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This page was generated on 2025-09-05 12:08 -0400 (Fri, 05 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 116/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
autonomics 1.17.0  (landing page)
Aditya Bhagwat
Snapshot Date: 2025-09-04 13:45 -0400 (Thu, 04 Sep 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: autonomics
Version: 1.17.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.17.0.tar.gz
StartedAt: 2025-09-05 04:16:41 -0000 (Fri, 05 Sep 2025)
EndedAt: 2025-09-05 04:34:23 -0000 (Fri, 05 Sep 2025)
EllapsedTime: 1062.5 seconds
RetCode: 0
Status:   OK  
CheckDir: autonomics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings autonomics_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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
fit_linmod               43.920  0.167  44.183
read_rnaseq_counts       41.754  1.426  43.343
plot_exprs_per_coef      34.688  0.060  34.837
read_diann_proteingroups 33.451  0.506  33.692
plot_exprs               33.031  0.215  33.336
default_formula          24.091  0.323  24.340
read_metabolon           20.996  0.112  21.166
analyze                  20.992  0.044  21.085
plot_summary             20.927  0.036  21.011
read_somascan            20.364  0.223  20.646
plot_volcano             17.341  0.116  17.499
ftype                    12.002  0.191  12.184
plot_densities           11.862  0.128  12.014
extract_coef_features     9.903  0.088  10.015
fcluster                  8.822  0.032   8.873
plot_sample_nas           8.632  0.075   8.727
read_fragpipe             8.518  0.104   8.482
rm_diann_contaminants     7.568  0.084   7.565
code                      7.522  0.008   7.547
reset_fit                 7.454  0.016   7.504
biplot_covariates         7.360  0.024   7.398
fit_survival              7.028  0.032   7.077
plot_subgroup_points      6.600  0.040   6.656
subtract_baseline         6.517  0.028   6.557
biplot                    5.842  0.068   5.924
plot_violins              5.652  0.032   5.698
modelvar                  5.271  0.008   5.288
plot_survival             5.201  0.028   5.244
log2transform             5.003  0.028   5.046
annotate_uniprot_rest     0.125  0.004   5.749
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/autonomics.Rcheck/00check.log’
for details.


Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
189.286   2.745 191.610 

Example timings

autonomics.Rcheck/autonomics-Ex.timings

nameusersystemelapsed
AUTONOMICS_DATASETS0.0000.0000.001
COMPOUNDDISCOVERER_PATTERNS000
FITSEP000
LINMODENGINES000
MAXQUANT_PATTERNS000
SURVIVALENGINES000
TAXON_TO_ORGNAME000
TESTS000
X2.7580.0762.849
abstract_fit2.4390.0202.462
add_adjusted_pvalues0.7990.0120.816
add_assay_means0.4840.0160.500
add_facetvars2.1160.0152.133
add_opentargets_by_uniprot0.5110.0040.521
add_psp0.7060.0640.775
add_smiles0.6060.0400.644
analysis0.5650.0000.566
analyze20.992 0.04421.085
annotate_maxquant1.2710.0281.305
annotate_uniprot_rest0.1250.0045.749
assert_is_valid_sumexp0.7540.0280.781
bin1.2040.0591.267
biplot5.8420.0685.924
biplot_corrections4.5830.0044.596
biplot_covariates7.3600.0247.398
block2lme0.0040.0000.004
center1.9480.0041.956
code7.5220.0087.547
coefs1.1220.0121.134
collapsed_entrezg_to_symbol0.0010.0000.001
contrast_subgroup_cols0.8130.0040.816
count_in0.0020.0000.001
counts0.4960.0040.503
counts2cpm0.4180.0000.419
counts2tpm0.4080.0000.409
cpm0.4880.0000.489
create_design0.9550.0040.959
default_formula24.091 0.32324.340
default_geom0.7070.0040.710
default_sfile0.0020.0000.002
demultiplex0.0210.0000.021
dequantify0.0030.0000.003
dequantify_compounddiscoverer0.0020.0000.001
dot-coxph0.5490.0080.560
dot-merge0.0240.0000.024
dot-read_maxquant_proteingroups0.1210.0080.129
download_data000
download_gtf0.0000.0000.001
download_mcclain21000
dt2mat0.0020.0020.004
enrichment2.6720.0082.688
entrezg_to_symbol0.0010.0000.001
extract_coef_features 9.903 0.08810.015
extract_rectangle0.1590.0000.159
fcluster8.8220.0328.873
fcor1.4140.0001.418
fdata0.7600.0080.771
fdr2p1.3700.0041.376
filter_exprs_replicated_in_some_subgroup1.4170.0161.431
filter_features0.6740.0080.681
filter_medoid1.0460.0001.049
filter_samples0.6910.0120.701
fit_linmod43.920 0.16744.183
fit_survival7.0280.0327.077
fitcoefs1.2450.0121.256
fits1.0440.0281.071
fix_xlgenes0.0020.0000.002
flevels0.5290.0080.539
fnames0.6980.0000.700
formula2str000
ftype12.002 0.19112.184
fvalues0.5540.0040.560
fvars0.5350.0000.537
genome_to_orgdb0.0010.0000.001
group_by_level0.0020.0000.002
guess_compounddiscoverer_quantity0.0020.0000.002
guess_fitsep0.6770.0040.684
guess_maxquant_quantity0.0070.0000.007
guess_sep0.6770.0160.691
has_multiple_levels0.0770.0040.082
hdlproteins0.0500.0200.083
impute4.1310.0244.167
invert_subgroups0.9180.0040.925
is_collapsed_subset0.0010.0000.000
is_correlation_matrix0.0020.0000.001
is_diann_report0.3020.0200.312
is_fastadt0.0960.0000.096
is_file000
is_fraction0.0020.0000.002
is_imputed0.9910.0000.994
is_positive_number0.0020.0000.002
is_scalar_subset0.4340.0000.434
is_sig2.4110.0042.422
is_valid_formula0.0650.0000.065
keep_connected_blocks0.7200.0160.734
keep_connected_features0.8900.0040.904
keep_replicated_features1.1090.0191.127
label2index0.0010.0000.001
list2mat0.0010.0000.000
log2counts0.4640.0000.465
log2cpm0.4460.0000.448
log2diffs0.4730.0080.482
log2proteins0.4610.0040.467
log2sites0.4420.0040.448
log2tpm0.4140.0000.415
log2transform5.0030.0285.046
logical2factor0.0020.0000.002
make_alpha_palette0.7120.0080.719
make_colors0.0110.0000.012
make_volcano_dt1.2480.0001.251
map_fvalues0.5460.0000.547
matrix2sumexp1.1750.0041.182
merge_sample_file0.5850.0000.586
merge_sdata0.7390.0040.743
message_df0.0030.0000.003
model_coefs0.9860.0161.002
modelvar5.2710.0085.288
order_on_p1.6790.0361.716
pca4.0230.0204.051
pg_to_canonical0.0080.0000.009
plot_coef_densities1.7730.0271.803
plot_contrast_venn3.6360.0083.643
plot_contrastogram4.1360.0484.203
plot_data1.7300.0201.752
plot_densities11.862 0.12812.014
plot_design0.8570.0080.867
plot_exprs33.031 0.21533.336
plot_exprs_per_coef34.688 0.06034.837
plot_fit_summary2.8420.0322.877
plot_heatmap3.0770.0083.094
plot_joint_density3.8400.0443.893
plot_matrix0.6470.0120.658
plot_sample_nas8.6320.0758.727
plot_subgroup_points6.6000.0406.656
plot_summary20.927 0.03621.011
plot_survival5.2010.0285.244
plot_venn0.0050.0000.006
plot_venn_heatmap0.0310.0000.031
plot_violins5.6520.0325.698
plot_volcano17.341 0.11617.499
preprocess_rnaseq_counts0.5480.0120.561
pull_columns0.0030.0000.003
read_affymetrix000
read_diann_proteingroups33.451 0.50633.692
read_fragpipe8.5180.1048.482
read_maxquant_phosphosites1.8890.0161.909
read_maxquant_proteingroups1.6390.0081.652
read_metabolon20.996 0.11221.166
read_msigdt0.0010.0000.001
read_olink1.6650.0201.671
read_rectangles0.2440.0000.245
read_rnaseq_counts41.754 1.42643.343
read_salmon000
read_somascan20.364 0.22320.646
read_uniprotdt0.3760.0080.385
reset_fit7.4540.0167.504
rm_diann_contaminants7.5680.0847.565
rm_missing_in_some_samples0.7460.0320.777
rm_unmatched_samples0.8620.0040.867
scaledlibsizes0.4270.0000.428
scoremat1.4470.0081.457
slevels0.6280.0080.639
snames0.5370.0040.542
split_extract_fixed0.6870.0120.697
split_samples1.6350.0191.657
stri_any_regex0.0010.0000.000
stri_detect_fixed_in_collapsed0.4710.0000.472
subgroup_matrix0.7800.0080.787
subtract_baseline6.5170.0286.557
sumexp_to_longdt3.6200.0923.714
sumexp_to_tsv0.6760.0000.678
sumexplist_to_longdt1.9390.0201.965
summarize_fit2.2790.0042.283
svalues0.5640.0000.565
svars0.5060.0160.524
systematic_nas0.7270.0360.765
tag_features1.3010.0201.324
tag_hdlproteins0.6920.0160.710
taxon2org0.0010.0000.001
tpm0.4470.0000.448
uncollapse0.0390.0000.039
values0.5910.0000.592
varlevels_dont_clash0.0280.0000.027
venn_detects0.7160.0000.719
weights0.4540.0000.456
write_xl0.9300.0120.941
zero_to_na0.0010.0000.001