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This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 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: 2025-08-29 13:45 -0400 (Fri, 29 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 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: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2025-08-29 19:12:08 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 19:30:01 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 1073.3 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.17.0’
* 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 108.436  1.954 111.395
read_rnaseq_counts        38.708  2.932  42.299
fit_linmod                33.962  0.310  34.483
plot_exprs_per_coef       26.399  0.200  26.728
plot_exprs                26.250  0.172  26.611
rm_diann_contaminants     23.965  0.452  24.666
read_somascan             18.662  0.150  19.038
default_formula           18.224  0.383  18.785
read_metabolon            16.438  0.174  16.751
plot_summary              16.344  0.145  16.583
analyze                   16.233  0.187  16.524
plot_volcano              13.744  0.119  13.921
ftype                      9.651  0.270   9.984
plot_densities             9.380  0.162   9.592
reset_fit                  7.505  0.168   7.733
extract_coef_features      7.322  0.072   7.423
plot_sample_nas            7.291  0.057   7.383
fcluster                   7.101  0.079   7.209
read_fragpipe              6.888  0.153   7.112
fit_survival               6.028  0.074   6.140
subtract_baseline          5.607  0.180   5.881
code                       5.625  0.079   5.728
biplot_covariates          5.541  0.068   5.636
plot_subgroup_points       5.288  0.107   5.435
* 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 ‘1.17.0’
** 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-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 
164.049   9.002 192.064 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0010.0000.001
COMPOUNDDISCOVERER_PATTERNS0.0000.0000.001
FITSEP0.0000.0010.000
LINMODENGINES000
MAXQUANT_PATTERNS0.0000.0010.000
SURVIVALENGINES000
TAXON_TO_ORGNAME0.0000.0010.000
TESTS0.0010.0000.000
X2.5650.0802.665
abstract_fit1.9160.0972.033
add_adjusted_pvalues0.6620.0200.686
add_assay_means0.3810.0090.392
add_facetvars1.6890.0601.761
add_opentargets_by_uniprot0.4560.0090.471
add_psp0.5790.0160.599
add_smiles0.5100.0420.557
analysis0.4430.0090.454
analyze16.233 0.18716.524
annotate_maxquant1.1240.1031.237
annotate_uniprot_rest0.0870.0132.041
assert_is_valid_sumexp0.5770.0340.613
bin1.1880.0161.209
biplot4.5320.0754.632
biplot_corrections3.3520.0573.428
biplot_covariates5.5410.0685.636
block2lme0.0040.0010.005
center1.4940.0191.521
code5.6250.0795.728
coefs0.8650.0480.923
collapsed_entrezg_to_symbol0.0010.0010.001
contrast_subgroup_cols0.6270.0400.670
count_in0.0010.0010.001
counts0.3490.0040.355
counts2cpm0.3530.0030.357
counts2tpm0.2960.0030.300
cpm0.3400.0040.344
create_design0.7470.0450.795
default_formula18.224 0.38318.785
default_geom0.5800.0480.633
default_sfile0.0020.0000.002
demultiplex0.0150.0010.015
dequantify0.0010.0000.002
dequantify_compounddiscoverer0.0010.0000.002
dot-coxph0.4660.0490.518
dot-merge0.0250.0010.026
dot-read_maxquant_proteingroups0.1170.0060.122
download_data0.0000.0000.001
download_gtf000
download_mcclain21000
dt2mat0.0020.0000.003
enrichment2.0440.0142.070
entrezg_to_symbol0.0010.0000.001
extract_coef_features7.3220.0727.423
extract_rectangle0.1440.0390.184
fcluster7.1010.0797.209
fcor1.1300.0321.173
fdata0.5520.0150.568
fdr2p1.1020.0451.155
filter_exprs_replicated_in_some_subgroup1.0200.0431.067
filter_features0.6050.0470.655
filter_medoid0.7650.0200.789
filter_samples0.5700.0430.618
fit_linmod33.962 0.31034.483
fit_survival6.0280.0746.140
fitcoefs0.9450.0430.998
fits0.9370.0510.995
fix_xlgenes0.0020.0010.003
flevels0.4380.0060.444
fnames0.5350.0070.544
formula2str0.0000.0000.001
ftype9.6510.2709.984
fvalues0.4790.0110.492
fvars0.4100.0070.420
genome_to_orgdb0.0010.0000.001
group_by_level0.0010.0000.001
guess_compounddiscoverer_quantity0.0020.0000.002
guess_fitsep0.4970.0060.506
guess_maxquant_quantity0.0060.0010.008
guess_sep0.5730.0550.653
has_multiple_levels0.0670.0030.070
hdlproteins0.0520.0320.086
impute3.4020.0423.476
invert_subgroups0.8180.0150.840
is_collapsed_subset0.0010.0000.001
is_correlation_matrix0.0020.0000.001
is_diann_report0.2690.0550.402
is_fastadt0.0740.0020.078
is_file0.0000.0010.001
is_fraction0.0020.0000.003
is_imputed0.8970.0120.917
is_positive_number0.0020.0000.002
is_scalar_subset0.4130.0070.423
is_sig2.1130.0222.152
is_valid_formula0.0600.0020.062
keep_connected_blocks0.6310.0590.702
keep_connected_features0.9070.0580.981
keep_replicated_features0.9920.0631.069
label2index0.0010.0010.001
list2mat0.0010.0000.001
log2counts0.4200.0050.432
log2cpm0.4440.0050.450
log2diffs0.3750.0070.384
log2proteins0.3830.0060.390
log2sites0.3950.0070.403
log2tpm0.3870.0020.392
log2transform4.3860.0554.472
logical2factor0.0020.0010.002
make_alpha_palette0.5880.0460.642
make_colors0.0100.0010.012
make_volcano_dt0.9910.0111.007
map_fvalues0.4670.0070.478
matrix2sumexp1.1680.0531.232
merge_sample_file0.5220.0080.532
merge_sdata0.6370.0600.704
message_df0.0030.0000.003
model_coefs0.9260.0500.988
modelvar4.5030.0704.599
order_on_p1.4120.0561.477
pca3.7010.0873.822
pg_to_canonical0.0050.0010.006
plot_coef_densities1.4820.0451.539
plot_contrast_venn3.0940.1843.325
plot_contrastogram3.2540.1113.387
plot_data1.4370.0511.496
plot_densities9.3800.1629.592
plot_design0.7200.0100.735
plot_exprs26.250 0.17226.611
plot_exprs_per_coef26.399 0.20026.728
plot_fit_summary2.2670.0572.337
plot_heatmap2.5920.0192.630
plot_joint_density3.4120.0703.502
plot_matrix0.5770.0470.628
plot_sample_nas7.2910.0577.383
plot_subgroup_points5.2880.1075.435
plot_summary16.344 0.14516.583
plot_survival3.9370.0323.988
plot_venn0.0040.0010.006
plot_venn_heatmap0.0240.0010.026
plot_violins4.2290.0814.335
plot_volcano13.744 0.11913.921
preprocess_rnaseq_counts0.4890.0240.515
pull_columns0.0020.0000.003
read_affymetrix0.0000.0000.001
read_diann_proteingroups108.436 1.954111.395
read_fragpipe6.8880.1537.112
read_maxquant_phosphosites1.7620.0381.812
read_maxquant_proteingroups1.3500.0241.386
read_metabolon16.438 0.17416.751
read_msigdt0.0000.0000.001
read_olink1.5360.0811.639
read_rectangles0.2060.0260.234
read_rnaseq_counts38.708 2.93242.299
read_salmon0.0000.0000.001
read_somascan18.662 0.15019.038
read_uniprotdt0.4320.0430.489
reset_fit7.5050.1687.733
rm_diann_contaminants23.965 0.45224.666
rm_missing_in_some_samples0.5680.0490.635
rm_unmatched_samples0.7540.0220.793
scaledlibsizes0.3430.0060.353
scoremat1.1390.0551.211
slevels0.4570.0100.472
snames0.4330.0110.447
split_extract_fixed0.8370.1671.017
split_samples1.3750.0651.456
stri_any_regex0.0010.0010.002
stri_detect_fixed_in_collapsed0.4130.0090.429
subgroup_matrix0.6560.0540.723
subtract_baseline5.6070.1805.881
sumexp_to_longdt2.1150.1742.338
sumexp_to_tsv0.6460.0110.662
sumexplist_to_longdt1.7210.0301.767
summarize_fit2.0430.0742.145
svalues0.4500.0070.460
svars0.4840.0070.497
systematic_nas0.6240.0070.636
tag_features1.1910.0321.237
tag_hdlproteins0.7310.0770.815
taxon2org0.0010.0000.002
tpm0.4190.0030.425
uncollapse0.0350.0010.036
values0.4970.0120.517
varlevels_dont_clash0.0240.0010.026
venn_detects0.7870.0250.822
weights0.4200.0030.429
write_xl0.9020.0600.969
zero_to_na0.0020.0010.003