Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:06 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | 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: 2024-07-22 12:02:26 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 12:18:27 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 961.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: autonomics.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.6 * 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 96.738 1.832 102.701 read_rnaseq_counts 30.655 1.219 35.218 plot_exprs 21.053 0.186 21.667 rm_diann_contaminants 20.690 0.362 25.601 plot_exprs_per_coef 19.302 0.151 20.360 default_formula 15.802 0.351 17.231 read_somascan 13.383 0.083 14.976 analyze 13.030 0.142 13.396 read_metabolon 12.879 0.162 14.553 fit 12.767 0.227 15.564 plot_summary 12.446 0.125 12.720 plot_densities 10.698 0.232 11.118 plot_volcano 10.473 0.141 10.755 plot_sample_nas 8.280 0.096 8.494 read_fragpipe 6.036 0.148 6.867 dot-plot_survival 5.328 0.385 6.207 code 5.164 0.083 5.453 biplot_covariates 5.151 0.080 5.457 extract_coef_features 5.005 0.123 5.399 subtract_baseline 4.814 0.086 5.979 reset_fit 4.537 0.075 5.128 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: FALSE attr(,"cause") [1] nonexistent attr(,"class") [1] "vector_with_cause" "logical" Backtrace: ▆ 1. └─autonomics::.read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") at test-8_fit.R:76:9 2. └─autonomics:::assert_all_are_existing_files(file) 3. └─autonomics:::assert_engine(...) 4. └─autonomics:::give_feedback(handler_type, msg, predicate_name) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 158 ] Error: Test failures Execution halted * 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 ERROR, 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-arm64/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.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 1 | WARN 0 | SKIP 0 | PASS 158 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-8_fit.R:76:9'): fit: mcclain21 ─────────────────────────────── <assertionError/assertionCondition/simpleError/error/condition> Error in `.read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id")`: is_existing_file : Some or all of the files specified by file do not exist. /Users/biocbuild/Library/Caches/org.R-project.R/R/autonomics/datasets/mcclain21/GSE161731_counts.csv.gz FALSE attr(,"cause") [1] nonexistent attr(,"class") [1] "vector_with_cause" "logical" Backtrace: ▆ 1. └─autonomics::.read_rnaseq_counts(file, sfile = sfile, by.y = "rna_id") at test-8_fit.R:76:9 2. └─autonomics:::assert_all_are_existing_files(file) 3. └─autonomics:::assert_engine(...) 4. └─autonomics:::give_feedback(handler_type, msg, predicate_name) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 158 ] Error: Test failures Execution halted
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 | 0.000 | 0.001 | 0.001 | |
TAXON_TO_ORGNAME | 0.000 | 0.000 | 0.001 | |
TESTS | 0 | 0 | 0 | |
abstract_fit | 1.225 | 0.078 | 1.487 | |
add_adjusted_pvalues | 0.578 | 0.016 | 0.629 | |
add_assay_means | 1.303 | 0.014 | 1.373 | |
add_facetvars | 1.311 | 0.078 | 1.442 | |
add_opentargets_by_uniprot | 0.333 | 0.009 | 0.375 | |
add_psp | 0.577 | 0.016 | 0.617 | |
add_smiles | 0.543 | 0.048 | 0.602 | |
analysis | 0.428 | 0.007 | 0.438 | |
analyze | 13.030 | 0.142 | 13.396 | |
annotate_maxquant | 1.018 | 0.037 | 1.070 | |
annotate_uniprot_rest | 0.097 | 0.018 | 0.720 | |
assert_is_valid_sumexp | 0.660 | 0.048 | 0.716 | |
bin | 0.455 | 0.012 | 0.471 | |
biplot | 4.779 | 0.078 | 4.945 | |
biplot_corrections | 3.382 | 0.064 | 3.549 | |
biplot_covariates | 5.151 | 0.080 | 5.457 | |
block2lme | 0.003 | 0.001 | 0.004 | |
center | 1.635 | 0.023 | 1.722 | |
code | 5.164 | 0.083 | 5.453 | |
coefs | 0.773 | 0.046 | 0.834 | |
collapsed_entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.642 | 0.043 | 0.689 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.509 | 0.004 | 0.523 | |
counts2cpm | 0.431 | 0.005 | 0.458 | |
counts2tpm | 0.446 | 0.004 | 0.455 | |
cpm | 0.342 | 0.004 | 0.374 | |
create_design | 0.560 | 0.030 | 0.636 | |
default_formula | 15.802 | 0.351 | 17.231 | |
default_geom | 0.623 | 0.053 | 0.717 | |
default_sfile | 0.002 | 0.001 | 0.002 | |
demultiplex | 0.013 | 0.001 | 0.014 | |
dequantify | 0.002 | 0.000 | 0.002 | |
dot-merge | 0.022 | 0.001 | 0.024 | |
dot-plot_survival | 5.328 | 0.385 | 6.207 | |
dot-read_maxquant_proteingroups | 0.146 | 0.007 | 0.160 | |
download_contaminants | 0.097 | 0.009 | 0.831 | |
download_data | 0.000 | 0.001 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.001 | 0.002 | |
dt2mat | 0.004 | 0.000 | 0.004 | |
enrichment | 1.334 | 0.056 | 1.474 | |
entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
explore_transformations | 3.793 | 0.110 | 4.161 | |
extract_coef_features | 5.005 | 0.123 | 5.399 | |
extract_rectangle | 0.161 | 0.048 | 0.223 | |
fdata | 0.643 | 0.018 | 0.919 | |
fdr2p | 1.019 | 0.057 | 1.442 | |
filter_exprs_replicated_in_some_subgroup | 1.092 | 0.056 | 1.430 | |
filter_features | 0.586 | 0.050 | 0.832 | |
filter_medoid | 0.897 | 0.025 | 1.190 | |
filter_samples | 0.603 | 0.051 | 0.717 | |
fit | 12.767 | 0.227 | 15.564 | |
fit_lmx | 4.340 | 0.080 | 4.643 | |
fitcoefs | 0.831 | 0.039 | 0.918 | |
fits | 0.813 | 0.049 | 0.891 | |
fitvars | 1.159 | 0.054 | 1.247 | |
fix_xlgenes | 0.002 | 0.000 | 0.003 | |
flevels | 0.474 | 0.008 | 0.488 | |
fnames | 0.522 | 0.009 | 0.538 | |
formula2str | 0.001 | 0.000 | 0.001 | |
fvalues | 0.469 | 0.010 | 0.493 | |
fvars | 0.490 | 0.008 | 0.499 | |
genome_to_orgdb | 0.000 | 0.001 | 0.001 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.549 | 0.007 | 0.572 | |
guess_maxquant_quantity | 0.005 | 0.001 | 0.006 | |
guess_sep | 0.582 | 0.050 | 0.649 | |
has_multiple_levels | 0.056 | 0.002 | 0.060 | |
hdlproteins | 0.063 | 0.029 | 0.096 | |
impute | 3.083 | 0.043 | 3.300 | |
invert_subgroups | 0.742 | 0.008 | 0.767 | |
is_collapsed_subset | 0 | 0 | 0 | |
is_diann_report | 0.309 | 0.048 | 0.422 | |
is_fastadt | 0.068 | 0.001 | 0.071 | |
is_file | 0.000 | 0.000 | 0.001 | |
is_fraction | 0.001 | 0.000 | 0.002 | |
is_imputed | 0.857 | 0.010 | 0.901 | |
is_positive_number | 0.002 | 0.001 | 0.003 | |
is_scalar_subset | 0.380 | 0.007 | 0.397 | |
is_sig | 1.305 | 0.016 | 1.362 | |
is_valid_formula | 0.049 | 0.002 | 0.052 | |
keep_connected_blocks | 0.628 | 0.047 | 0.698 | |
keep_connected_features | 0.780 | 0.050 | 0.855 | |
keep_replicated_features | 0.928 | 0.053 | 1.016 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.475 | 0.005 | 0.501 | |
log2cpm | 0.442 | 0.004 | 0.464 | |
log2diffs | 0.379 | 0.007 | 0.395 | |
log2proteins | 0.391 | 0.007 | 0.412 | |
log2sites | 0.55 | 0.01 | 0.57 | |
log2tpm | 0.453 | 0.004 | 0.472 | |
log2transform | 4.171 | 0.053 | 4.370 | |
logical2factor | 0.001 | 0.000 | 0.002 | |
make_alpha_palette | 0.609 | 0.048 | 0.679 | |
make_colors | 0.014 | 0.001 | 0.018 | |
make_volcano_dt | 0.997 | 0.012 | 1.036 | |
map_fvalues | 0.466 | 0.009 | 0.485 | |
matrix2sumexp | 1.082 | 0.051 | 1.170 | |
merge_sample_file | 0.582 | 0.012 | 0.611 | |
merge_sdata | 0.648 | 0.056 | 0.726 | |
message_df | 0.002 | 0.000 | 0.003 | |
modelvar | 1.716 | 0.059 | 1.831 | |
order_on_p | 0.993 | 0.048 | 1.075 | |
pca | 3.286 | 0.073 | 3.451 | |
pg_to_canonical | 0.006 | 0.000 | 0.006 | |
plot_contrast_venn | 2.028 | 0.060 | 2.113 | |
plot_contrastogram | 2.603 | 0.155 | 2.816 | |
plot_data | 1.440 | 0.061 | 1.548 | |
plot_densities | 10.698 | 0.232 | 11.118 | |
plot_design | 0.703 | 0.014 | 0.724 | |
plot_exprs | 21.053 | 0.186 | 21.667 | |
plot_exprs_per_coef | 19.302 | 0.151 | 20.360 | |
plot_fit_summary | 1.991 | 0.061 | 2.089 | |
plot_heatmap | 1.897 | 0.017 | 1.939 | |
plot_matrix | 0.581 | 0.049 | 0.638 | |
plot_sample_nas | 8.280 | 0.096 | 8.494 | |
plot_subgroup_points | 4.758 | 0.081 | 4.905 | |
plot_summary | 12.446 | 0.125 | 12.720 | |
plot_venn | 0.025 | 0.002 | 0.027 | |
plot_venn_heatmap | 0.045 | 0.005 | 0.049 | |
plot_violins | 4.172 | 0.098 | 4.339 | |
plot_volcano | 10.473 | 0.141 | 10.755 | |
preprocess_rnaseq_counts | 0.405 | 0.005 | 0.413 | |
pull_columns | 0.003 | 0.001 | 0.003 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.050 | 0.004 | 0.296 | |
read_diann_proteingroups | 96.738 | 1.832 | 102.701 | |
read_fragpipe | 6.036 | 0.148 | 6.867 | |
read_maxquant_phosphosites | 1.750 | 0.035 | 1.988 | |
read_maxquant_proteingroups | 1.469 | 0.031 | 1.655 | |
read_metabolon | 12.879 | 0.162 | 14.553 | |
read_msigdt | 0.000 | 0.001 | 0.001 | |
read_olink | 1.652 | 0.058 | 1.913 | |
read_rectangles | 0.215 | 0.026 | 0.266 | |
read_rnaseq_counts | 30.655 | 1.219 | 35.218 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 13.383 | 0.083 | 14.976 | |
read_uniprotdt | 0.396 | 0.025 | 0.482 | |
reset_fit | 4.537 | 0.075 | 5.128 | |
rm_diann_contaminants | 20.690 | 0.362 | 25.601 | |
rm_missing_in_some_samples | 0.582 | 0.048 | 0.728 | |
rm_unmatched_samples | 0.674 | 0.022 | 0.848 | |
scaledlibsizes | 0.434 | 0.005 | 0.531 | |
scoremat | 1.110 | 0.052 | 1.415 | |
slevels | 0.526 | 0.010 | 0.669 | |
snames | 0.476 | 0.009 | 0.613 | |
split_extract_fixed | 0.606 | 0.047 | 0.809 | |
split_samples | 1.335 | 0.051 | 1.723 | |
stri_any_regex | 0.000 | 0.001 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.412 | 0.008 | 0.500 | |
subgroup_matrix | 0.601 | 0.049 | 0.787 | |
subtract_baseline | 4.814 | 0.086 | 5.979 | |
sumexp_to_longdt | 2.067 | 0.088 | 2.464 | |
sumexp_to_tsv | 2.324 | 0.092 | 2.695 | |
sumexplist_to_longdt | 1.822 | 0.037 | 2.063 | |
summarize_fit | 1.678 | 0.070 | 1.889 | |
svalues | 0.483 | 0.009 | 0.521 | |
svars | 0.499 | 0.010 | 0.537 | |
systematic_nas | 0.622 | 0.008 | 0.671 | |
tag_features | 1.067 | 0.035 | 1.182 | |
tag_hdlproteins | 0.683 | 0.038 | 0.779 | |
taxon2org | 0.002 | 0.000 | 0.001 | |
tpm | 0.449 | 0.004 | 0.489 | |
uncollapse | 0.013 | 0.001 | 0.017 | |
values | 0.512 | 0.015 | 0.561 | |
varlevels_dont_clash | 0.033 | 0.001 | 0.037 | |
venn_detects | 0.635 | 0.009 | 0.680 | |
weights | 0.497 | 0.005 | 0.507 | |
write_xl | 0.793 | 0.048 | 0.918 | |
zero_to_na | 0.001 | 0.000 | 0.002 | |