Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:26 -0400 (Fri, 07 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" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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: 2024-06-05 18:49:15 -0400 (Wed, 05 Jun 2024) |
EndedAt: 2024-06-05 19:03:20 -0400 (Wed, 05 Jun 2024) |
EllapsedTime: 844.8 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 96.241 2.064 98.898 read_rnaseq_counts 29.133 3.177 32.504 plot_exprs 20.181 0.119 20.345 rm_diann_contaminants 19.632 0.431 20.124 plot_exprs_per_coef 19.810 0.099 19.950 default_formula 14.094 0.333 14.517 read_somascan 12.675 0.049 12.759 read_metabolon 12.546 0.082 12.653 analyze 12.386 0.108 12.518 fit 11.726 0.145 11.886 plot_summary 11.668 0.083 11.777 plot_volcano 10.524 0.081 10.631 plot_densities 9.068 0.265 9.372 plot_sample_nas 7.863 0.090 7.981 read_fragpipe 6.155 0.109 6.299 biplot_covariates 5.332 0.061 5.405 dot-plot_survival 4.535 0.561 5.125 * 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 141.417 8.461 150.615
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0 | 0 | 0 | |
CONTAMINANTSURL | 0 | 0 | 0 | |
FITSEP | 0 | 0 | 0 | |
LINMOD_ENGINES | 0.000 | 0.000 | 0.001 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0.000 | 0.000 | 0.001 | |
TESTS | 0 | 0 | 0 | |
abstract_fit | 1.307 | 0.069 | 1.383 | |
add_adjusted_pvalues | 0.595 | 0.018 | 0.614 | |
add_assay_means | 0.459 | 0.007 | 0.467 | |
add_facetvars | 2.452 | 0.122 | 2.582 | |
add_opentargets_by_uniprot | 0.464 | 0.010 | 0.477 | |
add_psp | 0.611 | 0.015 | 0.627 | |
add_smiles | 0.539 | 0.051 | 0.594 | |
analysis | 0.377 | 0.007 | 0.383 | |
analyze | 12.386 | 0.108 | 12.518 | |
annotate_maxquant | 0.901 | 0.033 | 0.940 | |
annotate_uniprot_rest | 0.087 | 0.013 | 2.786 | |
assert_is_valid_sumexp | 0.610 | 0.044 | 0.655 | |
bin | 0.465 | 0.009 | 0.476 | |
biplot | 3.817 | 0.076 | 3.906 | |
biplot_corrections | 3.306 | 0.058 | 3.373 | |
biplot_covariates | 5.332 | 0.061 | 5.405 | |
block2lme | 0.003 | 0.001 | 0.003 | |
center | 2.158 | 0.019 | 2.181 | |
code | 4.695 | 0.079 | 4.788 | |
coefs | 0.741 | 0.038 | 0.782 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.683 | 0.048 | 0.735 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.362 | 0.002 | 0.365 | |
counts2cpm | 0.479 | 0.004 | 0.504 | |
counts2tpm | 0.439 | 0.004 | 0.444 | |
cpm | 0.415 | 0.004 | 0.419 | |
create_design | 0.670 | 0.053 | 0.727 | |
default_formula | 14.094 | 0.333 | 14.517 | |
default_geom | 0.520 | 0.037 | 0.559 | |
default_sfile | 0.001 | 0.000 | 0.002 | |
demultiplex | 0.011 | 0.000 | 0.012 | |
dequantify | 0.002 | 0.000 | 0.002 | |
dot-merge | 0.019 | 0.001 | 0.020 | |
dot-plot_survival | 4.535 | 0.561 | 5.125 | |
dot-read_maxquant_proteingroups | 0.105 | 0.004 | 0.110 | |
download_contaminants | 0.023 | 0.006 | 4.094 | |
download_data | 0.000 | 0.001 | 0.002 | |
download_gtf | 0.000 | 0.000 | 0.001 | |
download_mcclain21 | 0.000 | 0.001 | 0.001 | |
dt2mat | 0.004 | 0.001 | 0.006 | |
enrichment | 1.321 | 0.031 | 1.355 | |
entrezg_to_symbol | 0.001 | 0.001 | 0.001 | |
explore_transformations | 3.571 | 0.094 | 3.671 | |
extract_coef_features | 4.710 | 0.117 | 4.841 | |
extract_rectangle | 0.161 | 0.044 | 0.206 | |
fdata | 0.590 | 0.012 | 0.603 | |
fdr2p | 0.956 | 0.068 | 1.034 | |
filter_exprs_replicated_in_some_subgroup | 1.062 | 0.066 | 1.151 | |
filter_features | 0.535 | 0.042 | 0.579 | |
filter_medoid | 0.781 | 0.019 | 0.800 | |
filter_samples | 0.607 | 0.045 | 0.654 | |
fit | 11.726 | 0.145 | 11.886 | |
fit_lmx | 4.165 | 0.072 | 4.251 | |
fitcoefs | 0.760 | 0.047 | 0.810 | |
fits | 0.768 | 0.042 | 0.813 | |
fitvars | 1.105 | 0.047 | 1.157 | |
fix_xlgenes | 0.001 | 0.000 | 0.001 | |
flevels | 0.389 | 0.004 | 0.393 | |
fnames | 0.521 | 0.007 | 0.528 | |
formula2str | 0.000 | 0.000 | 0.001 | |
fvalues | 0.390 | 0.005 | 0.395 | |
fvars | 0.343 | 0.004 | 0.347 | |
genome_to_orgdb | 0.000 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.001 | 0.002 | |
guess_fitsep | 0.534 | 0.008 | 0.544 | |
guess_maxquant_quantity | 0.004 | 0.001 | 0.005 | |
guess_sep | 0.454 | 0.035 | 0.490 | |
has_multiple_levels | 0.062 | 0.003 | 0.064 | |
hdlproteins | 0.050 | 0.041 | 0.094 | |
impute | 3.172 | 0.030 | 3.209 | |
invert_subgroups | 0.759 | 0.007 | 0.768 | |
is_collapsed_subset | 0.001 | 0.001 | 0.001 | |
is_diann_report | 0.247 | 0.047 | 0.369 | |
is_fastadt | 0.056 | 0.002 | 0.058 | |
is_file | 0.000 | 0.001 | 0.000 | |
is_fraction | 0.002 | 0.001 | 0.003 | |
is_imputed | 0.760 | 0.007 | 0.769 | |
is_positive_number | 0.001 | 0.000 | 0.002 | |
is_scalar_subset | 0.385 | 0.006 | 0.392 | |
is_sig | 1.340 | 0.011 | 1.354 | |
is_valid_formula | 0.047 | 0.001 | 0.048 | |
keep_connected_blocks | 0.577 | 0.052 | 0.641 | |
keep_connected_features | 0.822 | 0.052 | 0.879 | |
keep_replicated_features | 0.832 | 0.042 | 0.879 | |
label2index | 0 | 0 | 0 | |
list2mat | 0.000 | 0.000 | 0.001 | |
log2counts | 0.485 | 0.002 | 0.489 | |
log2cpm | 0.443 | 0.002 | 0.446 | |
log2diffs | 0.341 | 0.004 | 0.345 | |
log2proteins | 0.385 | 0.005 | 0.390 | |
log2sites | 0.372 | 0.006 | 0.378 | |
log2tpm | 0.394 | 0.002 | 0.396 | |
log2transform | 3.800 | 0.049 | 3.857 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.767 | 0.068 | 0.848 | |
make_colors | 0.010 | 0.001 | 0.011 | |
make_volcano_dt | 0.765 | 0.006 | 0.771 | |
map_fvalues | 0.375 | 0.004 | 0.379 | |
matrix2sumexp | 1.072 | 0.048 | 1.123 | |
merge_sample_file | 0.581 | 0.009 | 0.590 | |
merge_sdata | 0.612 | 0.061 | 0.677 | |
message_df | 0.003 | 0.000 | 0.004 | |
modelvar | 1.626 | 0.089 | 1.741 | |
order_on_p | 1.039 | 0.042 | 1.083 | |
pca | 3.028 | 0.068 | 3.119 | |
pg_to_canonical | 0.006 | 0.001 | 0.007 | |
plot_contrast_venn | 1.828 | 0.050 | 1.884 | |
plot_contrastogram | 2.334 | 0.156 | 2.502 | |
plot_data | 1.261 | 0.054 | 1.320 | |
plot_densities | 9.068 | 0.265 | 9.372 | |
plot_design | 0.639 | 0.009 | 0.649 | |
plot_exprs | 20.181 | 0.119 | 20.345 | |
plot_exprs_per_coef | 19.810 | 0.099 | 19.950 | |
plot_fit_summary | 1.944 | 0.055 | 2.006 | |
plot_heatmap | 1.565 | 0.007 | 1.571 | |
plot_matrix | 0.518 | 0.045 | 0.570 | |
plot_sample_nas | 7.863 | 0.090 | 7.981 | |
plot_subgroup_points | 4.843 | 0.067 | 4.927 | |
plot_summary | 11.668 | 0.083 | 11.777 | |
plot_venn | 0.016 | 0.001 | 0.018 | |
plot_venn_heatmap | 0.044 | 0.004 | 0.047 | |
plot_violins | 4.046 | 0.078 | 4.138 | |
plot_volcano | 10.524 | 0.081 | 10.631 | |
preprocess_rnaseq_counts | 0.439 | 0.003 | 0.443 | |
pull_columns | 0.002 | 0.001 | 0.002 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.006 | 0.001 | 0.008 | |
read_diann_proteingroups | 96.241 | 2.064 | 98.898 | |
read_fragpipe | 6.155 | 0.109 | 6.299 | |
read_maxquant_phosphosites | 1.469 | 0.025 | 1.495 | |
read_maxquant_proteingroups | 1.295 | 0.022 | 1.334 | |
read_metabolon | 12.546 | 0.082 | 12.653 | |
read_msigdt | 0.001 | 0.001 | 0.002 | |
read_olink | 1.481 | 0.053 | 1.543 | |
read_rectangles | 0.266 | 0.036 | 0.304 | |
read_rnaseq_counts | 29.133 | 3.177 | 32.504 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 12.675 | 0.049 | 12.759 | |
read_uniprotdt | 0.302 | 0.016 | 0.319 | |
reset_fit | 4.164 | 0.063 | 4.237 | |
rm_diann_contaminants | 19.632 | 0.431 | 20.124 | |
rm_missing_in_some_samples | 0.551 | 0.055 | 0.609 | |
rm_unmatched_samples | 0.634 | 0.007 | 0.643 | |
scaledlibsizes | 0.490 | 0.024 | 0.515 | |
scoremat | 1.124 | 0.041 | 1.168 | |
slevels | 0.484 | 0.011 | 0.496 | |
snames | 0.486 | 0.006 | 0.493 | |
split_extract_fixed | 0.600 | 0.048 | 0.652 | |
split_samples | 1.310 | 0.063 | 1.379 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.394 | 0.005 | 0.401 | |
subgroup_matrix | 0.526 | 0.060 | 0.589 | |
subtract_baseline | 4.870 | 0.078 | 4.976 | |
sumexp_to_longdt | 1.765 | 0.079 | 1.849 | |
sumexp_to_tsv | 0.451 | 0.005 | 0.457 | |
sumexplist_to_longdt | 1.665 | 0.018 | 1.686 | |
summarize_fit | 1.550 | 0.062 | 1.621 | |
svalues | 0.489 | 0.010 | 0.501 | |
svars | 0.477 | 0.006 | 0.485 | |
systematic_nas | 0.593 | 0.008 | 0.603 | |
tag_features | 0.949 | 0.029 | 0.982 | |
tag_hdlproteins | 0.521 | 0.023 | 0.545 | |
taxon2org | 0.001 | 0.001 | 0.000 | |
tpm | 0.478 | 0.003 | 0.482 | |
uncollapse | 0.014 | 0.000 | 0.014 | |
values | 0.508 | 0.012 | 0.521 | |
varlevels_dont_clash | 0.025 | 0.001 | 0.026 | |
venn_detects | 0.540 | 0.007 | 0.549 | |
weights | 0.362 | 0.002 | 0.364 | |
write_xl | 0.802 | 0.067 | 0.874 | |
zero_to_na | 0.002 | 0.000 | 0.003 | |