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This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 116/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: f051989
git_last_commit_date: 2025-04-15 12:21:58 -0400 (Tue, 15 Apr 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 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: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2025-08-31 20:22:49 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 20:38:32 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 942.1 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.17.0’
* 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 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
read_diann_proteingroups 90.410  0.858  86.700
read_rnaseq_counts       31.777  1.504  32.974
fit_linmod               30.059  0.081  29.351
plot_exprs_per_coef      22.486  0.126  22.511
plot_exprs               21.353  0.032  21.233
rm_diann_contaminants    18.530  0.214  17.455
default_formula          16.004  0.307  15.915
read_somascan            14.200  0.106  14.202
analyze                  14.097  0.174  14.110
read_metabolon           13.970  0.011  13.804
plot_summary             13.745  0.030  13.666
plot_volcano             11.586  0.015  11.512
ftype                     8.704  0.126   8.295
plot_densities            7.816  0.027   7.737
reset_fit                 6.437  0.116   6.395
extract_coef_features     6.348  0.059   6.386
fcluster                  5.951  0.020   5.914
plot_sample_nas           5.757  0.010   5.719
read_fragpipe             5.642  0.014   5.384
code                      4.988  0.048   5.004
* 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 ‘1.17.0’
** 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 (2025-06-13) -- "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 2 | SKIP 0 | PASS 158 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 158 ]
> 
> proc.time()
   user  system elapsed 
153.786   4.409 150.915 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS000
FITSEP0.0010.0000.000
LINMODENGINES000
MAXQUANT_PATTERNS000
SURVIVALENGINES0.0000.0000.001
TAXON_TO_ORGNAME000
TESTS000
X2.2230.0782.268
abstract_fit1.5980.0501.624
add_adjusted_pvalues0.5470.0040.553
add_assay_means0.3260.0310.357
add_facetvars1.4630.0111.451
add_opentargets_by_uniprot0.3560.0040.361
add_psp0.4760.0070.485
add_smiles0.4330.0330.430
analysis0.4070.0310.438
analyze14.097 0.17414.110
annotate_maxquant0.9600.0240.985
annotate_uniprot_rest0.3380.0272.029
assert_is_valid_sumexp0.5150.0300.523
bin1.1070.0621.169
biplot4.2020.2364.412
biplot_corrections2.9610.0963.010
biplot_covariates4.7570.1144.850
block2lme0.0020.0000.003
center1.3240.0111.335
code4.9880.0485.004
coefs0.7510.0090.738
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.5300.0060.515
count_in0.0010.0000.001
counts0.3310.0380.363
counts2cpm0.2930.0220.309
counts2tpm0.2670.0060.267
cpm0.3010.0010.295
create_design0.6430.0080.629
default_formula16.004 0.30715.915
default_geom0.5020.0050.486
default_sfile0.0010.0000.002
demultiplex0.0150.0000.015
dequantify0.0020.0000.002
dequantify_compounddiscoverer0.0010.0000.001
dot-coxph0.3700.0100.379
dot-merge0.0160.0000.016
dot-read_maxquant_proteingroups0.1100.0100.121
download_data000
download_gtf000
download_mcclain21000
dt2mat0.0020.0010.003
enrichment1.7850.0071.792
entrezg_to_symbol0.0000.0010.000
extract_coef_features6.3480.0596.386
extract_rectangle0.1000.0070.107
fcluster5.9510.0205.914
fcor0.9770.0030.980
fdata0.5400.0030.543
fdr2p0.8910.0100.879
filter_exprs_replicated_in_some_subgroup1.0310.0050.913
filter_features0.4860.0060.454
filter_medoid0.6560.0050.646
filter_samples0.5190.0080.489
fit_linmod30.059 0.08129.351
fit_survival4.8980.0564.943
fitcoefs0.9360.0090.907
fits0.7230.0050.707
fix_xlgenes0.0020.0000.002
flevels0.3740.0020.376
fnames0.4730.0030.476
formula2str000
ftype8.7040.1268.295
fvalues0.3710.0040.375
fvars0.3740.0150.389
genome_to_orgdb000
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4420.0040.446
guess_maxquant_quantity0.0050.0000.005
guess_sep0.4500.0070.435
has_multiple_levels0.0490.0000.049
hdlproteins0.0360.0140.054
impute2.7000.0112.711
invert_subgroups0.5830.0010.585
is_collapsed_subset000
is_correlation_matrix0.0010.0000.001
is_diann_report0.4100.0390.422
is_fastadt0.0560.0010.057
is_file0.0000.0000.001
is_fraction0.0010.0000.001
is_imputed0.6590.0030.661
is_positive_number0.0000.0010.001
is_scalar_subset0.2890.0010.290
is_sig1.5840.0051.589
is_valid_formula0.0410.0010.042
keep_connected_blocks0.4810.0110.466
keep_connected_features0.6340.0090.602
keep_replicated_features0.7890.0090.738
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.2900.0000.285
log2cpm0.2940.0000.289
log2diffs0.2890.0070.296
log2proteins0.2760.0110.286
log2sites0.3000.0000.299
log2tpm0.2790.0010.274
log2transform3.3770.0303.408
logical2factor0.0020.0000.001
make_alpha_palette0.5050.0070.482
make_colors0.0080.0010.009
make_volcano_dt0.8010.0020.803
map_fvalues0.3690.0020.372
matrix2sumexp0.8510.0080.820
merge_sample_file0.4140.0030.417
merge_sdata0.5330.0110.506
message_df0.0020.0000.002
model_coefs0.7080.0060.675
modelvar3.5600.0113.481
order_on_p1.1880.0051.154
pca2.6830.0082.654
pg_to_canonical0.0050.0000.005
plot_coef_densities1.1930.0141.174
plot_contrast_venn2.4160.0082.273
plot_contrastogram2.7780.0302.650
plot_data1.1690.0141.154
plot_densities7.8160.0277.737
plot_design0.6220.0010.624
plot_exprs21.353 0.03221.233
plot_exprs_per_coef22.486 0.12622.511
plot_fit_summary1.9220.0101.852
plot_heatmap2.1060.0032.109
plot_joint_density2.6380.0312.646
plot_matrix0.4580.0140.448
plot_sample_nas5.7570.0105.719
plot_subgroup_points4.3130.0084.280
plot_summary13.745 0.03013.666
plot_survival3.3060.0063.284
plot_venn0.0040.0000.004
plot_venn_heatmap0.0180.0010.019
plot_violins3.6720.0163.668
plot_volcano11.586 0.01511.512
preprocess_rnaseq_counts0.2710.0020.258
pull_columns0.0020.0000.002
read_affymetrix000
read_diann_proteingroups90.410 0.85886.700
read_fragpipe5.6420.0145.384
read_maxquant_phosphosites1.3920.0061.398
read_maxquant_proteingroups1.1340.0081.142
read_metabolon13.970 0.01113.804
read_msigdt0.0010.0000.001
read_olink1.2750.0061.194
read_rectangles0.1640.0010.164
read_rnaseq_counts31.777 1.50432.974
read_salmon000
read_somascan14.200 0.10614.202
read_uniprotdt0.3470.0100.356
reset_fit6.4370.1166.395
rm_diann_contaminants18.530 0.21417.455
rm_missing_in_some_samples0.4600.0220.459
rm_unmatched_samples0.6040.0090.614
scaledlibsizes0.2670.0020.263
scoremat0.9220.0070.907
slevels0.3500.0020.353
snames0.3580.0030.361
split_extract_fixed0.6210.0040.603
split_samples1.0950.0081.082
stri_any_regex0.0010.0000.001
stri_detect_fixed_in_collapsed0.2990.0020.301
subgroup_matrix0.4860.0030.453
subtract_baseline4.0650.0364.033
sumexp_to_longdt1.6910.0521.687
sumexp_to_tsv0.4860.0030.490
sumexplist_to_longdt1.3500.0081.352
summarize_fit1.5570.0071.499
svalues0.3550.0010.356
svars0.3460.0020.349
systematic_nas0.5220.0010.522
tag_features0.8830.0120.895
tag_hdlproteins0.5200.0010.521
taxon2org0.0010.0000.001
tpm0.2830.0000.269
uncollapse0.0250.0010.026
values0.3680.0030.372
varlevels_dont_clash0.0160.0000.017
venn_detects0.5280.0240.553
weights0.2890.0130.291
write_xl0.6810.0380.682
zero_to_na0.0010.0000.002