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This page was generated on 2025-08-20 12:03 -0400 (Wed, 20 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 116/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-08-19 13:45 -0400 (Tue, 19 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: 2025-08-19 20:11:15 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 20:26:43 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 928.0 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 24.04.3 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 89.721  0.773  85.950
read_rnaseq_counts       30.361  1.013  31.097
fit_linmod               29.167  0.192  28.844
plot_exprs_per_coef      22.009  0.131  22.015
plot_exprs               20.697  0.073  20.666
rm_diann_contaminants    18.405  0.195  17.396
default_formula          16.224  0.502  16.338
read_somascan            14.072  0.124  14.107
analyze                  13.970  0.204  14.039
read_metabolon           13.622  0.054  13.589
plot_summary             13.553  0.045  13.425
plot_volcano             11.342  0.098  11.382
ftype                     8.299  0.178   8.171
plot_densities            7.473  0.106   7.487
extract_coef_features     6.302  0.067   6.347
reset_fit                 6.017  0.178   6.099
fcluster                  5.790  0.069   5.774
plot_sample_nas           5.749  0.005   5.712
read_fragpipe             5.620  0.089   5.409
code                      5.059  0.118   5.145
fit_survival              4.967  0.035   4.991
* 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 
141.666   3.576 142.343 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0010.000
COMPOUNDDISCOVERER_PATTERNS000
FITSEP000
LINMODENGINES000
MAXQUANT_PATTERNS0.0000.0000.001
SURVIVALENGINES0.0000.0010.000
TAXON_TO_ORGNAME0.0000.0000.001
TESTS000
X2.1160.0162.109
abstract_fit1.5870.0661.631
add_adjusted_pvalues0.5280.0090.538
add_assay_means0.3250.0040.329
add_facetvars1.4420.0241.445
add_opentargets_by_uniprot0.3490.0060.357
add_psp0.4720.0080.482
add_smiles0.4080.0080.395
analysis0.3410.0020.343
analyze13.970 0.20414.039
annotate_maxquant0.9430.0380.981
annotate_uniprot_rest0.3140.0202.011
assert_is_valid_sumexp0.5480.0220.543
bin1.0920.0771.169
biplot4.0090.2134.199
biplot_corrections2.8310.1342.942
biplot_covariates4.6400.1874.804
block2lme0.0030.0000.003
center1.3040.0411.346
code5.0590.1185.145
coefs0.7580.0160.752
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.5590.0250.562
count_in0.0010.0000.001
counts0.3080.0020.311
counts2cpm0.2910.0010.292
counts2tpm0.2670.0080.276
cpm0.3050.0080.313
create_design0.6630.0080.650
default_formula16.224 0.50216.338
default_geom0.4880.0250.485
default_sfile0.0020.0000.002
demultiplex0.0140.0000.014
dequantify0.0020.0000.002
dequantify_compounddiscoverer0.0000.0000.001
dot-coxph0.3660.0100.376
dot-merge0.0150.0000.015
dot-read_maxquant_proteingroups0.1050.0030.108
download_data000
download_gtf000
download_mcclain210.0010.0000.000
dt2mat0.0030.0000.003
enrichment1.7380.0371.776
entrezg_to_symbol0.0000.0000.001
extract_coef_features6.3020.0676.347
extract_rectangle0.0980.0080.105
fcluster5.7900.0695.774
fcor0.9820.0040.986
fdata0.4660.0040.470
fdr2p0.9230.0570.959
filter_exprs_replicated_in_some_subgroup0.9380.0140.892
filter_features0.4940.0070.479
filter_medoid0.6400.0050.644
filter_samples0.4850.0080.471
fit_linmod29.167 0.19228.844
fit_survival4.9670.0354.991
fitcoefs0.8210.0130.812
fits0.7680.0070.738
fix_xlgenes0.0020.0000.001
flevels0.3730.0010.374
fnames0.4540.0030.458
formula2str000
ftype8.2990.1788.171
fvalues0.3890.0140.403
fvars0.3370.0000.338
genome_to_orgdb000
group_by_level0.0000.0000.001
guess_compounddiscoverer_quantity0.0010.0000.000
guess_fitsep0.4000.0080.408
guess_maxquant_quantity0.0030.0020.005
guess_sep0.4410.0070.427
has_multiple_levels0.0510.0000.050
hdlproteins0.0390.0160.058
impute2.6900.0152.707
invert_subgroups0.5710.0060.578
is_collapsed_subset0.0000.0000.001
is_correlation_matrix0.0010.0000.001
is_diann_report0.3680.0360.400
is_fastadt0.0560.0000.056
is_file0.0010.0000.001
is_fraction0.0010.0000.001
is_imputed0.6160.0040.620
is_positive_number0.0010.0000.001
is_scalar_subset0.2910.0020.294
is_sig1.5550.0021.557
is_valid_formula0.0410.0000.041
keep_connected_blocks0.4840.0050.445
keep_connected_features0.6970.0020.607
keep_replicated_features0.7750.0040.676
label2index000
list2mat0.0010.0000.000
log2counts0.2770.0000.276
log2cpm0.2910.0000.292
log2diffs0.2830.0030.286
log2proteins0.2990.0070.306
log2sites0.2890.0040.295
log2tpm0.2720.0000.273
log2transform3.3220.0283.351
logical2factor0.0010.0000.001
make_alpha_palette0.4660.0020.446
make_colors0.0090.0000.009
make_volcano_dt0.7830.0060.790
map_fvalues0.3400.0000.341
matrix2sumexp0.8170.0160.812
merge_sample_file0.3840.0080.393
merge_sdata0.4940.0100.469
message_df0.0020.0000.002
model_coefs0.6910.0060.658
modelvar3.4840.0133.407
order_on_p1.1460.0181.136
pca2.6550.0232.657
pg_to_canonical0.0050.0000.005
plot_coef_densities1.0900.0081.076
plot_contrast_venn2.4100.0182.345
plot_contrastogram2.6310.0612.622
plot_data1.1290.0151.113
plot_densities7.4730.1067.487
plot_design0.5900.0010.592
plot_exprs20.697 0.07320.666
plot_exprs_per_coef22.009 0.13122.015
plot_fit_summary2.0410.0201.936
plot_heatmap2.1360.0142.150
plot_joint_density2.6810.0142.672
plot_matrix0.4720.0090.458
plot_sample_nas5.7490.0055.712
plot_subgroup_points4.2980.0104.236
plot_summary13.553 0.04513.425
plot_survival3.2980.0063.285
plot_venn0.0050.0000.005
plot_venn_heatmap0.0210.0000.022
plot_violins3.5690.0393.588
plot_volcano11.342 0.09811.382
preprocess_rnaseq_counts0.4130.0150.428
pull_columns0.0020.0000.002
read_affymetrix0.0000.0000.001
read_diann_proteingroups89.721 0.77385.950
read_fragpipe5.6200.0895.409
read_maxquant_phosphosites1.3700.0091.379
read_maxquant_proteingroups1.0950.0061.101
read_metabolon13.622 0.05413.589
read_msigdt000
read_olink1.2570.0161.204
read_rectangles0.1620.0070.170
read_rnaseq_counts30.361 1.01331.097
read_salmon000
read_somascan14.072 0.12414.107
read_uniprotdt0.2940.0050.299
reset_fit6.0170.1786.099
rm_diann_contaminants18.405 0.19517.396
rm_missing_in_some_samples0.4400.0070.420
rm_unmatched_samples0.5870.0000.587
scaledlibsizes0.2650.0010.266
scoremat0.9150.0090.903
slevels0.3450.0010.346
snames0.3610.0000.361
split_extract_fixed0.6230.0090.593
split_samples1.0820.0051.065
stri_any_regex0.0010.0000.000
stri_detect_fixed_in_collapsed0.2980.0000.299
subgroup_matrix0.4870.0050.455
subtract_baseline4.0930.0254.048
sumexp_to_longdt1.6830.0141.644
sumexp_to_tsv0.4880.0040.492
sumexplist_to_longdt1.3220.0071.328
summarize_fit1.5510.0071.488
svalues0.3610.0020.361
svars0.3960.0000.396
systematic_nas0.480.000.48
tag_features0.8740.0090.883
tag_hdlproteins0.5240.0140.540
taxon2org0.0010.0000.001
tpm0.2720.0010.272
uncollapse0.0290.0000.030
values0.3620.0060.368
varlevels_dont_clash0.0160.0010.018
venn_detects0.5290.0010.530
weights0.2860.0010.287
write_xl0.6670.0050.650
zero_to_na0.0020.0000.001