Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-15 11:39 -0400 (Thu, 15 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 115/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.13.21 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.13.21 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings autonomics_1.13.21.tar.gz |
StartedAt: 2024-08-14 21:05:03 -0400 (Wed, 14 Aug 2024) |
EndedAt: 2024-08-14 21:19:46 -0400 (Wed, 14 Aug 2024) |
EllapsedTime: 883.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: autonomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings autonomics_1.13.21.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘autonomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘autonomics’ version ‘1.13.21’ * 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 loading without being on the library search path ... 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 89.892 0.956 86.194 read_rnaseq_counts 28.492 2.082 30.347 plot_exprs_per_coef 23.559 0.092 23.537 plot_exprs 23.206 0.176 23.285 rm_diann_contaminants 18.678 0.520 19.070 default_formula 14.120 0.328 14.010 fit 13.396 0.037 12.341 read_somascan 12.741 0.392 13.079 analyze 12.562 0.104 12.583 plot_summary 12.187 0.088 12.169 read_metabolon 11.846 0.028 11.763 plot_volcano 9.836 0.092 9.869 plot_densities 9.053 0.140 9.081 ftype 6.939 0.096 6.656 read_fragpipe 6.898 0.064 6.658 code 6.151 0.096 6.226 plot_sample_nas 5.683 0.036 5.676 biplot_covariates 5.451 0.104 5.533 fcluster 5.310 0.052 5.306 extract_coef_features 4.969 0.072 5.020 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck/00check.log’ for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 0 | PASS 159 ] > > proc.time() user system elapsed 138.059 3.786 139.492
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0 | 0 | 0 | |
COMPOUNDDISCOVERER_PATTERNS | 0.001 | 0.000 | 0.000 | |
CONTAMINANTSURL | 0.001 | 0.000 | 0.000 | |
FITSEP | 0.000 | 0.000 | 0.001 | |
LINMOD_ENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0.000 | 0.000 | 0.001 | |
TAXON_TO_ORGNAME | 0.001 | 0.000 | 0.000 | |
TESTS | 0 | 0 | 0 | |
X | 1.522 | 0.016 | 1.516 | |
abstract_fit | 1.070 | 0.056 | 1.105 | |
add_adjusted_pvalues | 1.239 | 0.044 | 1.284 | |
add_assay_means | 0.354 | 0.008 | 0.362 | |
add_facetvars | 1.903 | 0.024 | 1.905 | |
add_opentargets_by_uniprot | 0.400 | 0.004 | 0.405 | |
add_psp | 0.545 | 0.027 | 0.574 | |
add_smiles | 0.469 | 0.012 | 0.460 | |
analysis | 0.381 | 0.032 | 0.412 | |
analyze | 12.562 | 0.104 | 12.583 | |
annotate_maxquant | 0.832 | 0.052 | 0.884 | |
annotate_uniprot_rest | 0.342 | 0.012 | 2.593 | |
assert_is_valid_sumexp | 0.543 | 0.019 | 0.543 | |
bin | 0.388 | 0.000 | 0.388 | |
biplot | 3.451 | 0.020 | 3.435 | |
biplot_corrections | 2.946 | 0.032 | 2.957 | |
biplot_covariates | 5.451 | 0.104 | 5.533 | |
block2lme | 0.003 | 0.000 | 0.003 | |
center | 1.325 | 0.004 | 1.329 | |
code | 6.151 | 0.096 | 6.226 | |
coefs | 0.694 | 0.004 | 0.679 | |
collapsed_entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.551 | 0.008 | 0.539 | |
count_in | 0 | 0 | 0 | |
counts | 0.391 | 0.000 | 0.391 | |
counts2cpm | 0.342 | 0.000 | 0.342 | |
counts2tpm | 0.35 | 0.00 | 0.35 | |
cpm | 0.330 | 0.004 | 0.334 | |
create_design | 0.668 | 0.012 | 0.645 | |
default_coefs | 0.682 | 0.004 | 0.664 | |
default_formula | 14.120 | 0.328 | 14.010 | |
default_geom | 0.495 | 0.012 | 0.487 | |
default_sfile | 0.002 | 0.000 | 0.002 | |
demultiplex | 0.012 | 0.000 | 0.012 | |
dequantify | 0.002 | 0.000 | 0.002 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.001 | |
dot-merge | 0.015 | 0.000 | 0.015 | |
dot-plot_survival | 3.029 | 0.096 | 3.125 | |
dot-read_maxquant_proteingroups | 1.176 | 0.056 | 1.232 | |
download_contaminants | 0.226 | 0.000 | 2.541 | |
download_data | 0.001 | 0.000 | 0.000 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.000 | 0.001 | |
dt2mat | 0.006 | 0.000 | 0.005 | |
enrichment | 1.214 | 0.028 | 1.242 | |
entrezg_to_symbol | 0 | 0 | 0 | |
explore_transformations | 3.182 | 0.120 | 3.302 | |
extract_coef_features | 4.969 | 0.072 | 5.020 | |
extract_rectangle | 0.103 | 0.004 | 0.108 | |
fcluster | 5.310 | 0.052 | 5.306 | |
fcor | 0.950 | 0.008 | 0.958 | |
fdata | 0.530 | 0.004 | 0.533 | |
fdr2p | 0.903 | 0.008 | 0.890 | |
filter_exprs_replicated_in_some_subgroup | 1.003 | 0.012 | 0.900 | |
filter_features | 0.512 | 0.015 | 0.490 | |
filter_medoid | 0.724 | 0.012 | 0.736 | |
filter_samples | 0.525 | 0.012 | 0.499 | |
fit | 13.396 | 0.037 | 12.341 | |
fit_lmx | 4.370 | 0.064 | 4.200 | |
fitcoefs | 0.776 | 0.000 | 0.738 | |
fits | 0.721 | 0.000 | 0.685 | |
fitvars | 1.020 | 0.008 | 0.991 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.398 | 0.008 | 0.406 | |
fnames | 0.447 | 0.004 | 0.452 | |
formula2str | 0 | 0 | 0 | |
ftype | 6.939 | 0.096 | 6.656 | |
fvalues | 0.404 | 0.004 | 0.407 | |
fvars | 0.452 | 0.000 | 0.452 | |
genome_to_orgdb | 0 | 0 | 0 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.000 | 0.001 | 0.001 | |
guess_fitsep | 0.446 | 0.003 | 0.448 | |
guess_maxquant_quantity | 0.005 | 0.000 | 0.005 | |
guess_sep | 0.482 | 0.020 | 0.480 | |
has_multiple_levels | 0.046 | 0.006 | 0.052 | |
hdlproteins | 0.037 | 0.009 | 0.050 | |
impute | 2.806 | 0.060 | 2.866 | |
invert_subgroups | 0.617 | 0.000 | 0.617 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_correlation_matrix | 0.001 | 0.000 | 0.001 | |
is_diann_report | 0.513 | 0.044 | 0.469 | |
is_fastadt | 0.059 | 0.000 | 0.059 | |
is_file | 0 | 0 | 0 | |
is_fraction | 0.001 | 0.000 | 0.002 | |
is_imputed | 0.683 | 0.000 | 0.684 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.351 | 0.004 | 0.356 | |
is_sig | 1.481 | 0.000 | 1.481 | |
is_valid_formula | 0.040 | 0.000 | 0.039 | |
keep_connected_blocks | 0.530 | 0.012 | 0.513 | |
keep_connected_features | 0.713 | 0.004 | 0.673 | |
keep_replicated_features | 0.815 | 0.032 | 0.784 | |
label2index | 0.001 | 0.000 | 0.000 | |
list2mat | 0.001 | 0.000 | 0.000 | |
log2counts | 0.428 | 0.004 | 0.432 | |
log2cpm | 0.362 | 0.000 | 0.362 | |
log2diffs | 0.325 | 0.008 | 0.333 | |
log2proteins | 0.333 | 0.004 | 0.338 | |
log2sites | 0.323 | 0.004 | 0.327 | |
log2tpm | 0.411 | 0.000 | 0.412 | |
log2transform | 3.570 | 0.012 | 3.583 | |
logical2factor | 0.001 | 0.000 | 0.001 | |
make_alpha_palette | 0.553 | 0.008 | 0.540 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.864 | 0.004 | 0.868 | |
map_fvalues | 0.388 | 0.004 | 0.391 | |
matrix2sumexp | 0.946 | 0.000 | 0.924 | |
merge_sample_file | 0.454 | 0.004 | 0.457 | |
merge_sdata | 0.564 | 0.012 | 0.554 | |
message_df | 0.002 | 0.000 | 0.002 | |
modelvar | 3.498 | 0.000 | 3.443 | |
order_on_p | 0.951 | 0.008 | 0.929 | |
pca | 2.836 | 0.028 | 2.841 | |
pg_to_canonical | 0.006 | 0.000 | 0.006 | |
plot_contrast_venn | 2.323 | 0.012 | 2.254 | |
plot_contrastogram | 3.034 | 0.020 | 2.966 | |
plot_data | 1.198 | 0.008 | 1.185 | |
plot_densities | 9.053 | 0.140 | 9.081 | |
plot_design | 0.645 | 0.016 | 0.661 | |
plot_exprs | 23.206 | 0.176 | 23.285 | |
plot_exprs_per_coef | 23.559 | 0.092 | 23.537 | |
plot_fit_summary | 1.860 | 0.012 | 1.765 | |
plot_heatmap | 1.682 | 0.004 | 1.686 | |
plot_matrix | 0.503 | 0.008 | 0.472 | |
plot_sample_nas | 5.683 | 0.036 | 5.676 | |
plot_subgroup_points | 4.289 | 0.032 | 4.268 | |
plot_summary | 12.187 | 0.088 | 12.169 | |
plot_venn | 0.016 | 0.000 | 0.016 | |
plot_venn_heatmap | 0.02 | 0.00 | 0.02 | |
plot_violins | 3.600 | 0.012 | 3.574 | |
plot_volcano | 9.836 | 0.092 | 9.869 | |
preprocess_rnaseq_counts | 0.336 | 0.024 | 0.359 | |
pull_columns | 0.003 | 0.000 | 0.002 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.117 | 0.000 | 1.298 | |
read_diann_proteingroups | 89.892 | 0.956 | 86.194 | |
read_fragpipe | 6.898 | 0.064 | 6.658 | |
read_maxquant_phosphosites | 1.433 | 0.000 | 1.432 | |
read_maxquant_proteingroups | 1.200 | 0.012 | 1.211 | |
read_metabolon | 11.846 | 0.028 | 11.763 | |
read_msigdt | 0.001 | 0.000 | 0.000 | |
read_olink | 1.302 | 0.032 | 1.252 | |
read_rectangles | 0.164 | 0.008 | 0.172 | |
read_rnaseq_counts | 28.492 | 2.082 | 30.347 | |
read_salmon | 0.001 | 0.000 | 0.000 | |
read_somascan | 12.741 | 0.392 | 13.079 | |
read_uniprotdt | 0.273 | 0.012 | 0.285 | |
reset_fit | 4.740 | 0.052 | 4.682 | |
rm_diann_contaminants | 18.678 | 0.520 | 19.070 | |
rm_missing_in_some_samples | 0.533 | 0.009 | 0.521 | |
rm_unmatched_samples | 0.515 | 0.012 | 0.526 | |
scaledlibsizes | 0.426 | 0.016 | 0.442 | |
scoremat | 0.933 | 0.008 | 0.920 | |
slevels | 0.389 | 0.008 | 0.398 | |
snames | 0.471 | 0.004 | 0.475 | |
split_extract_fixed | 0.483 | 0.004 | 0.468 | |
split_samples | 1.157 | 0.004 | 1.141 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.329 | 0.004 | 0.333 | |
subgroup_matrix | 0.505 | 0.016 | 0.499 | |
subtract_baseline | 4.300 | 0.036 | 4.284 | |
sumexp_to_longdt | 1.779 | 0.040 | 1.763 | |
sumexp_to_tsv | 0.483 | 0.016 | 0.499 | |
sumexplist_to_longdt | 1.555 | 0.032 | 1.587 | |
summarize_fit | 1.643 | 0.048 | 1.628 | |
svalues | 0.433 | 0.020 | 0.454 | |
svars | 0.407 | 0.000 | 0.407 | |
systematic_nas | 0.528 | 0.008 | 0.536 | |
tag_features | 1.072 | 0.036 | 1.109 | |
tag_hdlproteins | 0.509 | 0.004 | 0.514 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.385 | 0.004 | 0.388 | |
uncollapse | 0.011 | 0.000 | 0.010 | |
values | 0.458 | 0.004 | 0.463 | |
varlevels_dont_clash | 0.096 | 0.012 | 0.108 | |
venn_detects | 0.572 | 0.004 | 0.577 | |
weights | 0.375 | 0.004 | 0.379 | |
write_xl | 0.671 | 0.004 | 0.653 | |
zero_to_na | 0.001 | 0.000 | 0.001 | |