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This page was generated on 2025-08-15 12:06 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-14 13:45 -0400 (Thu, 14 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
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 13.7.7 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 palomino8

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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings autonomics_1.17.0.tar.gz
StartedAt: 2025-08-15 00:36:08 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 00:56:06 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 1198.7 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings autonomics_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 153.29   6.40  156.38
read_rnaseq_counts        41.83   2.45   49.78
fit_linmod                38.92   0.47   39.56
rm_diann_contaminants     30.69   1.25   31.10
plot_exprs_per_coef       28.41   0.31   28.74
plot_exprs                26.62   0.33   27.48
default_formula           19.47   0.61   19.94
plot_summary              18.92   0.25   19.17
read_metabolon            18.77   0.16   18.92
read_somascan             18.83   0.05   18.87
analyze                   17.14   0.31   17.48
plot_volcano              16.50   0.27   16.94
ftype                     11.50   0.46   12.03
read_fragpipe             10.71   0.27   10.91
fcluster                   8.83   0.14    9.02
extract_coef_features      8.36   0.11    8.50
plot_densities             7.97   0.20    8.18
plot_sample_nas            7.66   0.08    7.75
code                       7.01   0.11    7.12
biplot_covariates          6.87   0.11    6.98
fit_survival               6.77   0.12    7.39
reset_fit                  6.55   0.11    6.68
subtract_baseline          6.20   0.13    6.33
plot_subgroup_points       6.06   0.07    6.14
plot_violins               5.08   0.19    5.26
biplot                     5.17   0.08    5.25
plot_survival              5.10   0.08    5.20
* 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
  'F:/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log'
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
 190.85   13.92  214.36 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS000
COMPOUNDDISCOVERER_PATTERNS000
FITSEP000
LINMODENGINES000
MAXQUANT_PATTERNS000
SURVIVALENGINES000
TAXON_TO_ORGNAME000
TESTS000
X2.830.112.98
abstract_fit2.190.202.39
add_adjusted_pvalues0.810.020.84
add_assay_means0.440.020.46
add_facetvars1.920.112.03
add_opentargets_by_uniprot0.530.000.55
add_psp0.690.060.75
add_smiles0.620.060.68
analysis0.580.050.63
analyze17.14 0.3117.48
annotate_maxquant1.000.111.11
annotate_uniprot_rest0.030.011.41
assert_is_valid_sumexp0.560.080.64
bin1.240.001.23
biplot5.170.085.25
biplot_corrections4.220.084.30
biplot_covariates6.870.116.98
block2lme000
center2.130.002.13
code7.010.117.12
coefs0.960.091.05
collapsed_entrezg_to_symbol000
contrast_subgroup_cols0.690.100.78
count_in000
counts0.450.000.45
counts2cpm0.390.000.39
counts2tpm0.410.000.41
cpm0.440.000.44
create_design0.810.060.88
default_formula19.47 0.6119.94
default_geom0.590.010.61
default_sfile000
demultiplex0.020.000.01
dequantify000
dequantify_compounddiscoverer000
dot-coxph0.450.040.49
dot-merge0.030.000.03
dot-read_maxquant_proteingroups0.100.010.11
download_data000
download_gtf000
download_mcclain21000
dt2mat0.010.000.02
enrichment2.380.002.37
entrezg_to_symbol000
extract_coef_features8.360.118.50
extract_rectangle0.180.060.25
fcluster8.830.149.02
fcor1.420.071.48
fdata0.610.010.63
fdr2p1.360.061.42
filter_exprs_replicated_in_some_subgroup1.320.111.42
filter_features0.710.050.76
filter_medoid1.040.031.07
filter_samples0.680.050.75
fit_linmod38.92 0.4739.56
fit_survival6.770.127.39
fitcoefs1.140.111.25
fits0.900.080.99
fix_xlgenes0.020.000.01
flevels0.650.000.66
fnames0.570.000.56
formula2str000
ftype11.50 0.4612.03
fvalues0.450.000.47
fvars0.550.020.56
genome_to_orgdb000
group_by_level000
guess_compounddiscoverer_quantity000
guess_fitsep0.630.030.65
guess_maxquant_quantity000
guess_sep0.440.080.52
has_multiple_levels0.060.000.06
hdlproteins0.080.000.30
impute3.780.053.84
invert_subgroups0.780.030.83
is_collapsed_subset000
is_correlation_matrix000
is_diann_report0.330.090.55
is_fastadt0.060.000.06
is_file000
is_fraction000
is_imputed0.920.030.95
is_positive_number000
is_scalar_subset0.380.000.39
is_sig2.070.032.11
is_valid_formula0.070.000.07
keep_connected_blocks0.680.070.75
keep_connected_features0.740.070.81
keep_replicated_features0.800.110.91
label2index000
list2mat000
log2counts0.340.000.34
log2cpm0.380.020.39
log2diffs0.340.010.36
log2proteins0.390.000.41
log2sites0.450.000.45
log2tpm0.420.000.42
log2transform4.210.104.47
logical2factor000
make_alpha_palette0.610.050.65
make_colors0.010.000.02
make_volcano_dt0.910.020.92
map_fvalues0.470.010.48
matrix2sumexp1.120.061.22
merge_sample_file0.690.000.71
merge_sdata0.670.100.76
message_df000
model_coefs0.860.110.97
modelvar4.830.124.96
order_on_p1.670.081.77
pca3.510.113.63
pg_to_canonical0.020.000.01
plot_coef_densities1.720.111.83
plot_contrast_venn2.650.172.83
plot_contrastogram2.580.143.06
plot_data1.160.051.48
plot_densities7.970.208.18
plot_design0.750.021.03
plot_exprs26.62 0.3327.48
plot_exprs_per_coef28.41 0.3128.74
plot_fit_summary2.370.122.51
plot_heatmap2.800.112.92
plot_joint_density3.580.143.91
plot_matrix0.450.100.55
plot_sample_nas7.660.087.75
plot_subgroup_points6.060.076.14
plot_summary18.92 0.2519.17
plot_survival5.100.085.20
plot_venn000
plot_venn_heatmap0.030.000.03
plot_violins5.080.195.26
plot_volcano16.50 0.2716.94
preprocess_rnaseq_counts0.630.020.65
pull_columns000
read_affymetrix000
read_diann_proteingroups153.29 6.40156.38
read_fragpipe10.71 0.2710.91
read_maxquant_phosphosites1.680.081.80
read_maxquant_proteingroups1.780.081.87
read_metabolon18.77 0.1618.92
read_msigdt000
read_olink1.850.092.63
read_rectangles0.220.080.31
read_rnaseq_counts41.83 2.4549.78
read_salmon000
read_somascan18.83 0.0518.87
read_uniprotdt0.360.040.41
reset_fit6.550.116.68
rm_diann_contaminants30.69 1.2531.10
rm_missing_in_some_samples0.620.100.72
rm_unmatched_samples0.890.000.90
scaledlibsizes0.400.000.39
scoremat1.250.081.33
slevels0.430.010.47
snames0.550.000.54
split_extract_fixed0.700.140.85
split_samples1.640.121.76
stri_any_regex000
stri_detect_fixed_in_collapsed0.490.020.52
subgroup_matrix0.580.120.70
subtract_baseline6.200.136.33
sumexp_to_longdt2.500.152.64
sumexp_to_tsv0.500.020.56
sumexplist_to_longdt1.700.051.77
summarize_fit1.700.041.75
svalues0.440.020.46
svars0.370.000.37
systematic_nas0.490.020.52
tag_features0.980.061.04
tag_hdlproteins0.560.080.72
taxon2org000
tpm0.520.010.53
uncollapse0.030.000.03
values0.600.020.61
varlevels_dont_clash0.010.000.02
venn_detects0.610.060.67
weights0.340.030.38
write_xl0.600.110.70
zero_to_na000