Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-06 11:38 -0400 (Sat, 06 Jul 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" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
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 112/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.13.19 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | 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: 1.13.19 |
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_1.13.19.tar.gz |
StartedAt: 2024-07-05 20:30:43 -0400 (Fri, 05 Jul 2024) |
EndedAt: 2024-07-05 20:45:22 -0400 (Fri, 05 Jul 2024) |
EllapsedTime: 878.9 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_1.13.19.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 ‘1.13.19’ * 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 89.647 3.352 88.543 plot_model_summary 39.384 0.224 39.053 read_rnaseq_counts 27.666 2.331 29.835 rm_diann_contaminants 18.925 0.583 19.565 plot_exprs 17.611 0.204 17.652 plot_exprs_per_coef 16.806 0.128 16.810 default_formula 13.904 0.558 14.068 fit 12.443 0.916 12.618 read_somascan 12.144 0.284 12.325 analyze 11.595 0.103 11.583 read_metabolon 11.411 0.056 11.347 plot_summary 10.614 0.019 10.538 plot_densities 8.576 0.248 8.741 plot_volcano 8.697 0.056 8.645 plot_sample_nas 5.689 0.068 5.701 fcluster 5.347 0.256 5.538 read_fragpipe 5.306 0.076 5.116 * 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 > > test_check("autonomics") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ] > > proc.time() user system elapsed 128.531 4.173 129.896
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.001 | 0.001 | 0.000 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
CONTAMINANTSURL | 0 | 0 | 0 | |
FITSEP | 0 | 0 | 0 | |
LINMOD_ENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
abstract_fit | 1.240 | 0.008 | 1.227 | |
add_adjusted_pvalues | 0.577 | 0.032 | 0.610 | |
add_assay_means | 1.046 | 0.072 | 1.119 | |
add_facetvars | 1.470 | 0.036 | 1.485 | |
add_opentargets_by_uniprot | 0.413 | 0.004 | 0.418 | |
add_psp | 0.512 | 0.000 | 0.512 | |
add_smiles | 0.471 | 0.000 | 0.446 | |
analysis | 0.365 | 0.000 | 0.364 | |
analyze | 11.595 | 0.103 | 11.583 | |
annotate_maxquant | 0.832 | 0.028 | 0.861 | |
annotate_uniprot_rest | 0.392 | 0.016 | 2.341 | |
assert_is_valid_sumexp | 0.562 | 0.060 | 0.602 | |
bin | 0.387 | 0.012 | 0.400 | |
biplot | 4.177 | 0.380 | 4.536 | |
biplot_corrections | 2.847 | 0.116 | 2.929 | |
biplot_covariates | 4.702 | 0.148 | 4.812 | |
block2lme | 0.003 | 0.000 | 0.003 | |
center | 1.356 | 0.020 | 1.377 | |
code | 3.815 | 0.076 | 3.870 | |
coefs | 0.681 | 0.012 | 0.673 | |
collapsed_entrezg_to_symbol | 0 | 0 | 0 | |
contrast_subgroup_cols | 0.559 | 0.016 | 0.556 | |
count_in | 0.000 | 0.000 | 0.001 | |
counts | 0.384 | 0.012 | 0.396 | |
counts2cpm | 0.328 | 0.000 | 0.328 | |
counts2tpm | 0.341 | 0.000 | 0.340 | |
cpm | 0.341 | 0.016 | 0.357 | |
create_design | 0.690 | 0.004 | 0.675 | |
default_coefs | 0.680 | 0.000 | 0.658 | |
default_formula | 13.904 | 0.558 | 14.068 | |
default_geom | 0.491 | 0.016 | 0.479 | |
default_sfile | 0.001 | 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 | 0.014 | |
dot-plot_survival | 3.824 | 0.212 | 4.035 | |
dot-read_maxquant_proteingroups | 0.115 | 0.004 | 0.119 | |
download_contaminants | 0.164 | 0.008 | 2.423 | |
download_data | 0.001 | 0.000 | 0.000 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.000 | 0.001 | |
dt2mat | 0.005 | 0.002 | 0.007 | |
enrichment | 1.165 | 0.120 | 1.286 | |
entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
explore_transformations | 3.214 | 0.442 | 3.655 | |
extract_coef_features | 4.260 | 0.376 | 4.614 | |
extract_rectangle | 0.091 | 0.024 | 0.115 | |
fcluster | 5.347 | 0.256 | 5.538 | |
fcor | 0.941 | 0.044 | 0.985 | |
fdata | 0.541 | 0.068 | 0.609 | |
fdr2p | 0.881 | 0.056 | 0.907 | |
filter_exprs_replicated_in_some_subgroup | 1.018 | 0.068 | 0.962 | |
filter_features | 0.526 | 0.000 | 0.498 | |
filter_medoid | 0.698 | 0.020 | 0.718 | |
filter_samples | 0.551 | 0.032 | 0.557 | |
fit | 12.443 | 0.916 | 12.618 | |
fit_lmx | 4.325 | 0.227 | 4.369 | |
fitcoefs | 0.743 | 0.020 | 0.741 | |
fits | 0.733 | 0.020 | 0.731 | |
fitvars | 0.964 | 0.044 | 0.986 | |
fix_xlgenes | 0.001 | 0.000 | 0.002 | |
flevels | 0.410 | 0.012 | 0.422 | |
fnames | 0.468 | 0.012 | 0.480 | |
formula2str | 0 | 0 | 0 | |
fvalues | 0.398 | 0.012 | 0.409 | |
fvars | 0.378 | 0.008 | 0.386 | |
genome_to_orgdb | 0 | 0 | 0 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.441 | 0.008 | 0.450 | |
guess_maxquant_quantity | 0.005 | 0.000 | 0.006 | |
guess_sep | 0.528 | 0.020 | 0.527 | |
has_multiple_levels | 0.055 | 0.000 | 0.055 | |
hdlproteins | 0.041 | 0.016 | 0.061 | |
impute | 2.874 | 0.108 | 2.982 | |
invert_subgroups | 0.671 | 0.032 | 0.703 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_correlation_matrix | 0.001 | 0.000 | 0.002 | |
is_diann_report | 0.525 | 0.036 | 0.468 | |
is_fastadt | 0.057 | 0.000 | 0.058 | |
is_file | 0 | 0 | 0 | |
is_fraction | 0.000 | 0.002 | 0.001 | |
is_imputed | 0.689 | 0.006 | 0.694 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.320 | 0.008 | 0.328 | |
is_sig | 1.304 | 0.016 | 1.320 | |
is_valid_formula | 0.039 | 0.000 | 0.039 | |
keep_connected_blocks | 0.515 | 0.012 | 0.486 | |
keep_connected_features | 0.701 | 0.008 | 0.656 | |
keep_replicated_features | 1.025 | 0.044 | 1.003 | |
label2index | 0.001 | 0.000 | 0.000 | |
list2mat | 0.001 | 0.000 | 0.000 | |
log2counts | 0.386 | 0.004 | 0.389 | |
log2cpm | 0.364 | 0.000 | 0.365 | |
log2diffs | 0.334 | 0.040 | 0.374 | |
log2proteins | 0.325 | 0.028 | 0.353 | |
log2sites | 0.324 | 0.016 | 0.340 | |
log2tpm | 0.365 | 0.012 | 0.377 | |
log2transform | 3.521 | 0.080 | 3.601 | |
logical2factor | 0.002 | 0.000 | 0.001 | |
make_alpha_palette | 0.514 | 0.012 | 0.502 | |
make_colors | 0.010 | 0.000 | 0.009 | |
make_volcano_dt | 0.815 | 0.016 | 0.830 | |
map_fvalues | 0.387 | 0.000 | 0.388 | |
matrix2sumexp | 0.876 | 0.004 | 0.857 | |
merge_sample_file | 0.460 | 0.016 | 0.477 | |
merge_sdata | 0.531 | 0.028 | 0.522 | |
message_df | 0.002 | 0.000 | 0.002 | |
modelvar | 3.162 | 0.052 | 3.116 | |
order_on_p | 0.890 | 0.008 | 0.877 | |
pca | 2.861 | 0.052 | 2.877 | |
pg_to_canonical | 0.006 | 0.000 | 0.006 | |
plot_contrast_venn | 2.230 | 0.020 | 2.104 | |
plot_contrastogram | 2.652 | 0.036 | 2.587 | |
plot_data | 1.208 | 0.024 | 1.211 | |
plot_densities | 8.576 | 0.248 | 8.741 | |
plot_design | 0.572 | 0.004 | 0.575 | |
plot_exprs | 17.611 | 0.204 | 17.652 | |
plot_exprs_per_coef | 16.806 | 0.128 | 16.810 | |
plot_fit_summary | 1.778 | 0.000 | 1.723 | |
plot_heatmap | 1.582 | 0.052 | 1.634 | |
plot_matrix | 0.521 | 0.004 | 0.488 | |
plot_model_summary | 39.384 | 0.224 | 39.053 | |
plot_sample_nas | 5.689 | 0.068 | 5.701 | |
plot_subgroup_points | 4.106 | 0.048 | 4.073 | |
plot_summary | 10.614 | 0.019 | 10.538 | |
plot_venn | 0.017 | 0.000 | 0.016 | |
plot_venn_heatmap | 0.020 | 0.000 | 0.019 | |
plot_violins | 3.534 | 0.020 | 3.516 | |
plot_volcano | 8.697 | 0.056 | 8.645 | |
preprocess_rnaseq_counts | 0.373 | 0.000 | 0.373 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.125 | 0.000 | 1.228 | |
read_diann_proteingroups | 89.647 | 3.352 | 88.543 | |
read_fragpipe | 5.306 | 0.076 | 5.116 | |
read_maxquant_phosphosites | 1.525 | 0.040 | 1.565 | |
read_maxquant_proteingroups | 1.245 | 0.016 | 1.261 | |
read_metabolon | 11.411 | 0.056 | 11.347 | |
read_msigdt | 0.000 | 0.000 | 0.001 | |
read_olink | 1.338 | 0.032 | 1.307 | |
read_rectangles | 0.164 | 0.012 | 0.176 | |
read_rnaseq_counts | 27.666 | 2.331 | 29.835 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 12.144 | 0.284 | 12.325 | |
read_uniprotdt | 0.272 | 0.016 | 0.288 | |
reset_fit | 3.767 | 0.176 | 3.848 | |
rm_diann_contaminants | 18.925 | 0.583 | 19.565 | |
rm_missing_in_some_samples | 0.614 | 0.048 | 0.630 | |
rm_unmatched_samples | 0.611 | 0.036 | 0.646 | |
scaledlibsizes | 0.421 | 0.032 | 0.453 | |
scoremat | 1.061 | 0.132 | 1.155 | |
slevels | 0.422 | 0.044 | 0.467 | |
snames | 0.408 | 0.044 | 0.452 | |
split_extract_fixed | 0.586 | 0.080 | 0.636 | |
split_samples | 1.102 | 0.116 | 1.179 | |
stri_any_regex | 0.001 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.317 | 0.052 | 0.369 | |
subgroup_matrix | 0.559 | 0.112 | 0.650 | |
subtract_baseline | 4.149 | 0.260 | 4.343 | |
sumexp_to_longdt | 1.861 | 0.112 | 1.863 | |
sumexp_to_tsv | 0.466 | 0.040 | 0.506 | |
sumexplist_to_longdt | 1.524 | 0.112 | 1.636 | |
summarize_fit | 1.504 | 0.044 | 1.483 | |
svalues | 0.401 | 0.012 | 0.412 | |
svars | 0.399 | 0.008 | 0.407 | |
systematic_nas | 0.585 | 0.056 | 0.642 | |
tag_features | 0.833 | 0.060 | 0.893 | |
tag_hdlproteins | 0.536 | 0.012 | 0.548 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.427 | 0.008 | 0.436 | |
uncollapse | 0.01 | 0.00 | 0.01 | |
values | 0.41 | 0.00 | 0.41 | |
varlevels_dont_clash | 0.021 | 0.004 | 0.025 | |
venn_detects | 0.521 | 0.000 | 0.521 | |
weights | 0.358 | 0.000 | 0.358 | |
write_xl | 0.707 | 0.032 | 0.718 | |
zero_to_na | 0.002 | 0.000 | 0.001 | |