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"	4717
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4478
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4489
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4442
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: 2025-02-04 23:08:45 -0500 (Tue, 04 Feb 2025)

EndedAt: 2025-02-04 23:27:32 -0500 (Tue, 04 Feb 2025)

EllapsedTime: 1127.3 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 141.20   4.97  143.20
read_rnaseq_counts        38.14   1.95   40.28
fit_linmod                39.31   0.55   40.90
rm_diann_contaminants     31.55   0.90   31.58
plot_exprs                26.83   0.24   27.07
plot_exprs_per_coef       26.81   0.21   27.04
default_formula           21.62   0.49   22.08
read_somascan             17.80   0.05   17.86
plot_summary              17.47   0.17   17.64
read_metabolon            17.03   0.22   17.23
plot_volcano              15.67   0.22   15.90
analyze                   14.79   0.19   16.95
read_fragpipe             12.66   0.30   12.83
plot_densities            10.43   0.27   10.70
ftype                      9.64   0.39   10.05
extract_coef_features      8.68   0.05    8.72
fcluster                   7.83   0.09    8.90
plot_sample_nas            7.22   0.11    7.33
reset_fit                  6.56   0.17    6.75
code                       6.42   0.14    6.60
biplot_covariates          6.39   0.15    6.57
fit_survival               6.25   0.08    6.66
plot_subgroup_points       5.93   0.12    6.06
subtract_baseline          5.78   0.14    5.93
biplot                     5.10   0.12    5.24
plot_violins               4.95   0.09    5.05
* 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 
 178.92   11.98  200.75

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	1.72	0.16	1.95
abstract_fit	2.04	0.06	2.11
add_adjusted_pvalues	1.28	0.00	1.28
add_assay_means	0.43	0.00	0.42
add_facetvars	1.39	0.11	1.50
add_opentargets_by_uniprot	0.33	0.03	0.45
add_psp	0.44	0.02	0.74
add_smiles	0.39	0.03	0.51
analysis	0.33	0.00	0.33
analyze	14.79	0.19	16.95
annotate_maxquant	1.08	0.04	1.18
annotate_uniprot_rest	0.03	0.06	1.46
assert_is_valid_sumexp	0.52	0.10	0.61
bin	0.44	0.03	0.47
biplot	5.10	0.12	5.24
biplot_corrections	4.11	0.15	4.25
biplot_covariates	6.39	0.15	6.57
block2lme	0	0	0
center	1.52	0.02	1.53
code	6.42	0.14	6.60
coefs	0.83	0.06	0.89
collapsed_entrezg_to_symbol	0	0	0
contrast_subgroup_cols	0.70	0.05	0.76
count_in	0	0	0
counts	0.41	0.00	0.46
counts2cpm	0.37	0.00	0.37
counts2tpm	0.41	0.00	0.41
cpm	0.29	0.00	0.29
create_design	0.83	0.09	0.93
default_formula	21.62	0.49	22.08
default_geom	0.63	0.03	0.66
default_sfile	0	0	0
demultiplex	0.01	0.00	0.01
dequantify	0	0	0
dequantify_compounddiscoverer	0	0	0
dot-coxph	0.60	0.09	1.28
dot-merge	0.01	0.00	0.02
dot-read_maxquant_proteingroups	0.14	0.00	0.16
download_data	0	0	0
download_gtf	0	0	0
download_mcclain21	0	0	0
dt2mat	0	0	0
enrichment	1.90	0.04	1.98
entrezg_to_symbol	0	0	0
extract_coef_features	8.68	0.05	8.72
extract_rectangle	0.17	0.05	0.22
fcluster	7.83	0.09	8.90
fcor	1.39	0.03	1.53
fdata	0.76	0.03	0.83
fdr2p	1.25	0.03	1.30
filter_exprs_replicated_in_some_subgroup	1.13	0.05	1.17
filter_features	0.69	0.08	0.76
filter_medoid	0.80	0.00	1.17
filter_samples	0.53	0.03	0.57
fit_linmod	39.31	0.55	40.90
fit_survival	6.25	0.08	6.66
fitcoefs	1.16	0.03	1.19
fits	0.84	0.09	0.93
fix_xlgenes	0	0	0
flevels	0.42	0.02	0.44
fnames	0.72	0.00	0.72
formula2str	0	0	0
ftype	9.64	0.39	10.05
fvalues	0.57	0.01	0.59
fvars	0.54	0.03	0.58
genome_to_orgdb	0	0	0
group_by_level	0	0	0
guess_compounddiscoverer_quantity	0.02	0.00	0.02
guess_fitsep	0.58	0.00	0.57
guess_maxquant_quantity	0	0	0
guess_sep	0.59	0.05	0.64
has_multiple_levels	0.08	0.00	0.08
hdlproteins	0.04	0.04	0.11
impute	4.18	0.00	4.17
invert_subgroups	0.82	0.02	0.86
is_collapsed_subset	0	0	0
is_correlation_matrix	0	0	0
is_diann_report	0.32	0.11	0.55
is_fastadt	0.09	0.00	0.09
is_file	0	0	0
is_fraction	0	0	0
is_imputed	2.06	0.03	2.09
is_positive_number	0	0	0
is_scalar_subset	0.38	0.01	0.41
is_sig	2.05	0.11	2.16
is_valid_formula	0.06	0.02	0.07
keep_connected_blocks	0.62	0.06	0.69
keep_connected_features	0.83	0.05	0.88
keep_replicated_features	0.86	0.01	0.89
label2index	0	0	0
list2mat	0	0	0
log2counts	0.27	0.00	0.26
log2cpm	0.36	0.00	0.36
log2diffs	0.37	0.02	0.39
log2proteins	0.42	0.02	0.44
log2sites	0.30	0.01	0.31
log2tpm	0.33	0.02	0.35
log2transform	4.23	0.06	4.29
logical2factor	0.02	0.00	0.02
make_alpha_palette	0.50	0.08	0.58
make_colors	0.01	0.00	0.01
make_volcano_dt	1.13	0.00	1.13
map_fvalues	0.57	0.00	0.57
matrix2sumexp	1.07	0.09	1.17
merge_sample_file	0.41	0.02	0.43
merge_sdata	0.64	0.09	0.74
message_df	0	0	0
model_coefs	0.64	0.05	0.69
modelvar	3.99	0.08	4.06
order_on_p	1.25	0.03	1.28
pca	3.57	0.08	3.72
pg_to_canonical	0	0	0
plot_coef_densities	1.63	0.09	1.72
plot_contrast_venn	2.70	0.11	2.83
plot_contrastogram	3.14	0.19	3.47
plot_data	1.57	0.06	1.64
plot_densities	10.43	0.27	10.70
plot_design	0.83	0.03	0.86
plot_exprs	26.83	0.24	27.07
plot_exprs_per_coef	26.81	0.21	27.04
plot_fit_summary	2.38	0.11	2.49
plot_heatmap	2.75	0.02	2.76
plot_joint_density	3.59	0.14	3.89
plot_matrix	0.69	0.05	0.74
plot_sample_nas	7.22	0.11	7.33
plot_subgroup_points	5.93	0.12	6.06
plot_summary	17.47	0.17	17.64
plot_survival	4.24	0.05	4.28
plot_venn	0	0	0
plot_venn_heatmap	0.03	0.00	0.03
plot_violins	4.95	0.09	5.05
plot_volcano	15.67	0.22	15.90
preprocess_rnaseq_counts	0.32	0.00	0.32
pull_columns	0	0	0
read_affymetrix	0	0	0
read_diann_proteingroups	141.20	4.97	143.20
read_fragpipe	12.66	0.30	12.83
read_maxquant_phosphosites	1.87	0.04	1.94
read_maxquant_proteingroups	1.41	0.05	1.45
read_metabolon	17.03	0.22	17.23
read_msigdt	0	0	0
read_olink	1.33	0.13	1.82
read_rectangles	0.20	0.01	0.21
read_rnaseq_counts	38.14	1.95	40.28
read_salmon	0	0	0
read_somascan	17.80	0.05	17.86
read_uniprotdt	0.39	0.02	0.41
reset_fit	6.56	0.17	6.75
rm_diann_contaminants	31.55	0.90	31.58
rm_missing_in_some_samples	0.65	0.00	0.65
rm_unmatched_samples	0.66	0.00	0.66
scaledlibsizes	0.39	0.00	0.39
scoremat	1.36	0.08	1.47
slevels	0.53	0.00	0.53
snames	0.50	0.03	0.53
split_extract_fixed	0.69	0.10	0.78
split_samples	1.29	0.08	1.38
stri_any_regex	0	0	0
stri_detect_fixed_in_collapsed	0.46	0.01	0.48
subgroup_matrix	0.70	0.03	0.73
subtract_baseline	5.78	0.14	5.93
sumexp_to_longdt	2.47	0.11	2.57
sumexp_to_tsv	0.64	0.00	0.66
sumexplist_to_longdt	2.17	0.00	2.20
summarize_fit	1.92	0.02	1.95
svalues	0.47	0.03	0.50
svars	0.52	0.02	0.53
systematic_nas	0.48	0.01	0.50
tag_features	1.39	0.00	1.39
tag_hdlproteins	0.50	0.03	0.53
taxon2org	0	0	0
tpm	0.25	0.02	0.27
uncollapse	0.04	0.00	0.04
values	0.71	0.01	0.72
varlevels_dont_clash	0.02	0.00	0.01
venn_detects	0.63	0.00	0.62
weights	0.31	0.00	0.32
write_xl	1.11	0.02	1.12
zero_to_na	0.02	0.00	0.02