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This page was generated on 2025-08-08 12:05 -0400 (Fri, 08 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 116/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2025-08-07 20:10:08 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 20:26:01 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 953.0 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_1.17.0.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 24.04.2 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 93.007  0.725  89.020
read_rnaseq_counts       31.790  2.232  33.805
fit_linmod               30.713  0.071  30.108
plot_exprs_per_coef      22.175  0.105  22.117
plot_exprs               21.444  0.076  21.417
rm_diann_contaminants    19.454  0.463  18.547
default_formula          16.730  0.394  16.673
read_somascan            14.701  0.358  15.003
analyze                  14.343  0.181  14.376
read_metabolon           14.104  0.015  13.986
plot_summary             13.757  0.011  13.633
plot_volcano             11.567  0.011  11.489
ftype                     8.568  0.123   8.387
plot_densities            7.834  0.047   7.754
reset_fit                 6.549  0.243   6.667
extract_coef_features     6.610  0.034   6.617
fcluster                  6.492  0.074   6.470
plot_sample_nas           5.836  0.007   5.798
read_fragpipe             5.791  0.014   5.505
code                      5.089  0.031   5.098
fit_survival              5.071  0.014   5.057
* 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

##############################################################################
##############################################################################
###
### 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 
146.796   3.467 147.550 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
FITSEP0.0010.0010.001
LINMODENGINES000
MAXQUANT_PATTERNS0.0000.0000.001
SURVIVALENGINES000
TAXON_TO_ORGNAME000
TESTS000
X2.2400.0722.289
abstract_fit1.6110.0411.629
add_adjusted_pvalues0.5690.0070.577
add_assay_means0.3350.0180.353
add_facetvars1.4790.0201.472
add_opentargets_by_uniprot0.3720.0030.376
add_psp0.4750.0100.486
add_smiles0.4340.0200.420
analysis0.3570.0200.377
analyze14.343 0.18114.376
annotate_maxquant0.9730.0321.005
annotate_uniprot_rest0.2980.0101.873
assert_is_valid_sumexp0.5150.0230.516
bin1.1220.0591.181
biplot4.1930.0154.187
biplot_corrections2.9430.0092.929
biplot_covariates4.8060.0114.795
block2lme0.0030.0000.003
center1.3520.0051.358
code5.0890.0315.098
coefs0.7740.0030.754
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.5830.0040.563
count_in0.0010.0000.001
counts0.3190.0000.320
counts2cpm0.3090.0170.325
counts2tpm0.2700.0010.272
cpm0.3120.0050.317
create_design0.6550.0080.642
default_formula16.730 0.39416.673
default_geom0.5200.0300.529
default_sfile0.0020.0000.002
demultiplex0.0140.0000.014
dequantify0.0020.0000.003
dequantify_compounddiscoverer0.0010.0010.001
dot-coxph0.3900.0100.401
dot-merge0.0180.0000.018
dot-read_maxquant_proteingroups0.1110.0020.113
download_data000
download_gtf000
download_mcclain21000
dt2mat0.0030.0000.003
enrichment1.8490.0041.853
entrezg_to_symbol0.0010.0000.000
extract_coef_features6.6100.0346.617
extract_rectangle0.1070.0040.111
fcluster6.4920.0746.470
fcor1.0810.0011.083
fdata0.5320.0070.539
fdr2p1.0120.0381.028
filter_exprs_replicated_in_some_subgroup1.0570.0060.938
filter_features0.5230.0060.498
filter_medoid0.6790.0060.685
filter_samples0.5200.0070.488
fit_linmod30.713 0.07130.108
fit_survival5.0710.0145.057
fitcoefs0.8460.0040.811
fits0.7780.0040.745
fix_xlgenes0.0020.0000.002
flevels0.3810.0100.392
fnames0.4870.0150.502
formula2str000
ftype8.5680.1238.387
fvalues0.4010.0200.421
fvars0.3490.0130.362
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0010.0000.001
guess_fitsep0.4190.0060.425
guess_maxquant_quantity0.0040.0010.005
guess_sep0.4610.0070.446
has_multiple_levels0.0490.0000.049
hdlproteins0.0370.0160.056
impute2.7940.0092.803
invert_subgroups0.5950.0110.606
is_collapsed_subset0.0000.0000.001
is_correlation_matrix0.0000.0010.001
is_diann_report0.4130.0370.427
is_fastadt0.0570.0000.057
is_file0.0010.0000.000
is_fraction0.0010.0000.002
is_imputed0.6590.0010.661
is_positive_number0.0010.0000.002
is_scalar_subset0.3340.0020.336
is_sig1.6340.0101.643
is_valid_formula0.0410.0000.041
keep_connected_blocks0.4600.0080.439
keep_connected_features0.7080.0030.652
keep_replicated_features0.8180.0090.718
label2index000
list2mat000
log2counts0.3060.0060.312
log2cpm0.3010.0000.301
log2diffs0.2860.0020.288
log2proteins0.3030.0040.307
log2sites0.3010.0030.303
log2tpm0.3010.0000.301
log2transform3.5350.0173.552
logical2factor0.0020.0000.001
make_alpha_palette0.4770.0060.462
make_colors0.010.000.01
make_volcano_dt0.8250.0000.825
map_fvalues0.3740.0020.376
matrix2sumexp0.8990.0080.871
merge_sample_file0.4070.0040.411
merge_sdata0.5180.0100.500
message_df0.0020.0000.002
model_coefs0.7170.0070.701
modelvar3.6210.0043.567
order_on_p1.1910.0051.173
pca2.7430.0062.729
pg_to_canonical0.0060.0000.006
plot_coef_densities1.1530.0131.128
plot_contrast_venn2.5870.0322.504
plot_contrastogram2.8060.0152.735
plot_data1.1990.0061.172
plot_densities7.8340.0477.754
plot_design0.6400.0080.648
plot_exprs21.444 0.07621.417
plot_exprs_per_coef22.175 0.10522.117
plot_fit_summary1.9240.0101.842
plot_heatmap2.0960.0042.100
plot_joint_density2.6820.0132.673
plot_matrix0.4520.0090.439
plot_sample_nas5.8360.0075.798
plot_subgroup_points4.4250.0084.352
plot_summary13.757 0.01113.633
plot_survival3.3920.0043.376
plot_venn0.0040.0000.004
plot_venn_heatmap0.0210.0000.022
plot_violins3.7350.0173.713
plot_volcano11.567 0.01111.489
preprocess_rnaseq_counts0.4040.0190.422
pull_columns0.0020.0000.002
read_affymetrix000
read_diann_proteingroups93.007 0.72589.020
read_fragpipe5.7910.0145.505
read_maxquant_phosphosites1.4430.0251.469
read_maxquant_proteingroups1.1720.0041.176
read_metabolon14.104 0.01513.986
read_msigdt0.0000.0000.001
read_olink1.2720.0141.215
read_rectangles0.1750.0140.188
read_rnaseq_counts31.790 2.23233.805
read_salmon000
read_somascan14.701 0.35815.003
read_uniprotdt0.3100.0090.319
reset_fit6.5490.2436.667
rm_diann_contaminants19.454 0.46318.547
rm_missing_in_some_samples0.4710.0280.471
rm_unmatched_samples0.6580.0270.686
scaledlibsizes0.2790.0120.290
scoremat1.0100.0161.003
slevels0.3600.0030.363
snames0.3720.0100.382
split_extract_fixed0.6700.0410.673
split_samples1.1620.0091.150
stri_any_regex000
stri_detect_fixed_in_collapsed0.3340.0110.345
subgroup_matrix0.5080.0060.489
subtract_baseline4.5180.0114.443
sumexp_to_longdt1.8450.0301.796
sumexp_to_tsv0.5230.0090.532
sumexplist_to_longdt1.4550.0071.463
summarize_fit1.7970.0231.703
svalues0.4090.0040.403
svars0.4650.0010.465
systematic_nas0.5210.0160.538
tag_features0.9980.0521.050
tag_hdlproteins0.5980.0160.614
taxon2org0.0010.0000.001
tpm0.2960.0010.297
uncollapse0.0300.0020.032
values0.3950.0010.396
varlevels_dont_clash0.0190.0000.019
venn_detects0.5840.0240.608
weights0.3370.0040.341
write_xl0.7560.0290.758
zero_to_na0.0010.0000.001