Multiple platform build/check report for BioC 3.21 - CHECK results for autonomics on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4720
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4482
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4493
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4446
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*

CHECK results for autonomics on palomino7

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: 1.15.143

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings autonomics_1.15.143.tar.gz

StartedAt: 2025-02-16 22:36:23 -0500 (Sun, 16 Feb 2025)

EndedAt: 2025-02-16 22:56:49 -0500 (Sun, 16 Feb 2025)

EllapsedTime: 1225.5 seconds

RetCode: 0

Status: OK

CheckDir: autonomics.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings autonomics_1.15.143.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.15.143'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... OK
* 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 144.77   4.42  146.12
read_rnaseq_counts        41.25   2.20   43.62
fit_linmod                38.00   0.50   38.53
rm_diann_contaminants     30.31   0.96   30.42
plot_exprs_per_coef       28.81   0.25   29.07
plot_exprs                26.82   0.29   27.13
default_formula           21.62   0.56   22.19
read_somascan             19.57   0.21   19.80
plot_summary              18.19   0.24   18.42
analyze                   17.30   0.28   17.59
read_metabolon            17.14   0.20   17.33
plot_volcano              15.64   0.25   15.89
read_fragpipe             10.69   0.25   10.82
ftype                      9.68   0.47   10.20
plot_densities             9.39   0.23    9.64
extract_coef_features      8.62   0.11    8.74
fcluster                   8.01   0.14    8.16
plot_sample_nas            7.66   0.08    7.75
reset_fit                  7.22   0.26    7.47
code                       6.53   0.11    6.66
fit_survival               6.37   0.12    6.61
plot_subgroup_points       6.18   0.09    6.28
biplot_covariates          5.92   0.17    6.13
subtract_baseline          6.01   0.08    6.09
biplot                     4.91   0.18    5.10
* 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: 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/autonomics.Rcheck/00check.log'
for details.

Installation output

autonomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL autonomics
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'autonomics' ...
** this is package 'autonomics' version '1.15.143'
** 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 Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
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 
 180.81   11.67  204.54

Example timings

autonomics.Rcheck/autonomics-Ex.timings

name	user	system	elapsed
AUTONOMICS_DATASETS	0	0	0
COMPOUNDDISCOVERER_PATTERNS	0	0	0
FITSEP	0	0	0
LINMODENGINES	0	0	0
MAXQUANT_PATTERNS	0	0	0
SURVIVALENGINES	0	0	0
TAXON_TO_ORGNAME	0	0	0
TESTS	0	0	0
X	1.73	0.05	1.86
abstract_fit	2.68	0.06	2.73
add_adjusted_pvalues	0.81	0.03	0.86
add_assay_means	0.42	0.03	0.45
add_facetvars	2.12	0.14	2.27
add_opentargets_by_uniprot	0.55	0.03	0.58
add_psp	0.70	0.03	0.75
add_smiles	0.63	0.04	0.65
analysis	0.37	0.00	0.38
analyze	17.30	0.28	17.59
annotate_maxquant	1.20	0.06	1.27
annotate_uniprot_rest	0.08	0.05	1.91
assert_is_valid_sumexp	0.53	0.11	0.64
bin	0.44	0.00	0.43
biplot	4.91	0.18	5.10
biplot_corrections	4.22	0.10	4.33
biplot_covariates	5.92	0.17	6.13
block2lme	0	0	0
center	1.84	0.02	1.86
code	6.53	0.11	6.66
coefs	0.83	0.08	0.90
collapsed_entrezg_to_symbol	0	0	0
contrast_subgroup_cols	0.75	0.05	0.80
count_in	0.02	0.00	0.01
counts	0.45	0.00	0.45
counts2cpm	0.38	0.02	0.40
counts2tpm	0.35	0.00	0.35
cpm	0.38	0.01	0.40
create_design	0.91	0.11	1.01
default_formula	21.62	0.56	22.19
default_geom	0.49	0.05	0.53
default_sfile	0	0	0
demultiplex	0.01	0.00	0.02
dequantify	0	0	0
dequantify_compounddiscoverer	0	0	0
dot-coxph	0.47	0.06	0.53
dot-merge	0.01	0.00	0.02
dot-read_maxquant_proteingroups	0.09	0.02	0.12
download_data	0	0	0
download_gtf	0	0	0
download_mcclain21	0.00	0.00	0.02
dt2mat	0	0	0
enrichment	2.38	0.01	2.39
entrezg_to_symbol	0	0	0
extract_coef_features	8.62	0.11	8.74
extract_rectangle	0.19	0.05	0.23
fcluster	8.01	0.14	8.16
fcor	1.25	0.03	1.28
fdata	0.78	0.03	0.81
fdr2p	1.17	0.03	1.20
filter_exprs_replicated_in_some_subgroup	1.06	0.05	1.11
filter_features	0.66	0.05	0.70
filter_medoid	0.94	0.01	0.96
filter_samples	0.61	0.07	0.67
fit_linmod	38.00	0.50	38.53
fit_survival	6.37	0.12	6.61
fitcoefs	1.02	0.08	1.09
fits	0.87	0.03	0.91
fix_xlgenes	0	0	0
flevels	0.5	0.0	0.5
fnames	0.60	0.03	0.62
formula2str	0	0	0
ftype	9.68	0.47	10.20
fvalues	0.55	0.01	0.57
fvars	0.53	0.03	0.56
genome_to_orgdb	0	0	0
group_by_level	0.02	0.00	0.01
guess_compounddiscoverer_quantity	0	0	0
guess_fitsep	0.69	0.00	0.69
guess_maxquant_quantity	0	0	0
guess_sep	0.54	0.03	0.60
has_multiple_levels	0.05	0.00	0.04
hdlproteins	0.08	0.04	0.13
impute	3.40	0.04	3.45
invert_subgroups	0.52	0.03	0.55
is_collapsed_subset	0	0	0
is_correlation_matrix	0.02	0.00	0.01
is_diann_report	0.34	0.08	0.53
is_fastadt	0.08	0.00	0.08
is_file	0	0	0
is_fraction	0	0	0
is_imputed	0.76	0.03	0.80
is_positive_number	0.00	0.02	0.02
is_scalar_subset	0.32	0.00	0.31
is_sig	1.90	0.05	1.95
is_valid_formula	0.06	0.00	0.06
keep_connected_blocks	0.69	0.03	0.72
keep_connected_features	0.58	0.09	0.67
keep_replicated_features	0.72	0.06	0.80
label2index	0	0	0
list2mat	0	0	0
log2counts	0.30	0.00	0.29
log2cpm	0.39	0.03	0.43
log2diffs	0.39	0.00	0.39
log2proteins	0.31	0.02	0.32
log2sites	0.38	0.02	0.39
log2tpm	0.28	0.00	0.29
log2transform	4.74	0.06	4.79
logical2factor	0	0	0
make_alpha_palette	0.56	0.08	0.66
make_colors	0.01	0.00	0.01
make_volcano_dt	0.99	0.01	1.02
map_fvalues	0.55	0.02	0.56
matrix2sumexp	1.05	0.04	1.09
merge_sample_file	0.59	0.00	0.60
merge_sdata	0.56	0.10	0.65
message_df	0	0	0
model_coefs	0.93	0.06	0.99
modelvar	4.20	0.11	4.32
order_on_p	1.28	0.14	1.43
pca	3.75	0.17	3.92
pg_to_canonical	0	0	0
plot_coef_densities	1.61	0.16	1.76
plot_contrast_venn	2.64	0.06	2.71
plot_contrastogram	3.53	0.08	3.68
plot_data	1.52	0.08	1.60
plot_densities	9.39	0.23	9.64
plot_design	0.90	0.02	0.92
plot_exprs	26.82	0.29	27.13
plot_exprs_per_coef	28.81	0.25	29.07
plot_fit_summary	2.33	0.07	2.41
plot_heatmap	2.53	0.00	2.53
plot_joint_density	3.36	0.11	3.47
plot_matrix	0.66	0.01	0.67
plot_sample_nas	7.66	0.08	7.75
plot_subgroup_points	6.18	0.09	6.28
plot_summary	18.19	0.24	18.42
plot_survival	4.45	0.11	4.56
plot_venn	0	0	0
plot_venn_heatmap	0.03	0.00	0.03
plot_violins	4.79	0.11	4.90
plot_volcano	15.64	0.25	15.89
preprocess_rnaseq_counts	0.4	0.0	0.4
pull_columns	0	0	0
read_affymetrix	0	0	0
read_diann_proteingroups	144.77	4.42	146.12
read_fragpipe	10.69	0.25	10.82
read_maxquant_phosphosites	1.87	0.00	1.90
read_maxquant_proteingroups	1.45	0.05	1.50
read_metabolon	17.14	0.20	17.33
read_msigdt	0.00	0.02	0.02
read_olink	1.77	0.09	1.89
read_rectangles	0.27	0.03	0.30
read_rnaseq_counts	41.25	2.20	43.62
read_salmon	0	0	0
read_somascan	19.57	0.21	19.80
read_uniprotdt	0.33	0.00	0.33
reset_fit	7.22	0.26	7.47
rm_diann_contaminants	30.31	0.96	30.42
rm_missing_in_some_samples	0.58	0.01	0.59
rm_unmatched_samples	0.88	0.02	0.88
scaledlibsizes	0.42	0.00	0.42
scoremat	1.37	0.06	1.45
slevels	0.35	0.03	0.38
snames	0.53	0.00	0.53
split_extract_fixed	0.67	0.06	0.73
split_samples	1.36	0.08	1.44
stri_any_regex	0	0	0
stri_detect_fixed_in_collapsed	0.48	0.00	0.49
subgroup_matrix	0.46	0.06	0.55
subtract_baseline	6.01	0.08	6.09
sumexp_to_longdt	1.94	0.06	2.00
sumexp_to_tsv	0.61	0.00	0.61
sumexplist_to_longdt	1.70	0.03	1.74
summarize_fit	1.96	0.08	2.04
svalues	0.36	0.00	0.36
svars	0.42	0.01	0.44
systematic_nas	0.71	0.02	0.72
tag_features	1.09	0.09	1.19
tag_hdlproteins	0.59	0.04	0.63
taxon2org	0	0	0
tpm	0.28	0.00	0.28
uncollapse	0.02	0.00	0.01
values	0.47	0.00	0.47
varlevels_dont_clash	0.01	0.00	0.02
venn_detects	0.54	0.03	0.56
weights	0.37	0.01	0.39
write_xl	0.74	0.05	0.80
zero_to_na	0.01	0.00	0.01