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This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1.16.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_21
git_last_commit: a47f4df
git_last_commit_date: 2025-04-15 12:21:58 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for autonomics on kjohnson1

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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2025-08-01 12:22:23 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 12:38:04 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 941.3 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 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
read_diann_proteingroups 97.389  2.211  96.532
read_rnaseq_counts       31.976  1.222  33.848
fit_linmod               30.167  0.272  30.572
plot_exprs_per_coef      22.729  0.166  23.209
rm_diann_contaminants    21.043  0.487  20.296
plot_exprs               21.305  0.163  21.781
default_formula          16.720  0.532  16.851
plot_summary             14.390  0.111  14.666
read_metabolon           13.865  0.112  14.437
read_somascan            13.518  0.069  13.886
analyze                  13.167  0.141  13.445
plot_volcano             11.739  0.115  11.898
ftype                     8.893  0.478   9.383
plot_densities            8.461  0.203   8.775
read_fragpipe             7.831  0.184   8.164
fcluster                  6.454  0.064   6.540
extract_coef_features     6.362  0.092   6.461
plot_sample_nas           5.767  0.048   6.068
fit_survival              5.253  0.053   5.315
code                      5.136  0.083   5.229
biplot_covariates         5.082  0.063   5.150
* 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-3.21-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-arm64/Resources/library’
* installing *source* package ‘autonomics’ ...
** this is package ‘autonomics’ version ‘1.16.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 2 | SKIP 0 | PASS 158 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 158 ]
> 
> proc.time()
   user  system elapsed 
160.991   9.137 168.533 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.001
COMPOUNDDISCOVERER_PATTERNS0.0000.0000.001
FITSEP0.0010.0000.000
LINMODENGINES0.0000.0000.001
MAXQUANT_PATTERNS0.0010.0000.001
SURVIVALENGINES0.0000.0000.001
TAXON_TO_ORGNAME0.0010.0010.001
TESTS000
X2.4280.1082.544
abstract_fit1.5800.0951.676
add_adjusted_pvalues0.5530.0160.572
add_assay_means0.3450.0090.355
add_facetvars1.4000.0561.458
add_opentargets_by_uniprot0.3760.0090.387
add_psp0.5240.0170.542
add_smiles0.4520.0460.501
analysis0.4510.0410.509
analyze13.167 0.14113.445
annotate_maxquant1.1450.0711.263
annotate_uniprot_rest0.0990.0190.795
assert_is_valid_sumexp1.6200.0501.671
bin0.3610.0080.369
biplot4.2530.0814.338
biplot_corrections3.0590.0593.155
biplot_covariates5.0820.0635.150
block2lme0.0040.0010.004
center1.4180.0221.443
code5.1360.0835.229
coefs0.7950.0450.840
collapsed_entrezg_to_symbol0.0000.0010.001
contrast_subgroup_cols0.5350.0500.618
count_in0.0010.0010.002
counts0.3770.0030.381
counts2cpm0.3060.0030.308
counts2tpm0.3160.0040.320
cpm0.2960.0020.298
create_design0.6720.0450.719
default_formula16.720 0.53216.851
default_geom0.4980.0440.543
default_sfile0.0020.0010.003
demultiplex0.0110.0010.012
dequantify0.0020.0010.003
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.4690.0290.500
dot-merge0.0220.0010.023
dot-read_maxquant_proteingroups0.1430.0040.147
download_data0.0000.0010.001
download_gtf000
download_mcclain210.0010.0000.002
dt2mat0.0040.0000.004
enrichment1.7560.0141.786
entrezg_to_symbol0.0010.0000.001
extract_coef_features6.3620.0926.461
extract_rectangle0.1530.0410.194
fcluster6.4540.0646.540
fcor1.1340.0321.171
fdata0.4870.0120.500
fdr2p0.9730.0431.018
filter_exprs_replicated_in_some_subgroup0.9750.0461.023
filter_features0.5410.0420.584
filter_medoid0.7050.0150.720
filter_samples0.5360.0420.580
fit_linmod30.167 0.27230.572
fit_survival5.2530.0535.315
fitcoefs0.9030.0500.985
fits0.8000.0430.844
fix_xlgenes0.0020.0000.002
flevels0.3950.0060.402
fnames0.5460.0060.553
formula2str000
ftype8.8930.4789.383
fvalues0.3840.0120.396
fvars0.4100.0080.418
genome_to_orgdb0.0000.0010.001
group_by_level0.0020.0010.001
guess_compounddiscoverer_quantity0.0010.0000.002
guess_fitsep0.4560.0060.463
guess_maxquant_quantity0.0050.0010.007
guess_sep0.4720.0410.513
has_multiple_levels0.0580.0020.060
hdlproteins0.0620.0350.099
impute2.9500.0422.995
invert_subgroups0.6370.0180.657
is_collapsed_subset0.0010.0000.001
is_correlation_matrix0.0020.0000.002
is_diann_report0.4210.0510.444
is_fastadt0.0560.0010.056
is_file0.0010.0000.001
is_fraction0.0020.0010.001
is_imputed0.7300.0090.739
is_positive_number0.0010.0010.002
is_scalar_subset0.3150.0050.320
is_sig1.7010.0141.722
is_valid_formula0.0520.0010.053
keep_connected_blocks0.5400.0450.592
keep_connected_features0.6760.0450.731
keep_replicated_features0.8170.0490.873
label2index000
list2mat0.0000.0010.001
log2counts0.3270.0030.331
log2cpm0.3260.0030.333
log2diffs0.3820.0080.392
log2proteins0.3350.0060.344
log2sites0.3210.0060.330
log2tpm0.3080.0030.314
log2transform3.8650.0573.962
logical2factor0.0010.0010.003
make_alpha_palette0.5200.0440.568
make_colors0.0140.0010.015
make_volcano_dt0.9080.0110.925
map_fvalues0.4030.0070.413
matrix2sumexp0.9670.0461.021
merge_sample_file0.4540.0100.465
merge_sdata0.5720.0510.630
message_df0.0020.0000.003
model_coefs0.7670.0450.840
modelvar3.5610.0653.658
order_on_p1.2620.0481.326
pca2.8670.0642.957
pg_to_canonical0.0050.0000.007
plot_coef_densities1.3750.0751.457
plot_contrast_venn2.4840.0762.588
plot_contrastogram2.9250.1263.100
plot_data1.2540.0531.317
plot_densities8.4610.2038.775
plot_design0.6010.0080.621
plot_exprs21.305 0.16321.781
plot_exprs_per_coef22.729 0.16623.209
plot_fit_summary2.0430.0572.146
plot_heatmap2.1450.0132.177
plot_joint_density2.9870.0783.099
plot_matrix0.5540.0480.608
plot_sample_nas5.7670.0486.068
plot_subgroup_points4.6850.0734.815
plot_summary14.390 0.11114.666
plot_survival3.6660.0333.727
plot_venn0.0050.0010.006
plot_venn_heatmap0.0260.0010.028
plot_violins3.9960.0834.111
plot_volcano11.739 0.11511.898
preprocess_rnaseq_counts0.5010.0120.516
pull_columns0.0040.0010.004
read_affymetrix000
read_diann_proteingroups97.389 2.21196.532
read_fragpipe7.8310.1848.164
read_maxquant_phosphosites1.5540.0391.680
read_maxquant_proteingroups1.1820.0291.251
read_metabolon13.865 0.11214.437
read_msigdt0.0000.0000.001
read_olink1.4430.0631.511
read_rectangles0.2110.0240.237
read_rnaseq_counts31.976 1.22233.848
read_salmon0.0000.0000.001
read_somascan13.518 0.06913.886
read_uniprotdt0.3290.0230.362
reset_fit4.8620.0744.997
rm_diann_contaminants21.043 0.48720.296
rm_missing_in_some_samples0.4640.0470.525
rm_unmatched_samples0.5870.0070.594
scaledlibsizes0.3020.0030.305
scoremat0.9380.0440.985
slevels0.3840.0070.391
snames0.3840.0050.389
split_extract_fixed0.5160.0410.565
split_samples1.0470.0441.105
stri_any_regex0.0010.0000.001
stri_detect_fixed_in_collapsed0.3760.0050.381
subgroup_matrix0.4910.0400.534
subtract_baseline4.1690.0634.266
sumexp_to_longdt1.8750.1362.035
sumexp_to_tsv0.4880.0130.508
sumexplist_to_longdt1.5580.0211.589
summarize_fit1.3400.0491.481
svalues0.2660.0050.275
svars0.3600.0060.366
systematic_nas0.5660.0070.574
tag_features1.0480.0271.082
tag_hdlproteins0.6110.0290.669
taxon2org0.0010.0010.001
tpm0.3020.0030.305
uncollapse0.0300.0020.032
values0.4070.0060.414
varlevels_dont_clash0.0220.0010.023
venn_detects0.5870.0080.596
weights0.2990.0020.301
write_xl0.6360.0440.683
zero_to_na0.0010.0000.002