Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-11 14:41 -0400 (Tue, 11 Jun 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" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
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 1.12.1 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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: 1.12.1 |
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_1.12.1.tar.gz |
StartedAt: 2024-06-09 18:48:09 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 19:02:17 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 847.8 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_1.12.1.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 ‘1.12.1’ * 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 95.597 2.102 98.309 read_rnaseq_counts 28.860 3.247 32.559 plot_exprs 20.967 0.116 21.126 rm_diann_contaminants 20.018 0.373 20.454 plot_exprs_per_coef 19.386 0.099 19.525 default_formula 14.298 0.330 14.728 plot_summary 12.516 0.085 12.631 analyze 12.247 0.119 12.398 read_metabolon 12.092 0.082 12.196 fit 11.946 0.159 12.120 read_somascan 11.968 0.035 12.020 plot_volcano 10.871 0.118 11.030 plot_densities 8.551 0.261 8.841 plot_sample_nas 7.589 0.090 7.697 read_fragpipe 5.844 0.097 5.967 biplot_covariates 5.371 0.069 5.456 dot-plot_survival 4.670 0.552 5.248 extract_coef_features 4.940 0.134 5.090 download_contaminants 0.026 0.008 9.587 * 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 140.498 8.119 149.418
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.001 | |
CONTAMINANTSURL | 0 | 0 | 0 | |
FITSEP | 0 | 0 | 0 | |
LINMOD_ENGINES | 0.000 | 0.001 | 0.000 | |
MAXQUANT_PATTERNS | 0.001 | 0.000 | 0.000 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0.001 | 0.000 | 0.000 | |
abstract_fit | 1.381 | 0.066 | 1.453 | |
add_adjusted_pvalues | 0.648 | 0.022 | 0.675 | |
add_assay_means | 0.497 | 0.007 | 0.506 | |
add_facetvars | 2.401 | 0.124 | 2.537 | |
add_opentargets_by_uniprot | 0.468 | 0.008 | 0.482 | |
add_psp | 0.571 | 0.013 | 0.585 | |
add_smiles | 0.595 | 0.049 | 0.649 | |
analysis | 0.430 | 0.007 | 0.446 | |
analyze | 12.247 | 0.119 | 12.398 | |
annotate_maxquant | 0.884 | 0.032 | 0.919 | |
annotate_uniprot_rest | 0.077 | 0.013 | 2.670 | |
assert_is_valid_sumexp | 0.592 | 0.049 | 0.646 | |
bin | 0.481 | 0.012 | 0.494 | |
biplot | 3.714 | 0.069 | 3.795 | |
biplot_corrections | 3.139 | 0.057 | 3.205 | |
biplot_covariates | 5.371 | 0.069 | 5.456 | |
block2lme | 0.002 | 0.001 | 0.003 | |
center | 2.257 | 0.034 | 2.299 | |
code | 4.781 | 0.072 | 4.867 | |
coefs | 0.752 | 0.042 | 0.796 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.000 | |
contrast_subgroup_cols | 0.609 | 0.039 | 0.650 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.447 | 0.004 | 0.452 | |
counts2cpm | 0.382 | 0.003 | 0.386 | |
counts2tpm | 0.374 | 0.003 | 0.377 | |
cpm | 0.337 | 0.001 | 0.338 | |
create_design | 0.678 | 0.042 | 0.721 | |
default_formula | 14.298 | 0.330 | 14.728 | |
default_geom | 0.559 | 0.050 | 0.613 | |
default_sfile | 0.001 | 0.000 | 0.001 | |
demultiplex | 0.018 | 0.000 | 0.019 | |
dequantify | 0.002 | 0.000 | 0.003 | |
dot-merge | 0.025 | 0.001 | 0.026 | |
dot-plot_survival | 4.670 | 0.552 | 5.248 | |
dot-read_maxquant_proteingroups | 0.130 | 0.006 | 0.136 | |
download_contaminants | 0.026 | 0.008 | 9.587 | |
download_data | 0.000 | 0.001 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.001 | 0.001 | |
dt2mat | 0.005 | 0.001 | 0.006 | |
enrichment | 1.127 | 0.023 | 1.152 | |
entrezg_to_symbol | 0.001 | 0.001 | 0.001 | |
explore_transformations | 3.131 | 0.102 | 3.236 | |
extract_coef_features | 4.940 | 0.134 | 5.090 | |
extract_rectangle | 0.159 | 0.047 | 0.210 | |
fdata | 0.582 | 0.011 | 0.594 | |
fdr2p | 1.000 | 0.057 | 1.061 | |
filter_exprs_replicated_in_some_subgroup | 1.038 | 0.054 | 1.094 | |
filter_features | 0.574 | 0.060 | 0.645 | |
filter_medoid | 0.735 | 0.016 | 0.752 | |
filter_samples | 0.636 | 0.046 | 0.691 | |
fit | 11.946 | 0.159 | 12.120 | |
fit_lmx | 4.366 | 0.062 | 4.439 | |
fitcoefs | 0.885 | 0.050 | 0.960 | |
fits | 0.767 | 0.049 | 0.822 | |
fitvars | 1.051 | 0.056 | 1.116 | |
fix_xlgenes | 0.001 | 0.000 | 0.002 | |
flevels | 0.372 | 0.004 | 0.378 | |
fnames | 0.399 | 0.004 | 0.403 | |
formula2str | 0.000 | 0.000 | 0.001 | |
fvalues | 0.365 | 0.003 | 0.369 | |
fvars | 0.359 | 0.005 | 0.364 | |
genome_to_orgdb | 0 | 0 | 0 | |
group_by_level | 0.001 | 0.000 | 0.002 | |
guess_fitsep | 0.594 | 0.007 | 0.603 | |
guess_maxquant_quantity | 0.006 | 0.001 | 0.007 | |
guess_sep | 0.586 | 0.042 | 0.630 | |
has_multiple_levels | 0.049 | 0.002 | 0.050 | |
hdlproteins | 0.051 | 0.032 | 0.088 | |
impute | 3.085 | 0.032 | 3.122 | |
invert_subgroups | 0.808 | 0.008 | 0.819 | |
is_collapsed_subset | 0.000 | 0.000 | 0.001 | |
is_diann_report | 0.229 | 0.043 | 0.351 | |
is_fastadt | 0.051 | 0.001 | 0.051 | |
is_file | 0.000 | 0.000 | 0.001 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.746 | 0.007 | 0.755 | |
is_positive_number | 0.002 | 0.000 | 0.001 | |
is_scalar_subset | 0.366 | 0.006 | 0.373 | |
is_sig | 1.195 | 0.012 | 1.208 | |
is_valid_formula | 0.055 | 0.001 | 0.056 | |
keep_connected_blocks | 0.643 | 0.053 | 0.706 | |
keep_connected_features | 0.899 | 0.048 | 0.951 | |
keep_replicated_features | 0.888 | 0.048 | 0.938 | |
label2index | 0.000 | 0.000 | 0.001 | |
list2mat | 0 | 0 | 0 | |
log2counts | 0.417 | 0.002 | 0.420 | |
log2cpm | 0.440 | 0.003 | 0.444 | |
log2diffs | 0.289 | 0.004 | 0.292 | |
log2proteins | 0.378 | 0.005 | 0.383 | |
log2sites | 0.317 | 0.006 | 0.322 | |
log2tpm | 0.346 | 0.002 | 0.348 | |
log2transform | 3.821 | 0.050 | 3.884 | |
logical2factor | 0.002 | 0.001 | 0.003 | |
make_alpha_palette | 0.635 | 0.060 | 0.697 | |
make_colors | 0.010 | 0.001 | 0.011 | |
make_volcano_dt | 0.926 | 0.010 | 0.938 | |
map_fvalues | 0.448 | 0.008 | 0.456 | |
matrix2sumexp | 1.006 | 0.046 | 1.058 | |
merge_sample_file | 0.528 | 0.010 | 0.539 | |
merge_sdata | 0.606 | 0.060 | 0.667 | |
message_df | 0.003 | 0.001 | 0.003 | |
modelvar | 1.842 | 0.060 | 1.908 | |
order_on_p | 0.965 | 0.051 | 1.022 | |
pca | 3.266 | 0.065 | 3.341 | |
pg_to_canonical | 0.005 | 0.000 | 0.006 | |
plot_contrast_venn | 1.993 | 0.048 | 2.048 | |
plot_contrastogram | 2.730 | 0.176 | 2.928 | |
plot_data | 1.558 | 0.075 | 1.643 | |
plot_densities | 8.551 | 0.261 | 8.841 | |
plot_design | 0.627 | 0.008 | 0.636 | |
plot_exprs | 20.967 | 0.116 | 21.126 | |
plot_exprs_per_coef | 19.386 | 0.099 | 19.525 | |
plot_fit_summary | 1.992 | 0.050 | 2.050 | |
plot_heatmap | 1.954 | 0.011 | 1.970 | |
plot_matrix | 0.557 | 0.039 | 0.596 | |
plot_sample_nas | 7.589 | 0.090 | 7.697 | |
plot_subgroup_points | 4.418 | 0.054 | 4.483 | |
plot_summary | 12.516 | 0.085 | 12.631 | |
plot_venn | 0.016 | 0.002 | 0.018 | |
plot_venn_heatmap | 0.047 | 0.004 | 0.051 | |
plot_violins | 4.105 | 0.076 | 4.192 | |
plot_volcano | 10.871 | 0.118 | 11.030 | |
preprocess_rnaseq_counts | 0.335 | 0.002 | 0.338 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0.000 | 0.001 | 0.000 | |
read_contaminants | 0.008 | 0.001 | 0.009 | |
read_diann_proteingroups | 95.597 | 2.102 | 98.309 | |
read_fragpipe | 5.844 | 0.097 | 5.967 | |
read_maxquant_phosphosites | 1.710 | 0.025 | 1.754 | |
read_maxquant_proteingroups | 1.428 | 0.020 | 1.487 | |
read_metabolon | 12.092 | 0.082 | 12.196 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.369 | 0.058 | 1.437 | |
read_rectangles | 0.299 | 0.045 | 0.359 | |
read_rnaseq_counts | 28.860 | 3.247 | 32.559 | |
read_salmon | 0.000 | 0.000 | 0.001 | |
read_somascan | 11.968 | 0.035 | 12.020 | |
read_uniprotdt | 0.302 | 0.029 | 0.331 | |
reset_fit | 4.235 | 0.059 | 4.300 | |
rm_diann_contaminants | 20.018 | 0.373 | 20.454 | |
rm_missing_in_some_samples | 0.519 | 0.058 | 0.582 | |
rm_unmatched_samples | 0.611 | 0.005 | 0.618 | |
scaledlibsizes | 0.509 | 0.038 | 0.551 | |
scoremat | 1.017 | 0.054 | 1.075 | |
slevels | 0.417 | 0.008 | 0.426 | |
snames | 0.493 | 0.009 | 0.505 | |
split_extract_fixed | 0.616 | 0.050 | 0.671 | |
split_samples | 1.168 | 0.053 | 1.227 | |
stri_any_regex | 0.000 | 0.001 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.390 | 0.006 | 0.396 | |
subgroup_matrix | 0.573 | 0.047 | 0.623 | |
subtract_baseline | 4.774 | 0.070 | 4.858 | |
sumexp_to_longdt | 2.062 | 0.091 | 2.161 | |
sumexp_to_tsv | 0.611 | 0.007 | 0.619 | |
sumexplist_to_longdt | 1.710 | 0.013 | 1.727 | |
summarize_fit | 1.765 | 0.053 | 1.822 | |
svalues | 0.443 | 0.005 | 0.449 | |
svars | 0.393 | 0.004 | 0.397 | |
systematic_nas | 0.664 | 0.006 | 0.671 | |
tag_features | 0.957 | 0.029 | 0.991 | |
tag_hdlproteins | 0.523 | 0.049 | 0.575 | |
taxon2org | 0.001 | 0.000 | 0.002 | |
tpm | 0.456 | 0.002 | 0.460 | |
uncollapse | 0.01 | 0.00 | 0.01 | |
values | 0.593 | 0.026 | 0.629 | |
varlevels_dont_clash | 0.022 | 0.001 | 0.024 | |
venn_detects | 0.527 | 0.008 | 0.537 | |
weights | 0.417 | 0.002 | 0.421 | |
write_xl | 0.761 | 0.060 | 0.826 | |
zero_to_na | 0.002 | 0.002 | 0.003 | |