Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-30 11:35:25 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 112/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.12.0 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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. |
Package: autonomics |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.12.0.tar.gz |
StartedAt: 2024-05-29 19:06:30 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 19:21:35 -0400 (Wed, 29 May 2024) |
EllapsedTime: 905.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: autonomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘autonomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘autonomics’ version ‘1.12.0’ * 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 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 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 ... NOTE checkRd: (-1) dequantify.Rd:24: Lost braces; missing escapes or markup? 24 | Encode {channel} as suffix. | ^ * 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 103.660 2.467 107.308 read_rnaseq_counts 31.212 3.262 35.021 rm_diann_contaminants 22.640 0.587 23.453 plot_exprs 21.321 0.311 21.816 plot_exprs_per_coef 20.339 0.225 20.704 default_formula 15.369 0.390 15.963 analyze 13.719 0.234 14.092 read_metabolon 13.698 0.170 13.984 read_somascan 13.602 0.142 13.861 fit 13.410 0.268 13.810 plot_summary 12.743 0.178 13.034 plot_volcano 10.467 0.159 10.704 plot_densities 9.791 0.324 10.219 plot_sample_nas 6.704 0.085 6.846 read_fragpipe 6.128 0.128 6.316 plot_subgroup_points 6.128 0.124 6.314 biplot_covariates 5.844 0.111 6.010 code 5.351 0.111 5.514 extract_coef_features 5.123 0.158 5.327 subtract_baseline 5.144 0.131 5.334 dot-plot_survival 4.618 0.569 5.249 reset_fit 4.912 0.115 5.075 * 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’ for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)
autonomics.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 153.577 8.817 164.608
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.001 | 0.000 | 0.000 | |
CONTAMINANTSURL | 0 | 0 | 0 | |
FITSEP | 0.000 | 0.000 | 0.001 | |
LINMOD_ENGINES | 0.001 | 0.000 | 0.000 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0.001 | 0.000 | 0.000 | |
abstract_fit | 1.430 | 0.081 | 1.528 | |
add_adjusted_pvalues | 0.651 | 0.025 | 0.682 | |
add_assay_means | 0.538 | 0.012 | 0.553 | |
add_facetvars | 2.457 | 0.120 | 2.598 | |
add_opentargets_by_uniprot | 0.468 | 0.012 | 0.487 | |
add_psp | 0.621 | 0.018 | 0.647 | |
add_smiles | 0.568 | 0.071 | 0.652 | |
analysis | 0.469 | 0.010 | 0.482 | |
analyze | 13.719 | 0.234 | 14.092 | |
annotate_maxquant | 0.909 | 0.041 | 0.959 | |
annotate_uniprot_rest | 0.085 | 0.015 | 2.191 | |
assert_is_valid_sumexp | 0.662 | 0.054 | 0.725 | |
bin | 0.448 | 0.013 | 0.464 | |
biplot | 4.049 | 0.116 | 4.206 | |
biplot_corrections | 3.556 | 0.098 | 3.693 | |
biplot_covariates | 5.844 | 0.111 | 6.010 | |
block2lme | 0.003 | 0.000 | 0.003 | |
center | 2.422 | 0.042 | 2.489 | |
code | 5.351 | 0.111 | 5.514 | |
coefs | 0.814 | 0.067 | 0.896 | |
collapsed_entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.656 | 0.046 | 0.707 | |
count_in | 0.001 | 0.001 | 0.001 | |
counts | 0.439 | 0.006 | 0.448 | |
counts2cpm | 0.440 | 0.009 | 0.454 | |
counts2tpm | 0.387 | 0.005 | 0.395 | |
cpm | 0.418 | 0.006 | 0.429 | |
create_design | 0.775 | 0.056 | 0.843 | |
default_formula | 15.369 | 0.390 | 15.963 | |
default_geom | 0.638 | 0.059 | 0.706 | |
default_sfile | 0.002 | 0.001 | 0.003 | |
demultiplex | 0.018 | 0.002 | 0.020 | |
dequantify | 0.002 | 0.000 | 0.002 | |
dot-merge | 0.022 | 0.001 | 0.023 | |
dot-plot_survival | 4.618 | 0.569 | 5.249 | |
dot-read_maxquant_proteingroups | 0.125 | 0.008 | 0.135 | |
download_contaminants | 0.024 | 0.008 | 2.850 | |
download_data | 0.001 | 0.001 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.001 | 0.001 | |
dt2mat | 0.004 | 0.001 | 0.004 | |
enrichment | 1.245 | 0.039 | 1.297 | |
entrezg_to_symbol | 0.000 | 0.001 | 0.002 | |
explore_transformations | 3.719 | 0.126 | 3.873 | |
extract_coef_features | 5.123 | 0.158 | 5.327 | |
extract_rectangle | 0.157 | 0.048 | 0.207 | |
fdata | 0.625 | 0.018 | 0.647 | |
fdr2p | 1.039 | 0.073 | 1.122 | |
filter_exprs_replicated_in_some_subgroup | 1.152 | 0.076 | 1.241 | |
filter_features | 0.610 | 0.054 | 0.675 | |
filter_medoid | 0.815 | 0.025 | 0.844 | |
filter_samples | 0.676 | 0.050 | 0.733 | |
fit | 13.410 | 0.268 | 13.810 | |
fit_lmx | 4.325 | 0.079 | 4.430 | |
fitcoefs | 0.825 | 0.049 | 0.882 | |
fits | 0.726 | 0.047 | 0.778 | |
fitvars | 1.101 | 0.051 | 1.160 | |
fix_xlgenes | 0.033 | 0.001 | 0.034 | |
flevels | 0.460 | 0.010 | 0.472 | |
fnames | 0.504 | 0.010 | 0.517 | |
formula2str | 0 | 0 | 0 | |
fvalues | 0.422 | 0.006 | 0.429 | |
fvars | 0.433 | 0.008 | 0.443 | |
genome_to_orgdb | 0.000 | 0.001 | 0.001 | |
group_by_level | 0.001 | 0.001 | 0.001 | |
guess_fitsep | 0.570 | 0.008 | 0.581 | |
guess_maxquant_quantity | 0.007 | 0.001 | 0.008 | |
guess_sep | 0.541 | 0.046 | 0.593 | |
has_multiple_levels | 0.060 | 0.002 | 0.064 | |
hdlproteins | 0.051 | 0.034 | 0.093 | |
impute | 3.151 | 0.045 | 3.217 | |
invert_subgroups | 0.721 | 0.008 | 0.731 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_diann_report | 0.241 | 0.051 | 0.370 | |
is_fastadt | 0.069 | 0.001 | 0.071 | |
is_file | 0.000 | 0.001 | 0.000 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.785 | 0.008 | 0.796 | |
is_positive_number | 0.001 | 0.001 | 0.002 | |
is_scalar_subset | 0.405 | 0.010 | 0.419 | |
is_sig | 1.366 | 0.018 | 1.395 | |
is_valid_formula | 0.052 | 0.001 | 0.054 | |
keep_connected_blocks | 0.591 | 0.055 | 0.660 | |
keep_connected_features | 0.816 | 0.059 | 0.887 | |
keep_replicated_features | 0.921 | 0.051 | 0.981 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.442 | 0.007 | 0.453 | |
log2cpm | 0.443 | 0.006 | 0.453 | |
log2diffs | 0.373 | 0.009 | 0.387 | |
log2proteins | 0.341 | 0.007 | 0.349 | |
log2sites | 0.392 | 0.009 | 0.407 | |
log2tpm | 0.482 | 0.008 | 0.495 | |
log2transform | 4.010 | 0.079 | 4.133 | |
logical2factor | 0.001 | 0.000 | 0.002 | |
make_alpha_palette | 0.716 | 0.060 | 0.783 | |
make_colors | 0.009 | 0.001 | 0.010 | |
make_volcano_dt | 0.915 | 0.014 | 0.935 | |
map_fvalues | 0.460 | 0.010 | 0.475 | |
matrix2sumexp | 1.164 | 0.060 | 1.239 | |
merge_sample_file | 0.538 | 0.013 | 0.558 | |
merge_sdata | 0.627 | 0.058 | 0.692 | |
message_df | 0.002 | 0.000 | 0.003 | |
modelvar | 1.760 | 0.062 | 1.836 | |
order_on_p | 1.071 | 0.075 | 1.161 | |
pca | 3.253 | 0.131 | 3.434 | |
pg_to_canonical | 0.005 | 0.001 | 0.005 | |
plot_contrast_venn | 2.117 | 0.072 | 2.213 | |
plot_contrastogram | 2.631 | 0.186 | 2.846 | |
plot_data | 1.441 | 0.066 | 1.522 | |
plot_densities | 9.791 | 0.324 | 10.219 | |
plot_design | 0.703 | 0.014 | 0.725 | |
plot_exprs | 21.321 | 0.311 | 21.816 | |
plot_exprs_per_coef | 20.339 | 0.225 | 20.704 | |
plot_fit_summary | 1.904 | 0.068 | 1.991 | |
plot_heatmap | 1.882 | 0.020 | 1.925 | |
plot_matrix | 0.606 | 0.053 | 0.668 | |
plot_sample_nas | 6.704 | 0.085 | 6.846 | |
plot_subgroup_points | 6.128 | 0.124 | 6.314 | |
plot_summary | 12.743 | 0.178 | 13.034 | |
plot_venn | 0.018 | 0.001 | 0.021 | |
plot_venn_heatmap | 0.046 | 0.004 | 0.050 | |
plot_violins | 4.010 | 0.099 | 4.182 | |
plot_volcano | 10.467 | 0.159 | 10.704 | |
preprocess_rnaseq_counts | 0.445 | 0.006 | 0.453 | |
pull_columns | 0.002 | 0.001 | 0.004 | |
read_affymetrix | 0.000 | 0.001 | 0.000 | |
read_contaminants | 0.010 | 0.002 | 0.012 | |
read_diann_proteingroups | 103.660 | 2.467 | 107.308 | |
read_fragpipe | 6.128 | 0.128 | 6.316 | |
read_maxquant_phosphosites | 1.582 | 0.032 | 1.621 | |
read_maxquant_proteingroups | 1.333 | 0.026 | 1.390 | |
read_metabolon | 13.698 | 0.170 | 13.984 | |
read_msigdt | 0.001 | 0.001 | 0.001 | |
read_olink | 1.439 | 0.060 | 1.517 | |
read_rectangles | 0.288 | 0.043 | 0.335 | |
read_rnaseq_counts | 31.212 | 3.262 | 35.021 | |
read_salmon | 0.000 | 0.001 | 0.000 | |
read_somascan | 13.602 | 0.142 | 13.861 | |
read_uniprotdt | 0.307 | 0.025 | 0.335 | |
reset_fit | 4.912 | 0.115 | 5.075 | |
rm_diann_contaminants | 22.640 | 0.587 | 23.453 | |
rm_missing_in_some_samples | 0.587 | 0.054 | 0.651 | |
rm_unmatched_samples | 0.645 | 0.010 | 0.661 | |
scaledlibsizes | 0.469 | 0.037 | 0.509 | |
scoremat | 1.137 | 0.065 | 1.224 | |
slevels | 0.502 | 0.015 | 0.521 | |
snames | 0.447 | 0.013 | 0.463 | |
split_extract_fixed | 0.566 | 0.051 | 0.627 | |
split_samples | 1.364 | 0.067 | 1.449 | |
stri_any_regex | 0.001 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.419 | 0.010 | 0.435 | |
subgroup_matrix | 0.645 | 0.056 | 0.716 | |
subtract_baseline | 5.144 | 0.131 | 5.334 | |
sumexp_to_longdt | 2.144 | 0.141 | 2.321 | |
sumexp_to_tsv | 0.603 | 0.016 | 0.629 | |
sumexplist_to_longdt | 1.851 | 0.035 | 1.906 | |
summarize_fit | 1.715 | 0.072 | 1.810 | |
svalues | 0.486 | 0.011 | 0.501 | |
svars | 0.458 | 0.011 | 0.477 | |
systematic_nas | 0.579 | 0.009 | 0.592 | |
tag_features | 1.025 | 0.043 | 1.084 | |
tag_hdlproteins | 0.558 | 0.075 | 0.640 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.406 | 0.009 | 0.419 | |
uncollapse | 0.013 | 0.001 | 0.015 | |
values | 0.476 | 0.016 | 0.495 | |
varlevels_dont_clash | 0.020 | 0.001 | 0.021 | |
venn_detects | 0.590 | 0.016 | 0.611 | |
weights | 0.450 | 0.009 | 0.465 | |
write_xl | 0.829 | 0.082 | 0.928 | |
zero_to_na | 0.002 | 0.001 | 0.004 | |