matrix0.1600.0010.161
is_collapsed_subset000
is_compounddiscoverer_output0.0490.0330.165
is_correlation_matrix0.0010.0010.001
is_diann_report0.0900.0140.105
is_fastadt0.0650.0010.067
is_file0.0010.0000.000
is_fraction0.0010.0010.002
is_fragpipe_tsv0.0560.0080.065
is_imputed0.7280.0070.738
is_maxquant_phosphosites0.0530.0070.061
is_maxquant_proteingroups0.0540.0070.063
is_positive_number0.0020.0000.002
is_scalar_subset0.3340.0050.338
is_sig1.4650.0131.484
is_valid_formula0.0530.0010.054
keep_estimable_features0.8340.0440.886
label2index0.0010.0000.001
list2mat0.0000.0010.001
log2counts0.3340.0030.339
log2cpm0.3470.0030.351
log2diffs0.3720.0070.381
log2proteins0.3420.0060.348
log2sites0.3490.0050.357
log2tpm0.3580.0030.363
log2transform5.2140.0455.286
logical2factor0.0020.0000.003
make_alpha_palette0.5510.0460.603
make_colors0.0100.0010.011
make_volcano_dt0.9530.0120.971
map_fvalues0.4180.0110.432
matrix2sumexp1.1620.0551.241
mclust_breaks0.5680.0970.670
merge_sample_file0.7050.0490.761
merge_sdata0.5940.0660.670
message_df0.0030.0000.003
model_coefs0.7750.0450.825
modelvar3.4930.0753.602
object10.5990.0050.607
order_on_p1.4940.0631.578
overall_parameters0.0230.0000.024
pca3.9930.0744.096
pg_to_canonical0.0070.0010.008
plot_coef_densities1.5630.0571.637
plot_contrast_venn2.6360.0632.723
plot_contrastogram3.1330.1253.289
plot_data1.4330.0751.984
plot_densities10.391 0.41812.357
plot_design0.7270.0110.770
plot_detections7.9440.0608.077
plot_exprs22.498 0.23323.033
plot_exprs_per_coef22.014 0.19822.376
plot_fit_summary2.3550.0622.568
plot_heatmap1.6390.0212.185
plot_matrix0.5650.1010.965
plot_subgroup_points6.5420.1456.935
plot_summary14.878 0.11815.063
plot_venn0.0190.0020.021
plot_venn_heatmap0.0270.0020.029
plot_violins5.6090.1175.769
plot_volcano16.057 0.16616.306
plot_xy_density7.9780.0668.100
preprocess_rnaseq_counts0.3960.0050.404
pull_columns0.0030.0000.004
pvalues_estimable0.0510.0060.056
read_affymetrix0.0010.0000.000
read_diann_proteingroups117.651 3.850127.954
read_fragpipe8.3350.2058.651
read_maxquant_phosphosites1.8130.0471.884
read_maxquant_proteingroups1.5360.0321.587
read_metabolon15.582 0.19015.967
read_msigdt0.0010.0010.002
read_olink1.5760.0801.714
read_rectangles0.2440.0300.287
read_rnaseq_counts35.969 3.79240.909
read_salmon0.0000.0010.001
read_somascan16.105 0.14816.420
read_uniprotdt0.3660.0530.433
reset_fit5.4140.1525.657
rm_diann_contaminants26.818 0.52927.660
rm_missing_in_some_samples0.5980.0730.699
rm_unmatched_samples0.8350.0360.886
sbind5.0100.1025.244
scaledlibsizes0.3540.0060.367
scoremat0.9790.0591.056
slevels0.4590.0130.482
snames0.4580.0110.476
split_extract_fixed0.6420.0580.718
split_samples1.4520.0631.533
stepauc0.3790.0070.392
stri_any_regex0.0000.0010.001
stri_detect_fixed_in_collapsed0.3800.0080.393
subgroup_matrix0.6710.0520.738
subtract_baseline6.2390.1466.462
sumexp_to_longdt2.3160.1852.657
sumexp_to_tsv0.6000.0130.617
sumexplist_to_longdt2.0000.0352.076
summarize_fit2.2200.0782.331
survobj0.1950.0020.202
svalues0.5230.0130.551
svars0.5190.0110.544
systematic_nas0.7920.0130.821
tag_features1.4490.0691.576
tag_hdlproteins0.7760.0450.836
taxon2org0.0010.0010.002
tpm0.4270.0080.441
uncollapse0.0390.0040.049
values0.5560.0160.586
varlevels_dont_clash0.0280.0020.032
venn_detects0.8290.0200.866
weights0.4340.0070.445
write_xl173.515 11.247254.738
zero_to_na0.0020.0060.065