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This page was generated on 2025-09-29 12:04 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4833
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4621
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4566
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 116/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.2  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025)
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: devel
git_last_commit: b9e7bf3
git_last_commit_date: 2025-09-25 03:15:20 -0400 (Thu, 25 Sep 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 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: 1.17.2
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_1.17.2.tar.gz
StartedAt: 2025-09-28 19:33:31 -0400 (Sun, 28 Sep 2025)
EndedAt: 2025-09-28 19:55:11 -0400 (Sun, 28 Sep 2025)
EllapsedTime: 1299.5 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.17.2.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 ‘1.17.2’
* 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
read_diann_proteingroups  116.890  2.331 120.825
awblinmod                  47.486  0.256  47.936
read_rnaseq_counts         37.169  3.461  41.572
LINMOD                     27.322  0.334  27.812
rm_diann_contaminants      24.865  0.507  25.680
default_formula            22.158  0.486  22.847
plot_exprs_per_coef        22.111  0.155  22.355
plot_exprs                 21.376  0.138  21.641
plot_volcano               17.427  0.162  17.753
read_metabolon             16.831  0.238  17.304
read_somascan              16.130  0.178  16.477
analyze                    15.585  0.217  15.888
fit_survival               14.753  0.216  15.097
plot_summary               14.824  0.135  15.059
plot_densities             12.878  0.245  13.201
explore-transforms         12.709  0.115  12.918
fcluster                   11.199  0.080  11.330
ftype                       9.617  0.285   9.953
plot_detections             8.710  0.045   8.781
biplot_covariates           8.114  0.076   8.229
plot_xy_density             8.129  0.058   8.246
read_fragpipe               7.719  0.162   7.990
plot_subgroup_points        6.541  0.085   6.664
subtract_baseline           6.275  0.116   6.455
extract_contrast_features   6.048  0.143   6.255
log2transform               6.130  0.054   6.218
code                        5.548  0.066   5.634
plot_violins                5.526  0.083   5.636
sbind                       5.474  0.077   5.621
reset_fit                   5.265  0.175   5.533
* 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 ‘1.17.2’
** 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 
151.733  17.893 319.896 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS000
LINMOD27.322 0.33427.812
LINMODENGINES0.0000.0010.001
MAXQUANT_PATTERNS0.0000.0000.001
TAXON_TO_ORGNAME000
TESTS0.0000.0010.000
X1.3800.0561.448
abstract_fit1.1200.0511.181
add_adjusted_pvalues0.6350.0130.654
add_assay_means0.3960.0060.403
add_facetvars1.5720.0501.628
add_opentargets_by_uniprot0.4540.0080.465
add_psp0.5900.0150.609
add_smiles0.5380.0380.578
all_non_numeric0.7230.0060.739
analysis0.4620.0090.472
analyze15.585 0.21715.888
annotate_maxquant1.0360.1111.159
annotate_uniprot_rest0.0800.0132.128
assert_is_valid_sumexp0.7420.0440.791
awblinmod47.486 0.25647.936
biplot4.4760.0654.567
biplot_corrections4.3010.0714.411
biplot_covariates8.1140.0768.229
block2limma0.0030.0010.002
block2lm0.0030.0010.003
block2lme0.0030.0010.004
block2lmer0.0050.0000.005
block_has_two_levels0.7590.0510.825
center2.1380.0182.163
code5.5480.0665.634
collapsed_entrezg_to_symbol1.1100.0801.196
contrast_subgroup_cols0.7730.0580.848
contrastdt0.4110.0020.416
count_in0.0010.0010.001
counts0.3990.0040.406
counts2cpm0.3910.0040.396
counts2tpm0.3390.0030.342
cpm0.4000.0030.406
create_design0.8070.0450.856
default_formula22.158 0.48622.847
default_geom0.6190.0510.678
default_sfile0.0020.0010.003
demultiplex0.0200.0010.021
densities0.2720.0050.278
dequantify0.0020.0010.003
dequantify_compounddiscoverer0.0010.0010.002
dot-coxph0.4890.0520.548
dot-merge0.0320.0010.033
dot-read_maxquant_proteingroups0.1230.0060.129
download_data0.0000.0000.001
download_gtf000
download_mcclain210.0010.0010.000
dt2mat0.0030.0010.004
enrichment1.3240.0171.350
entrezg_to_symbol0.1820.0050.187
explore-transforms12.709 0.11512.918
extract_contrast_features6.0480.1436.255
extract_rectangle0.1910.0590.258
factor.vars0.2690.0020.273
factorize1.0780.0191.107
fcluster11.199 0.08011.330
fcor1.6800.0351.723
fdata0.6170.0140.636
fdr2p1.1530.0521.214
filter_exprs_replicated_in_some_subgroup1.2040.0491.264
filter_features0.5680.0470.622
filter_medoid0.6930.0070.704
filter_samples0.6940.0570.760
fit_survival14.753 0.21615.097
fits0.4780.0030.487
fix_xlgenes0.0030.0000.002
flevels0.5180.0070.527
fnames0.6850.0100.700
formula2str000
ftype9.6170.2859.953
fvalues0.4470.0050.454
fvars0.4330.0060.441
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0010.002
guess_compounddiscoverer_quantity0.0010.0010.002
guess_fitsep0.6210.0080.631
guess_maxquant_quantity0.0070.0020.008
guess_sep0.5700.0420.614
has_multiple_levels0.0690.0010.070
hdlproteins0.0490.0360.090
impute4.0200.0354.076
invert_subgroups0.7440.0080.756
is_character_matrix0.1770.0010.179
is_collapsed_subset0.0010.0010.001
is_correlation_matrix0.0010.0010.002
is_diann_report0.2620.0510.390
is_fastadt0.0740.0010.076
is_file0.0000.0010.001
is_fraction0.0010.0010.002
is_imputed0.8770.0090.890
is_positive_number0.0020.0010.002
is_scalar_subset0.3640.0050.371
is_sig1.6430.0131.666
is_valid_formula0.0460.0010.047
keep_estimable_features0.8670.0520.933
label2index0.0010.0000.001
list2mat0.0010.0000.001
log2counts0.4600.0040.465
log2cpm0.3780.0020.383
log2diffs0.3580.0050.366
log2proteins0.3730.0050.380
log2sites0.4630.0060.473
log2tpm0.3930.0040.398
log2transform6.1300.0546.218
logical2factor0.0010.0010.001
make_alpha_palette0.6370.0480.691
make_colors0.0110.0020.013
make_volcano_dt1.1540.0181.178
map_fvalues0.5010.0080.513
matrix2sumexp1.3260.0571.401
mclust_breaks0.6830.1050.799
merge_sample_file0.5690.0080.579
merge_sdata0.7170.0560.779
message_df0.0040.0000.003
model_coefs0.8450.0590.945
modelvar4.0800.0674.176
object10.6400.0030.645
order_on_p1.6380.0531.701
overall_parameters0.0320.0010.033
pca4.0020.0744.098
pg_to_canonical0.0080.0000.009
plot_coef_densities1.6750.0491.737
plot_contrast_venn2.7140.0592.789
plot_contrastogram3.4890.1393.670
plot_data2.0810.0602.161
plot_densities12.878 0.24513.201
plot_design0.8240.0120.840
plot_detections8.7100.0458.781
plot_exprs21.376 0.13821.641
plot_exprs_per_coef22.111 0.15522.355
plot_fit_summary2.3920.0752.490
plot_heatmap2.1920.0182.224
plot_matrix0.5910.0460.642
plot_subgroup_points6.5410.0856.664
plot_summary14.824 0.13515.059
plot_venn0.0160.0020.017
plot_venn_heatmap0.0220.0010.023
plot_violins5.5260.0835.636
plot_volcano17.427 0.16217.753
plot_xy_density8.1290.0588.246
preprocess_rnaseq_counts0.4060.0030.411
pull_columns0.0020.0010.003
pvalues_estimable0.0480.0060.054
read_affymetrix000
read_diann_proteingroups116.890 2.331120.825
read_fragpipe7.7190.1627.990
read_maxquant_phosphosites2.0770.0552.164
read_maxquant_proteingroups1.5730.0261.620
read_metabolon16.831 0.23817.304
read_msigdt0.0010.0010.003
read_olink1.7130.0861.857
read_rectangles0.2280.0310.265
read_rnaseq_counts37.169 3.46141.572
read_salmon0.0000.0010.001
read_somascan16.130 0.17816.477
read_uniprotdt0.3600.0410.405
reset_fit5.2650.1755.533
rm_diann_contaminants24.865 0.50725.680
rm_missing_in_some_samples0.5830.0530.672
rm_unmatched_samples0.7920.0380.837
sbind5.4740.0775.621
scaledlibsizes0.3780.0060.389
scoremat1.1290.0731.234
slevels0.4440.0100.463
snames0.4290.0100.448
split_extract_fixed0.6590.0840.785
split_samples1.6080.1071.746
stepauc0.4060.0080.420
stri_any_regex0.0010.0020.002
stri_detect_fixed_in_collapsed0.4360.0130.463
subgroup_matrix0.7560.0650.832
subtract_baseline6.2750.1166.455
sumexp_to_longdt2.3510.1192.506
sumexp_to_tsv0.6090.0090.623
sumexplist_to_longdt1.9350.0261.976
summarize_fit2.2010.0702.294
survobj0.1840.0020.191
svalues0.4930.0110.508
svars0.4910.0080.503
systematic_nas0.7260.0090.742
tag_features1.1870.0341.230
tag_hdlproteins0.7370.0530.801
taxon2org0.0020.0000.002
tpm0.4010.0050.409
uncollapse0.0350.0020.037
values0.4880.0070.499
varlevels_dont_clash0.0260.0010.027
venn_detects0.7470.0100.762
weights0.4010.0040.408
write_xl0.8850.0490.943
zero_to_na0.0020.0010.002