Multiple platform build/check report for BioC 3.20 - CHECK results for autonomics on palomino4

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4669
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4404
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4431
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4384
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: autonomics

Version: 1.13.10

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings autonomics_1.13.10.tar.gz

StartedAt: 2024-05-29 19:35:18 -0400 (Wed, 29 May 2024)

EndedAt: 2024-05-29 19:51:28 -0400 (Wed, 29 May 2024)

EllapsedTime: 969.5 seconds

RetCode: 0

Status: OK

CheckDir: autonomics.Rcheck

Warnings: 0

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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings autonomics_1.13.10.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.13.10'
* 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 132.08   5.09  134.68
read_rnaseq_counts        32.30   2.02   34.43
rm_diann_contaminants     25.14   1.03   26.00
plot_exprs                22.55   0.27   22.89
plot_exprs_per_coef       20.64   0.17   20.87
default_formula           18.02   0.67   18.72
fit                       14.53   0.31   15.35
read_metabolon            14.17   0.22   14.52
analyze                   13.22   0.21   14.17
plot_summary              12.67   0.23   12.97
read_somascan             12.73   0.12   12.86
plot_volcano              11.50   0.22   11.86
plot_densities             9.76   0.16   10.00
read_fragpipe              8.21   0.17    8.19
fcluster                   6.74   0.11    7.30
biplot_covariates          6.28   0.21    6.55
plot_sample_nas            6.13   0.16    6.28
plot_subgroup_points       5.75   0.11    5.93
extract_coef_features      5.03   0.17    5.31
dot-plot_survival          4.52   0.56    5.53
fit_lmx                    4.89   0.17    5.16
log2transform              4.93   0.13    5.08
biplot                     4.89   0.14    5.09
code                       4.73   0.23    5.06
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck/00check.log'
for details.

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### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL autonomics
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'autonomics' ...
** 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)


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 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

> 
> test_check("autonomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
 156.03   13.39  178.43

name	user	system	elapsed
AUTONOMICS_DATASETS	0	0	0
COMPOUNDDISCOVERER_PATTERNS	0	0	0
CONTAMINANTSURL	0	0	0
FITSEP	0	0	0
LINMOD_ENGINES	0	0	0
MAXQUANT_PATTERNS	0	0	0
TAXON_TO_ORGNAME	0	0	0
TESTS	0	0	0
abstract_fit	1.51	0.10	1.89
add_adjusted_pvalues	0.63	0.01	0.69
add_assay_means	1.03	0.03	1.07
add_facetvars	1.64	0.11	1.82
add_opentargets_by_uniprot	0.41	0.02	0.43
add_psp	0.48	0.00	0.54
add_smiles	0.49	0.08	0.68
analysis	0.40	0.00	0.41
analyze	13.22	0.21	14.17
annotate_maxquant	1.08	0.02	1.16
annotate_uniprot_rest	0.06	0.05	1.39
assert_is_valid_sumexp	0.69	0.08	0.86
bin	0.39	0.04	0.44
biplot	4.89	0.14	5.09
biplot_corrections	3.12	0.11	3.33
biplot_covariates	6.28	0.21	6.55
block2lme	0	0	0
center	1.91	0.03	2.00
code	4.73	0.23	5.06
coefs	0.88	0.13	1.11
collapsed_entrezg_to_symbol	0	0	0
contrast_subgroup_cols	0.61	0.07	0.78
count_in	0.01	0.00	0.02
counts	0.42	0.00	0.44
counts2cpm	0.35	0.02	0.36
counts2tpm	0.36	0.00	0.35
cpm	0.42	0.02	0.44
create_design	0.84	0.06	0.99
default_formula	18.02	0.67	18.72
default_geom	0.78	0.06	0.93
default_sfile	0.02	0.00	0.02
demultiplex	0.01	0.00	0.01
dequantify	0	0	0
dequantify_compounddiscoverer	0.02	0.00	0.02
dot-merge	0.01	0.02	0.03
dot-plot_survival	4.52	0.56	5.53
dot-read_maxquant_proteingroups	0.14	0.02	0.16
download_contaminants	0.03	0.01	1.14
download_data	0	0	0
download_gtf	0	0	0
download_mcclain21	0	0	0
dt2mat	0	0	0
enrichment	1.59	0.25	1.87
entrezg_to_symbol	0	0	0
explore_transformations	4.30	0.16	4.49
extract_coef_features	5.03	0.17	5.31
extract_rectangle	0.14	0.09	0.33
fcluster	6.74	0.11	7.30
fcor	1.26	0.02	1.34
fdata	0.71	0.01	0.75
fdr2p	1.04	0.10	1.28
filter_exprs_replicated_in_some_subgroup	1.17	0.17	1.39
filter_features	0.52	0.08	0.70
filter_medoid	0.91	0.00	1.22
filter_samples	0.75	0.08	0.93
fit	14.53	0.31	15.35
fit_lmx	4.89	0.17	5.16
fitcoefs	0.76	0.14	0.97
fits	0.89	0.09	1.11
fitvars	1.50	0.13	1.72
fix_xlgenes	0	0	0
flevels	0.44	0.00	0.45
fnames	0.69	0.02	0.74
formula2str	0	0	0
fvalues	0.64	0.03	0.70
fvars	0.52	0.01	0.55
genome_to_orgdb	0	0	0
group_by_level	0	0	0
guess_compounddiscoverer_quantity	0	0	0
guess_fitsep	0.79	0.02	0.81
guess_maxquant_quantity	0.00	0.00	0.01
guess_sep	0.58	0.11	0.77
has_multiple_levels	0.05	0.00	0.05
hdlproteins	0.07	0.01	0.11
impute	3.60	0.05	3.72
invert_subgroups	0.65	0.03	0.70
is_collapsed_subset	0	0	0
is_correlation_matrix	0	0	0
is_diann_report	0.4	0.1	0.6
is_fastadt	0.1	0.0	0.1
is_file	0	0	0
is_fraction	0	0	0
is_imputed	0.78	0.03	0.83
is_positive_number	0	0	0
is_scalar_subset	0.34	0.02	0.39
is_sig	1.84	0.03	1.89
is_valid_formula	0.07	0.00	0.06
keep_connected_blocks	0.67	0.06	0.83
keep_connected_features	1.03	0.10	1.22
keep_replicated_features	0.83	0.06	1.00
label2index	0	0	0
list2mat	0	0	0
log2counts	0.34	0.01	0.37
log2cpm	0.49	0.00	0.50
log2diffs	0.42	0.02	0.45
log2proteins	0.33	0.03	0.36
log2sites	0.34	0.00	0.36
log2tpm	0.37	0.00	0.39
log2transform	4.93	0.13	5.08
logical2factor	0.01	0.00	0.02
make_alpha_palette	0.81	0.14	0.97
make_colors	0.02	0.00	0.01
make_volcano_dt	0.91	0.03	0.95
map_fvalues	0.39	0.01	0.41
matrix2sumexp	1.08	0.08	1.27
merge_sample_file	0.60	0.00	0.62
merge_sdata	0.68	0.14	0.89
message_df	0	0	0
modelvar	1.76	0.10	1.92
order_on_p	1.03	0.07	1.21
pca	3.28	0.19	3.61
pg_to_canonical	0	0	0
plot_contrast_venn	2.25	0.11	2.45
plot_contrastogram	2.55	0.17	2.93
plot_data	1.74	0.12	1.94
plot_densities	9.76	0.16	10.00
plot_design	0.81	0.00	0.83
plot_exprs	22.55	0.27	22.89
plot_exprs_per_coef	20.64	0.17	20.87
plot_fit_summary	2.00	0.08	2.18
plot_heatmap	1.89	0.01	1.92
plot_matrix	0.61	0.09	0.76
plot_sample_nas	6.13	0.16	6.28
plot_subgroup_points	5.75	0.11	5.93
plot_summary	12.67	0.23	12.97
plot_venn	0.06	0.00	0.06
plot_venn_heatmap	0.05	0.00	0.04
plot_violins	4.73	0.08	4.97
plot_volcano	11.50	0.22	11.86
preprocess_rnaseq_counts	0.56	0.00	0.57
pull_columns	0	0	0
read_affymetrix	0	0	0
read_contaminants	0.00	0.02	0.39
read_diann_proteingroups	132.08	5.09	134.68
read_fragpipe	8.21	0.17	8.19
read_maxquant_phosphosites	1.89	0.07	2.02
read_maxquant_proteingroups	1.37	0.06	1.45
read_metabolon	14.17	0.22	14.52
read_msigdt	0.02	0.00	0.01
read_olink	2.06	0.06	2.47
read_rectangles	0.25	0.09	0.37
read_rnaseq_counts	32.30	2.02	34.43
read_salmon	0	0	0
read_somascan	12.73	0.12	12.86
read_uniprotdt	0.32	0.00	0.31
reset_fit	3.84	0.08	4.01
rm_diann_contaminants	25.14	1.03	26.00
rm_missing_in_some_samples	0.67	0.08	0.85
rm_unmatched_samples	0.75	0.00	0.75
scaledlibsizes	0.50	0.00	0.51
scoremat	1.05	0.14	1.25
slevels	0.53	0.00	0.55
snames	0.53	0.00	0.55
split_extract_fixed	0.64	0.05	0.72
split_samples	1.53	0.05	1.64
stri_any_regex	0	0	0
stri_detect_fixed_in_collapsed	0.32	0.01	0.36
subgroup_matrix	0.46	0.09	0.65
subtract_baseline	4.39	0.11	4.58
sumexp_to_longdt	1.82	0.19	2.15
sumexp_to_tsv	0.64	0.01	0.67
sumexplist_to_longdt	1.50	0.07	1.63
summarize_fit	1.72	0.04	1.89
svalues	0.43	0.03	0.50
svars	0.39	0.03	0.44
systematic_nas	0.79	0.00	0.81
tag_features	0.98	0.05	1.03
tag_hdlproteins	0.73	0.00	0.76
taxon2org	0	0	0
tpm	0.38	0.00	0.38
uncollapse	0.02	0.00	0.01
values	0.51	0.00	0.52
varlevels_dont_clash	0.03	0.00	0.03
venn_detects	0.53	0.01	0.56
weights	0.57	0.00	0.56
write_xl	0.68	0.11	0.91
zero_to_na	0	0	0

CHECK results for autonomics on palomino4

Summary

Command output

Installation output

Tests output

Example timings