Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 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 117/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.14.7 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | 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 | 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: 1.14.7 |
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_1.14.7.tar.gz |
StartedAt: 2024-12-20 11:42:02 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 11:56:59 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 896.6 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_1.14.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘autonomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘autonomics’ version ‘1.14.7’ * 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 102.442 3.169 95.666 read_rnaseq_counts 33.387 1.413 32.652 plot_exprs 26.177 0.393 24.740 plot_exprs_per_coef 24.934 0.346 23.458 rm_diann_contaminants 24.323 0.813 20.319 fit 18.681 0.939 13.713 default_formula 17.636 0.785 15.992 analyze 13.867 0.304 12.705 read_metabolon 13.660 0.243 12.841 read_somascan 13.354 0.232 12.446 plot_summary 13.054 0.265 11.898 plot_densities 11.213 0.349 10.417 plot_volcano 10.287 0.206 9.802 ftype 9.837 0.642 8.211 read_fragpipe 7.865 0.378 6.825 plot_sample_nas 6.883 0.126 6.193 fcluster 6.490 0.148 6.033 fit_lmx 6.269 0.333 4.588 code 6.208 0.102 6.095 reset_fit 5.695 0.216 4.722 dot-plot_survival 5.092 0.298 5.402 biplot_covariates 5.249 0.100 5.123 plot_subgroup_points 5.186 0.136 4.676 extract_coef_features 4.918 0.109 4.806 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-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
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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 The following object is masked from 'package:base': beta > > test_check("autonomics") [ FAIL 0 | WARN 0 | SKIP 2 | PASS 157 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test-8_fit.R:89:5', 'test-8_fit.R:99:5' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 157 ] > > proc.time() user system elapsed 173.366 10.457 165.214
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
CONTAMINANTSURL | 0 | 0 | 0 | |
FITSEP | 0 | 0 | 0 | |
LINMOD_ENGINES | 0.000 | 0.001 | 0.000 | |
MAXQUANT_PATTERNS | 0.000 | 0.000 | 0.001 | |
TAXON_TO_ORGNAME | 0.000 | 0.001 | 0.001 | |
TESTS | 0.000 | 0.000 | 0.001 | |
X | 1.905 | 0.111 | 1.784 | |
abstract_fit | 2.034 | 0.121 | 1.921 | |
add_adjusted_pvalues | 0.591 | 0.028 | 0.622 | |
add_assay_means | 0.387 | 0.008 | 0.396 | |
add_facetvars | 2.116 | 0.085 | 1.975 | |
add_opentargets_by_uniprot | 0.432 | 0.009 | 0.443 | |
add_psp | 0.537 | 0.016 | 0.554 | |
add_smiles | 0.669 | 0.063 | 0.595 | |
analysis | 0.498 | 0.023 | 0.409 | |
analyze | 13.867 | 0.304 | 12.705 | |
annotate_maxquant | 0.989 | 0.037 | 1.028 | |
annotate_uniprot_rest | 0.099 | 0.019 | 0.872 | |
assert_is_valid_sumexp | 0.849 | 0.073 | 0.767 | |
bin | 1.530 | 0.033 | 1.491 | |
biplot | 3.514 | 0.094 | 3.394 | |
biplot_corrections | 3.299 | 0.082 | 3.157 | |
biplot_covariates | 5.249 | 0.100 | 5.123 | |
block2lme | 0.003 | 0.000 | 0.003 | |
center | 1.466 | 0.018 | 1.485 | |
code | 6.208 | 0.102 | 6.095 | |
coefs | 0.962 | 0.070 | 0.801 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.813 | 0.072 | 0.660 | |
count_in | 0.003 | 0.001 | 0.001 | |
counts | 0.448 | 0.004 | 0.448 | |
counts2cpm | 0.364 | 0.003 | 0.368 | |
counts2tpm | 1.428 | 0.007 | 1.437 | |
cpm | 0.405 | 0.003 | 0.408 | |
create_design | 0.911 | 0.082 | 0.769 | |
default_coefs | 0.947 | 0.073 | 0.801 | |
default_formula | 17.636 | 0.785 | 15.992 | |
default_geom | 0.752 | 0.074 | 0.633 | |
default_sfile | 0.004 | 0.001 | 0.003 | |
demultiplex | 0.020 | 0.002 | 0.012 | |
dequantify | 0.004 | 0.001 | 0.002 | |
dequantify_compounddiscoverer | 0.003 | 0.001 | 0.002 | |
dot-merge | 0.029 | 0.002 | 0.022 | |
dot-plot_survival | 5.092 | 0.298 | 5.402 | |
dot-read_maxquant_proteingroups | 0.145 | 0.004 | 0.149 | |
download_contaminants | 0.093 | 0.009 | 0.882 | |
download_data | 0.000 | 0.001 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.000 | 0.000 | |
dt2mat | 0.004 | 0.000 | 0.004 | |
enrichment | 1.239 | 0.077 | 1.317 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
explore_transformations | 3.425 | 0.126 | 3.553 | |
extract_coef_features | 4.918 | 0.109 | 4.806 | |
extract_rectangle | 0.144 | 0.041 | 0.186 | |
fcluster | 6.490 | 0.148 | 6.033 | |
fcor | 1.068 | 0.033 | 1.104 | |
fdata | 0.566 | 0.017 | 0.584 | |
fdr2p | 1.154 | 0.077 | 1.002 | |
filter_exprs_replicated_in_some_subgroup | 1.544 | 0.125 | 1.067 | |
filter_features | 0.812 | 0.084 | 0.587 | |
filter_medoid | 0.873 | 0.026 | 0.821 | |
filter_samples | 0.668 | 0.062 | 0.582 | |
fit | 18.681 | 0.939 | 13.713 | |
fit_lmx | 6.269 | 0.333 | 4.588 | |
fitcoefs | 1.007 | 0.076 | 0.836 | |
fits | 0.960 | 0.073 | 0.800 | |
fitvars | 1.303 | 0.076 | 1.154 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.484 | 0.008 | 0.495 | |
fnames | 0.497 | 0.008 | 0.506 | |
formula2str | 0.000 | 0.001 | 0.001 | |
ftype | 9.837 | 0.642 | 8.211 | |
fvalues | 0.603 | 0.021 | 0.535 | |
fvars | 0.474 | 0.011 | 0.485 | |
genome_to_orgdb | 0.000 | 0.001 | 0.000 | |
group_by_level | 0.001 | 0.000 | 0.002 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.511 | 0.010 | 0.526 | |
guess_maxquant_quantity | 0.005 | 0.001 | 0.006 | |
guess_sep | 0.685 | 0.060 | 0.614 | |
has_multiple_levels | 0.122 | 0.010 | 0.070 | |
hdlproteins | 0.075 | 0.035 | 0.099 | |
impute | 3.240 | 0.040 | 3.291 | |
invert_subgroups | 0.700 | 0.008 | 0.710 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_correlation_matrix | 0.002 | 0.000 | 0.002 | |
is_diann_report | 0.713 | 0.088 | 0.455 | |
is_fastadt | 0.129 | 0.008 | 0.071 | |
is_file | 0.001 | 0.001 | 0.001 | |
is_fraction | 0.003 | 0.000 | 0.002 | |
is_imputed | 0.859 | 0.013 | 0.838 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.368 | 0.006 | 0.375 | |
is_sig | 1.667 | 0.014 | 1.686 | |
is_valid_formula | 0.046 | 0.001 | 0.047 | |
keep_connected_blocks | 0.682 | 0.058 | 0.601 | |
keep_connected_features | 1.183 | 0.090 | 0.802 | |
keep_replicated_features | 1.364 | 0.115 | 0.953 | |
label2index | 0.002 | 0.000 | 0.000 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.585 | 0.019 | 0.445 | |
log2cpm | 0.448 | 0.004 | 0.453 | |
log2diffs | 0.369 | 0.008 | 0.383 | |
log2proteins | 0.424 | 0.008 | 0.433 | |
log2sites | 0.388 | 0.006 | 0.396 | |
log2tpm | 0.422 | 0.004 | 0.428 | |
log2transform | 3.941 | 0.049 | 4.010 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.693 | 0.068 | 0.649 | |
make_colors | 0.026 | 0.003 | 0.015 | |
make_volcano_dt | 1.041 | 0.017 | 1.009 | |
map_fvalues | 0.430 | 0.009 | 0.442 | |
matrix2sumexp | 1.226 | 0.068 | 1.069 | |
merge_sample_file | 0.578 | 0.010 | 0.590 | |
merge_sdata | 0.789 | 0.071 | 0.674 | |
message_df | 0.006 | 0.001 | 0.004 | |
modelvar | 4.238 | 0.132 | 3.698 | |
order_on_p | 1.182 | 0.070 | 1.036 | |
pca | 3.347 | 0.085 | 3.218 | |
pg_to_canonical | 0.007 | 0.000 | 0.007 | |
plot_contrast_venn | 3.019 | 0.123 | 2.496 | |
plot_contrastogram | 3.880 | 0.215 | 3.555 | |
plot_data | 1.573 | 0.083 | 1.378 | |
plot_densities | 11.213 | 0.349 | 10.417 | |
plot_design | 0.657 | 0.010 | 0.674 | |
plot_exprs | 26.177 | 0.393 | 24.740 | |
plot_exprs_per_coef | 24.934 | 0.346 | 23.458 | |
plot_fit_summary | 2.480 | 0.113 | 1.983 | |
plot_heatmap | 1.818 | 0.013 | 1.837 | |
plot_matrix | 0.660 | 0.063 | 0.594 | |
plot_sample_nas | 6.883 | 0.126 | 6.193 | |
plot_subgroup_points | 5.186 | 0.136 | 4.676 | |
plot_summary | 13.054 | 0.265 | 11.898 | |
plot_venn | 0.027 | 0.002 | 0.028 | |
plot_venn_heatmap | 0.023 | 0.001 | 0.024 | |
plot_violins | 3.923 | 0.124 | 3.851 | |
plot_volcano | 10.287 | 0.206 | 9.802 | |
preprocess_rnaseq_counts | 0.373 | 0.005 | 0.377 | |
pull_columns | 0.002 | 0.001 | 0.003 | |
read_affymetrix | 0.000 | 0.001 | 0.001 | |
read_contaminants | 0.047 | 0.004 | 0.302 | |
read_diann_proteingroups | 102.442 | 3.169 | 95.666 | |
read_fragpipe | 7.865 | 0.378 | 6.825 | |
read_maxquant_phosphosites | 1.644 | 0.026 | 1.674 | |
read_maxquant_proteingroups | 1.400 | 0.023 | 1.429 | |
read_metabolon | 13.660 | 0.243 | 12.841 | |
read_msigdt | 0.000 | 0.000 | 0.001 | |
read_olink | 1.622 | 0.079 | 1.367 | |
read_rectangles | 0.204 | 0.024 | 0.229 | |
read_rnaseq_counts | 33.387 | 1.413 | 32.652 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 13.354 | 0.232 | 12.446 | |
read_uniprotdt | 0.420 | 0.023 | 0.443 | |
reset_fit | 5.695 | 0.216 | 4.722 | |
rm_diann_contaminants | 24.323 | 0.813 | 20.319 | |
rm_missing_in_some_samples | 0.689 | 0.070 | 0.622 | |
rm_unmatched_samples | 0.618 | 0.008 | 0.525 | |
scaledlibsizes | 0.377 | 0.003 | 0.380 | |
scoremat | 1.215 | 0.060 | 1.039 | |
slevels | 0.417 | 0.007 | 0.425 | |
snames | 0.419 | 0.008 | 0.427 | |
split_extract_fixed | 0.730 | 0.055 | 0.597 | |
split_samples | 1.388 | 0.063 | 1.112 | |
stri_any_regex | 0.000 | 0.001 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.362 | 0.006 | 0.367 | |
subgroup_matrix | 0.679 | 0.049 | 0.590 | |
subtract_baseline | 4.313 | 0.101 | 3.834 | |
sumexp_to_longdt | 2.417 | 0.115 | 1.864 | |
sumexp_to_tsv | 0.493 | 0.008 | 0.502 | |
sumexplist_to_longdt | 1.627 | 0.017 | 1.644 | |
summarize_fit | 2.475 | 0.133 | 1.610 | |
svalues | 0.426 | 0.007 | 0.434 | |
svars | 0.493 | 0.006 | 0.499 | |
systematic_nas | 0.556 | 0.006 | 0.563 | |
tag_features | 1.013 | 0.027 | 1.042 | |
tag_hdlproteins | 0.554 | 0.029 | 0.584 | |
taxon2org | 0.002 | 0.000 | 0.002 | |
tpm | 0.505 | 0.007 | 0.512 | |
uncollapse | 0.011 | 0.001 | 0.012 | |
values | 0.439 | 0.006 | 0.445 | |
varlevels_dont_clash | 0.023 | 0.001 | 0.025 | |
venn_detects | 0.547 | 0.005 | 0.552 | |
weights | 0.464 | 0.003 | 0.468 | |
write_xl | 0.900 | 0.083 | 0.778 | |
zero_to_na | 0.001 | 0.001 | 0.002 | |