Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-11 20:42 -0400 (Fri, 11 Oct 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" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
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: 2024-10-10 12:25:35 -0400 (Thu, 10 Oct 2024) |
EndedAt: 2024-10-10 12:41:01 -0400 (Thu, 10 Oct 2024) |
EllapsedTime: 926.1 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 103.257 2.942 113.278 read_rnaseq_counts 31.043 1.458 35.205 plot_exprs 21.934 0.245 22.680 plot_exprs_per_coef 20.987 0.204 21.609 rm_diann_contaminants 20.449 0.564 20.970 default_formula 18.327 0.681 17.636 fit 16.980 0.661 13.349 analyze 12.992 0.185 14.382 plot_summary 12.428 0.165 13.291 read_metabolon 12.278 0.141 13.477 read_somascan 12.277 0.097 12.612 plot_volcano 10.337 0.143 10.734 plot_densities 9.933 0.325 9.515 read_fragpipe 8.228 0.286 9.573 fit_lmx 6.020 0.237 4.620 plot_sample_nas 6.047 0.065 6.641 dot-plot_survival 5.299 0.376 5.704 biplot_covariates 5.056 0.085 5.309 code 4.974 0.080 5.200 subtract_baseline 4.880 0.090 5.120 plot_subgroup_points 4.683 0.087 5.405 * 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 | 0.000 | 0.000 | 0.001 | |
CONTAMINANTSURL | 0 | 0 | 0 | |
FITSEP | 0.000 | 0.001 | 0.000 | |
LINMOD_ENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.001 | 0.001 | 0.000 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0.001 | 0.000 | 0.000 | |
abstract_fit | 1.553 | 0.136 | 1.504 | |
add_adjusted_pvalues | 0.736 | 0.022 | 0.774 | |
add_assay_means | 1.244 | 0.036 | 1.320 | |
add_facetvars | 1.646 | 0.091 | 1.788 | |
add_opentargets_by_uniprot | 0.363 | 0.008 | 0.516 | |
add_psp | 0.495 | 0.014 | 0.752 | |
add_smiles | 0.530 | 0.051 | 0.807 | |
analysis | 0.450 | 0.011 | 0.569 | |
analyze | 12.992 | 0.185 | 14.382 | |
annotate_maxquant | 0.738 | 0.030 | 0.816 | |
annotate_uniprot_rest | 0.094 | 0.020 | 0.832 | |
assert_is_valid_sumexp | 0.769 | 0.053 | 1.113 | |
bin | 1.465 | 0.018 | 1.547 | |
biplot | 3.584 | 0.073 | 3.746 | |
biplot_corrections | 3.501 | 0.089 | 3.516 | |
biplot_covariates | 5.056 | 0.085 | 5.309 | |
block2lme | 0.002 | 0.000 | 0.002 | |
center | 1.610 | 0.025 | 1.777 | |
code | 4.974 | 0.080 | 5.200 | |
coefs | 0.976 | 0.066 | 0.838 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.824 | 0.065 | 0.692 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.468 | 0.004 | 0.474 | |
counts2cpm | 0.438 | 0.004 | 0.443 | |
counts2tpm | 0.377 | 0.004 | 0.382 | |
cpm | 0.432 | 0.004 | 0.438 | |
create_design | 0.963 | 0.076 | 0.854 | |
default_formula | 18.327 | 0.681 | 17.636 | |
default_geom | 0.707 | 0.064 | 0.629 | |
default_sfile | 0.004 | 0.000 | 0.003 | |
demultiplex | 0.019 | 0.001 | 0.011 | |
dequantify | 0.003 | 0.000 | 0.002 | |
dot-merge | 0.036 | 0.002 | 0.022 | |
dot-plot_survival | 5.299 | 0.376 | 5.704 | |
dot-read_maxquant_proteingroups | 0.148 | 0.009 | 0.158 | |
download_contaminants | 0.096 | 0.009 | 0.839 | |
download_data | 0.000 | 0.001 | 0.001 | |
download_gtf | 0.000 | 0.001 | 0.000 | |
download_mcclain21 | 0.001 | 0.001 | 0.002 | |
dt2mat | 0.004 | 0.001 | 0.004 | |
enrichment | 1.273 | 0.070 | 1.352 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
explore_transformations | 3.700 | 0.076 | 3.834 | |
extract_coef_features | 4.440 | 0.095 | 4.389 | |
extract_rectangle | 0.154 | 0.046 | 0.201 | |
fdata | 0.600 | 0.015 | 0.617 | |
fdr2p | 1.182 | 0.071 | 1.054 | |
filter_exprs_replicated_in_some_subgroup | 1.522 | 0.100 | 1.089 | |
filter_features | 0.900 | 0.077 | 0.659 | |
filter_medoid | 0.872 | 0.024 | 0.889 | |
filter_samples | 0.701 | 0.061 | 0.619 | |
fit | 16.980 | 0.661 | 13.349 | |
fit_lmx | 6.020 | 0.237 | 4.620 | |
fitcoefs | 1.017 | 0.069 | 0.870 | |
fits | 0.993 | 0.068 | 0.857 | |
fitvars | 1.293 | 0.072 | 1.160 | |
fix_xlgenes | 0.003 | 0.000 | 0.002 | |
flevels | 0.457 | 0.008 | 0.467 | |
fnames | 0.526 | 0.011 | 0.538 | |
formula2str | 0 | 0 | 0 | |
fvalues | 0.466 | 0.008 | 0.476 | |
fvars | 0.453 | 0.009 | 0.463 | |
genome_to_orgdb | 0.000 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.001 | 0.001 | |
guess_fitsep | 0.527 | 0.009 | 0.539 | |
guess_maxquant_quantity | 0.005 | 0.002 | 0.006 | |
guess_sep | 0.916 | 0.066 | 0.875 | |
has_multiple_levels | 0.113 | 0.007 | 0.066 | |
hdlproteins | 0.085 | 0.030 | 0.091 | |
impute | 3.279 | 0.038 | 3.332 | |
invert_subgroups | 0.754 | 0.010 | 0.767 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_diann_report | 0.690 | 0.091 | 0.464 | |
is_fastadt | 0.115 | 0.006 | 0.071 | |
is_file | 0.001 | 0.001 | 0.001 | |
is_fraction | 0.005 | 0.000 | 0.003 | |
is_imputed | 0.797 | 0.011 | 0.809 | |
is_positive_number | 0.002 | 0.001 | 0.002 | |
is_scalar_subset | 0.398 | 0.006 | 0.407 | |
is_sig | 1.193 | 0.011 | 1.211 | |
is_valid_formula | 0.043 | 0.001 | 0.045 | |
keep_connected_blocks | 0.769 | 0.063 | 0.683 | |
keep_connected_features | 0.995 | 0.079 | 0.819 | |
keep_replicated_features | 1.337 | 0.099 | 0.886 | |
label2index | 0.001 | 0.001 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.485 | 0.008 | 0.487 | |
log2cpm | 0.399 | 0.003 | 0.403 | |
log2diffs | 0.358 | 0.005 | 0.363 | |
log2proteins | 0.358 | 0.005 | 0.364 | |
log2sites | 0.409 | 0.006 | 0.416 | |
log2tpm | 0.410 | 0.003 | 0.414 | |
log2transform | 3.861 | 0.046 | 3.949 | |
logical2factor | 0.001 | 0.001 | 0.002 | |
make_alpha_palette | 0.692 | 0.057 | 0.608 | |
make_colors | 0.024 | 0.003 | 0.015 | |
make_volcano_dt | 0.984 | 0.018 | 0.964 | |
map_fvalues | 0.451 | 0.008 | 0.461 | |
matrix2sumexp | 1.243 | 0.078 | 1.142 | |
merge_sample_file | 0.534 | 0.012 | 0.548 | |
merge_sdata | 0.778 | 0.080 | 0.675 | |
message_df | 0.005 | 0.001 | 0.003 | |
modelvar | 2.172 | 0.109 | 1.705 | |
order_on_p | 1.159 | 0.071 | 1.028 | |
pca | 3.315 | 0.091 | 3.221 | |
pg_to_canonical | 0.006 | 0.001 | 0.006 | |
plot_contrast_venn | 2.556 | 0.125 | 2.064 | |
plot_contrastogram | 2.986 | 0.191 | 2.689 | |
plot_data | 1.672 | 0.087 | 1.455 | |
plot_densities | 9.933 | 0.325 | 9.515 | |
plot_design | 0.673 | 0.011 | 0.724 | |
plot_exprs | 21.934 | 0.245 | 22.680 | |
plot_exprs_per_coef | 20.987 | 0.204 | 21.609 | |
plot_fit_summary | 1.989 | 0.078 | 2.092 | |
plot_heatmap | 1.759 | 0.017 | 1.807 | |
plot_matrix | 0.564 | 0.051 | 0.703 | |
plot_sample_nas | 6.047 | 0.065 | 6.641 | |
plot_subgroup_points | 4.683 | 0.087 | 5.405 | |
plot_summary | 12.428 | 0.165 | 13.291 | |
plot_venn | 0.025 | 0.002 | 0.027 | |
plot_venn_heatmap | 0.045 | 0.004 | 0.054 | |
plot_violins | 4.280 | 0.114 | 4.481 | |
plot_volcano | 10.337 | 0.143 | 10.734 | |
preprocess_rnaseq_counts | 0.404 | 0.005 | 0.428 | |
pull_columns | 0.002 | 0.001 | 0.003 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.050 | 0.005 | 0.301 | |
read_diann_proteingroups | 103.257 | 2.942 | 113.278 | |
read_fragpipe | 8.228 | 0.286 | 9.573 | |
read_maxquant_phosphosites | 1.758 | 0.037 | 1.877 | |
read_maxquant_proteingroups | 1.389 | 0.029 | 1.537 | |
read_metabolon | 12.278 | 0.141 | 13.477 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.386 | 0.066 | 1.504 | |
read_rectangles | 0.216 | 0.027 | 0.250 | |
read_rnaseq_counts | 31.043 | 1.458 | 35.205 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 12.277 | 0.097 | 12.612 | |
read_uniprotdt | 0.324 | 0.025 | 0.355 | |
reset_fit | 4.416 | 0.110 | 4.574 | |
rm_diann_contaminants | 20.449 | 0.564 | 20.970 | |
rm_missing_in_some_samples | 0.603 | 0.056 | 0.692 | |
rm_unmatched_samples | 0.679 | 0.010 | 0.709 | |
scaledlibsizes | 0.419 | 0.005 | 0.435 | |
scoremat | 1.179 | 0.056 | 1.254 | |
slevels | 0.479 | 0.008 | 0.493 | |
snames | 0.478 | 0.008 | 0.508 | |
split_extract_fixed | 0.592 | 0.050 | 0.656 | |
split_samples | 1.361 | 0.056 | 1.620 | |
stri_any_regex | 0.001 | 0.001 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.421 | 0.009 | 0.442 | |
subgroup_matrix | 0.715 | 0.057 | 0.767 | |
subtract_baseline | 4.88 | 0.09 | 5.12 | |
sumexp_to_longdt | 2.606 | 0.166 | 2.796 | |
sumexp_to_tsv | 0.562 | 0.011 | 0.589 | |
sumexplist_to_longdt | 1.888 | 0.034 | 2.142 | |
summarize_fit | 1.615 | 0.065 | 2.343 | |
svalues | 0.585 | 0.012 | 0.666 | |
svars | 0.493 | 0.009 | 0.565 | |
systematic_nas | 0.636 | 0.011 | 0.729 | |
tag_features | 1.208 | 0.035 | 1.303 | |
tag_hdlproteins | 0.617 | 0.035 | 0.668 | |
taxon2org | 0.001 | 0.000 | 0.002 | |
tpm | 0.431 | 0.003 | 0.437 | |
uncollapse | 0.012 | 0.000 | 0.012 | |
values | 0.460 | 0.009 | 0.482 | |
varlevels_dont_clash | 0.026 | 0.001 | 0.028 | |
venn_detects | 0.669 | 0.007 | 0.690 | |
weights | 0.422 | 0.003 | 0.426 | |
write_xl | 1.012 | 0.072 | 0.876 | |
zero_to_na | 0.002 | 0.001 | 0.002 | |