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This page was generated on 2024-05-20 11:32:08 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 112/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.13.7 (landing page) Aditya Bhagwat
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the autonomics package: - 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: 1.13.7 |
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_1.13.7.tar.gz |
StartedAt: 2024-05-19 05:40:22 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 05:54:21 -0400 (Sun, 19 May 2024) |
EllapsedTime: 839.4 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_1.13.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/autonomics.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 ‘1.13.7’ * 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 ... OK * 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 91.981 1.824 94.466 read_rnaseq_counts 27.098 1.309 29.042 plot_exprs 19.467 0.153 19.662 rm_diann_contaminants 18.442 0.376 18.872 plot_exprs_per_coef 18.644 0.137 18.856 default_formula 14.334 0.343 14.736 fit 11.953 0.167 12.132 plot_summary 11.752 0.088 11.885 read_metabolon 11.666 0.103 11.853 read_somascan 11.585 0.045 11.660 analyze 11.300 0.127 11.581 plot_volcano 10.167 0.111 10.338 plot_densities 8.060 0.244 8.308 plot_sample_nas 5.913 0.046 6.035 read_fragpipe 5.746 0.137 5.938 fcluster 5.537 0.098 5.642 dot-plot_survival 5.139 0.371 5.513 biplot_covariates 5.127 0.066 5.221 * 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, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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 | 0.001 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0.000 | 0.000 | 0.001 | |
CONTAMINANTSURL | 0.000 | 0.001 | 0.000 | |
FITSEP | 0 | 0 | 0 | |
LINMOD_ENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.000 | 0.000 | 0.001 | |
TAXON_TO_ORGNAME | 0.000 | 0.000 | 0.001 | |
TESTS | 0.000 | 0.000 | 0.001 | |
abstract_fit | 1.316 | 0.067 | 1.387 | |
add_adjusted_pvalues | 0.576 | 0.016 | 0.593 | |
add_assay_means | 0.515 | 0.007 | 0.522 | |
add_facetvars | 2.334 | 0.103 | 2.438 | |
add_opentargets_by_uniprot | 0.430 | 0.009 | 0.442 | |
add_psp | 0.522 | 0.013 | 0.536 | |
add_smiles | 0.462 | 0.041 | 0.505 | |
analysis | 0.402 | 0.007 | 0.409 | |
analyze | 11.300 | 0.127 | 11.581 | |
annotate_maxquant | 0.970 | 0.029 | 1.007 | |
annotate_uniprot_rest | 0.100 | 0.017 | 0.646 | |
assert_is_valid_sumexp | 0.651 | 0.049 | 0.713 | |
bin | 0.430 | 0.009 | 0.445 | |
biplot | 3.612 | 0.072 | 3.713 | |
biplot_corrections | 3.038 | 0.053 | 3.107 | |
biplot_covariates | 5.127 | 0.066 | 5.221 | |
block2lme | 0.004 | 0.001 | 0.004 | |
center | 2.420 | 0.020 | 2.441 | |
code | 3.859 | 0.076 | 3.957 | |
coefs | 0.665 | 0.027 | 0.696 | |
collapsed_entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.442 | 0.042 | 0.485 | |
count_in | 0.001 | 0.000 | 0.000 | |
counts | 0.254 | 0.003 | 0.261 | |
counts2cpm | 0.327 | 0.002 | 0.331 | |
counts2tpm | 0.255 | 0.003 | 0.261 | |
cpm | 0.372 | 0.003 | 0.414 | |
create_design | 0.706 | 0.046 | 0.753 | |
default_formula | 14.334 | 0.343 | 14.736 | |
default_geom | 0.551 | 0.059 | 0.656 | |
default_sfile | 0.002 | 0.001 | 0.003 | |
demultiplex | 0.011 | 0.001 | 0.012 | |
dequantify | 0.002 | 0.001 | 0.002 | |
dequantify_compounddiscoverer | 0.002 | 0.001 | 0.001 | |
dot-merge | 0.019 | 0.001 | 0.020 | |
dot-plot_survival | 5.139 | 0.371 | 5.513 | |
dot-read_maxquant_proteingroups | 0.144 | 0.005 | 0.150 | |
download_contaminants | 0.052 | 0.010 | 0.821 | |
download_data | 0.001 | 0.001 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.000 | 0.003 | |
dt2mat | 0.003 | 0.000 | 0.005 | |
enrichment | 1.228 | 0.093 | 1.322 | |
entrezg_to_symbol | 0.000 | 0.001 | 0.001 | |
explore_transformations | 3.424 | 0.099 | 3.537 | |
extract_coef_features | 4.460 | 0.097 | 4.559 | |
extract_rectangle | 0.146 | 0.040 | 0.186 | |
fcluster | 5.537 | 0.098 | 5.642 | |
fcor | 0.666 | 0.023 | 0.696 | |
fdata | 0.566 | 0.010 | 0.575 | |
fdr2p | 0.920 | 0.050 | 0.969 | |
filter_exprs_replicated_in_some_subgroup | 0.912 | 0.046 | 0.957 | |
filter_features | 0.511 | 0.047 | 0.581 | |
filter_medoid | 0.871 | 0.016 | 0.886 | |
filter_samples | 0.531 | 0.042 | 0.573 | |
fit | 11.953 | 0.167 | 12.132 | |
fit_lmx | 4.218 | 0.068 | 4.287 | |
fitcoefs | 0.726 | 0.044 | 0.770 | |
fits | 0.828 | 0.044 | 0.871 | |
fitvars | 1.001 | 0.047 | 1.055 | |
fix_xlgenes | 0.001 | 0.000 | 0.002 | |
flevels | 0.464 | 0.005 | 0.469 | |
fnames | 0.490 | 0.006 | 0.495 | |
formula2str | 0.001 | 0.000 | 0.001 | |
fvalues | 0.420 | 0.005 | 0.425 | |
fvars | 0.420 | 0.007 | 0.427 | |
genome_to_orgdb | 0.000 | 0.001 | 0.000 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.493 | 0.008 | 0.501 | |
guess_maxquant_quantity | 0.005 | 0.001 | 0.006 | |
guess_sep | 0.531 | 0.046 | 0.584 | |
has_multiple_levels | 0.049 | 0.002 | 0.050 | |
hdlproteins | 0.060 | 0.030 | 0.092 | |
impute | 2.913 | 0.035 | 2.950 | |
invert_subgroups | 0.728 | 0.006 | 0.735 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_correlation_matrix | 0.002 | 0.000 | 0.002 | |
is_diann_report | 0.308 | 0.046 | 0.413 | |
is_fastadt | 0.059 | 0.001 | 0.061 | |
is_file | 0.000 | 0.000 | 0.001 | |
is_fraction | 0.001 | 0.001 | 0.002 | |
is_imputed | 0.688 | 0.008 | 0.696 | |
is_positive_number | 0.002 | 0.001 | 0.001 | |
is_scalar_subset | 0.359 | 0.007 | 0.366 | |
is_sig | 1.122 | 0.012 | 1.134 | |
is_valid_formula | 0.046 | 0.001 | 0.046 | |
keep_connected_blocks | 0.515 | 0.045 | 0.559 | |
keep_connected_features | 2.183 | 0.059 | 2.265 | |
keep_replicated_features | 0.744 | 0.049 | 0.801 | |
label2index | 0.000 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.001 | 0.001 | |
log2counts | 0.394 | 0.003 | 0.397 | |
log2cpm | 0.375 | 0.003 | 0.378 | |
log2diffs | 0.315 | 0.004 | 0.320 | |
log2proteins | 0.324 | 0.005 | 0.330 | |
log2sites | 0.315 | 0.005 | 0.321 | |
log2tpm | 0.361 | 0.003 | 0.363 | |
log2transform | 3.514 | 0.044 | 3.571 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.550 | 0.045 | 0.595 | |
make_colors | 0.014 | 0.001 | 0.016 | |
make_volcano_dt | 0.806 | 0.011 | 0.824 | |
map_fvalues | 0.402 | 0.006 | 0.408 | |
matrix2sumexp | 0.959 | 0.046 | 1.005 | |
merge_sample_file | 0.445 | 0.009 | 0.454 | |
merge_sdata | 0.547 | 0.058 | 0.605 | |
message_df | 0.003 | 0.001 | 0.003 | |
modelvar | 1.433 | 0.051 | 1.484 | |
order_on_p | 0.924 | 0.048 | 0.982 | |
pca | 2.699 | 0.065 | 2.766 | |
pg_to_canonical | 0.005 | 0.000 | 0.005 | |
plot_contrast_venn | 1.687 | 0.055 | 1.742 | |
plot_contrastogram | 2.292 | 0.135 | 2.433 | |
plot_data | 1.186 | 0.054 | 1.245 | |
plot_densities | 8.060 | 0.244 | 8.308 | |
plot_design | 0.652 | 0.025 | 0.677 | |
plot_exprs | 19.467 | 0.153 | 19.662 | |
plot_exprs_per_coef | 18.644 | 0.137 | 18.856 | |
plot_fit_summary | 1.894 | 0.075 | 1.976 | |
plot_heatmap | 1.753 | 0.013 | 1.774 | |
plot_matrix | 0.556 | 0.047 | 0.606 | |
plot_sample_nas | 5.913 | 0.046 | 6.035 | |
plot_subgroup_points | 4.427 | 0.057 | 4.575 | |
plot_summary | 11.752 | 0.088 | 11.885 | |
plot_venn | 0.026 | 0.002 | 0.028 | |
plot_venn_heatmap | 0.022 | 0.002 | 0.024 | |
plot_violins | 3.923 | 0.087 | 4.029 | |
plot_volcano | 10.167 | 0.111 | 10.338 | |
preprocess_rnaseq_counts | 0.408 | 0.003 | 0.412 | |
pull_columns | 0.003 | 0.000 | 0.003 | |
read_affymetrix | 0.000 | 0.001 | 0.000 | |
read_contaminants | 0.011 | 0.001 | 0.013 | |
read_diann_proteingroups | 91.981 | 1.824 | 94.466 | |
read_fragpipe | 5.746 | 0.137 | 5.938 | |
read_maxquant_phosphosites | 3.313 | 0.134 | 3.528 | |
read_maxquant_proteingroups | 1.415 | 0.046 | 1.481 | |
read_metabolon | 11.666 | 0.103 | 11.853 | |
read_msigdt | 0.000 | 0.001 | 0.001 | |
read_olink | 1.574 | 0.055 | 1.641 | |
read_rectangles | 0.211 | 0.025 | 0.242 | |
read_rnaseq_counts | 27.098 | 1.309 | 29.042 | |
read_salmon | 0.000 | 0.001 | 0.000 | |
read_somascan | 11.585 | 0.045 | 11.660 | |
read_uniprotdt | 0.304 | 0.022 | 0.329 | |
reset_fit | 4.376 | 0.090 | 4.504 | |
rm_diann_contaminants | 18.442 | 0.376 | 18.872 | |
rm_missing_in_some_samples | 0.588 | 0.047 | 0.636 | |
rm_unmatched_samples | 0.565 | 0.004 | 0.571 | |
scaledlibsizes | 0.490 | 0.013 | 0.504 | |
scoremat | 1.012 | 0.047 | 1.062 | |
slevels | 0.437 | 0.013 | 0.454 | |
snames | 0.529 | 0.012 | 0.542 | |
split_extract_fixed | 0.555 | 0.044 | 0.600 | |
split_samples | 1.267 | 0.053 | 1.324 | |
stri_any_regex | 0.001 | 0.001 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.376 | 0.007 | 0.383 | |
subgroup_matrix | 0.569 | 0.053 | 0.625 | |
subtract_baseline | 4.576 | 0.070 | 4.674 | |
sumexp_to_longdt | 2.027 | 0.086 | 2.119 | |
sumexp_to_tsv | 0.995 | 0.044 | 1.047 | |
sumexplist_to_longdt | 1.753 | 0.025 | 1.782 | |
summarize_fit | 1.520 | 0.047 | 1.571 | |
svalues | 0.549 | 0.007 | 0.558 | |
svars | 0.449 | 0.006 | 0.455 | |
systematic_nas | 0.576 | 0.006 | 0.584 | |
tag_features | 1.385 | 0.035 | 1.427 | |
tag_hdlproteins | 0.588 | 0.046 | 0.636 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.402 | 0.003 | 0.405 | |
uncollapse | 0.010 | 0.001 | 0.011 | |
values | 0.442 | 0.007 | 0.450 | |
varlevels_dont_clash | 0.022 | 0.001 | 0.023 | |
venn_detects | 0.707 | 0.010 | 0.721 | |
weights | 0.423 | 0.004 | 0.428 | |
write_xl | 0.723 | 0.048 | 0.772 | |
zero_to_na | 0.001 | 0.001 | 0.002 | |