Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:39 -0400 (Tue, 27 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" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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: 2024-08-26 20:36:05 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 20:50:48 -0400 (Mon, 26 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 88.397 3.288 87.215 read_rnaseq_counts 27.676 1.036 28.520 plot_exprs_per_coef 23.762 0.184 23.861 plot_exprs 23.159 0.176 23.201 rm_diann_contaminants 17.852 0.164 18.094 default_formula 14.057 0.439 14.102 fit 12.651 0.279 12.242 analyze 12.264 0.076 12.259 read_somascan 12.131 0.148 12.228 read_metabolon 11.900 0.097 11.918 plot_summary 11.797 0.104 11.819 plot_volcano 9.339 0.040 9.329 plot_densities 8.025 0.160 8.112 ftype 6.687 0.172 6.573 read_fragpipe 6.396 0.160 6.287 code 6.062 0.172 6.213 fcluster 5.459 0.248 5.603 biplot_covariates 5.431 0.232 5.642 extract_coef_features 5.219 0.364 5.618 plot_sample_nas 5.411 0.100 5.466 * 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 135.678 3.863 136.829
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.001 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0.000 | 0.000 | 0.001 | |
CONTAMINANTSURL | 0.001 | 0.000 | 0.000 | |
FITSEP | 0 | 0 | 0 | |
LINMOD_ENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
X | 1.468 | 0.009 | 1.456 | |
abstract_fit | 1.025 | 0.072 | 1.074 | |
add_adjusted_pvalues | 1.192 | 0.040 | 1.233 | |
add_assay_means | 0.344 | 0.000 | 0.345 | |
add_facetvars | 1.860 | 0.031 | 1.864 | |
add_opentargets_by_uniprot | 0.405 | 0.001 | 0.407 | |
add_psp | 0.513 | 0.004 | 0.518 | |
add_smiles | 0.462 | 0.015 | 0.444 | |
analysis | 0.375 | 0.036 | 0.411 | |
analyze | 12.264 | 0.076 | 12.259 | |
annotate_maxquant | 0.842 | 0.024 | 0.866 | |
annotate_uniprot_rest | 0.287 | 0.016 | 2.111 | |
assert_is_valid_sumexp | 0.553 | 0.020 | 0.552 | |
bin | 0.394 | 0.032 | 0.427 | |
biplot | 3.426 | 0.256 | 3.661 | |
biplot_corrections | 2.954 | 0.112 | 3.016 | |
biplot_covariates | 5.431 | 0.232 | 5.642 | |
block2lme | 0.003 | 0.000 | 0.003 | |
center | 1.325 | 0.028 | 1.353 | |
code | 6.062 | 0.172 | 6.213 | |
coefs | 0.700 | 0.016 | 0.695 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.537 | 0.028 | 0.545 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.387 | 0.012 | 0.407 | |
counts2cpm | 0.337 | 0.000 | 0.337 | |
counts2tpm | 0.342 | 0.000 | 0.341 | |
cpm | 0.351 | 0.024 | 0.375 | |
create_design | 0.679 | 0.032 | 0.691 | |
default_coefs | 0.676 | 0.016 | 0.671 | |
default_formula | 14.057 | 0.439 | 14.102 | |
default_geom | 0.504 | 0.008 | 0.492 | |
default_sfile | 0.001 | 0.000 | 0.001 | |
demultiplex | 0.012 | 0.000 | 0.013 | |
dequantify | 0.002 | 0.000 | 0.002 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.001 | |
dot-merge | 0.014 | 0.000 | 0.014 | |
dot-plot_survival | 2.994 | 0.140 | 3.134 | |
dot-read_maxquant_proteingroups | 1.088 | 0.052 | 1.140 | |
download_contaminants | 0.184 | 0.016 | 2.451 | |
download_data | 0.000 | 0.000 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.003 | 0.000 | 0.003 | |
enrichment | 1.235 | 0.068 | 1.303 | |
entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
explore_transformations | 3.318 | 0.372 | 3.690 | |
extract_coef_features | 5.219 | 0.364 | 5.618 | |
extract_rectangle | 0.104 | 0.008 | 0.112 | |
fcluster | 5.459 | 0.248 | 5.603 | |
fcor | 0.985 | 0.072 | 1.057 | |
fdata | 0.526 | 0.016 | 0.542 | |
fdr2p | 0.922 | 0.040 | 0.940 | |
filter_exprs_replicated_in_some_subgroup | 0.960 | 0.048 | 0.948 | |
filter_features | 0.519 | 0.040 | 0.536 | |
filter_medoid | 0.714 | 0.036 | 0.750 | |
filter_samples | 0.522 | 0.004 | 0.504 | |
fit | 12.651 | 0.279 | 12.242 | |
fit_lmx | 4.277 | 0.148 | 4.242 | |
fitcoefs | 0.716 | 0.020 | 0.712 | |
fits | 0.697 | 0.000 | 0.678 | |
fitvars | 1.006 | 0.012 | 0.998 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.407 | 0.000 | 0.407 | |
fnames | 0.458 | 0.004 | 0.462 | |
formula2str | 0.000 | 0.000 | 0.001 | |
ftype | 6.687 | 0.172 | 6.573 | |
fvalues | 0.421 | 0.011 | 0.432 | |
fvars | 0.422 | 0.028 | 0.450 | |
genome_to_orgdb | 0.000 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.444 | 0.000 | 0.443 | |
guess_maxquant_quantity | 0.005 | 0.000 | 0.006 | |
guess_sep | 0.484 | 0.016 | 0.479 | |
has_multiple_levels | 0.048 | 0.000 | 0.049 | |
hdlproteins | 0.032 | 0.020 | 0.055 | |
impute | 2.824 | 0.028 | 2.853 | |
invert_subgroups | 0.629 | 0.004 | 0.634 | |
is_collapsed_subset | 0 | 0 | 0 | |
is_correlation_matrix | 0.001 | 0.000 | 0.002 | |
is_diann_report | 0.515 | 0.048 | 0.470 | |
is_fastadt | 0.063 | 0.000 | 0.064 | |
is_file | 0.000 | 0.000 | 0.001 | |
is_fraction | 0.001 | 0.000 | 0.001 | |
is_imputed | 0.703 | 0.008 | 0.711 | |
is_positive_number | 0.001 | 0.000 | 0.002 | |
is_scalar_subset | 0.353 | 0.004 | 0.357 | |
is_sig | 1.488 | 0.004 | 1.492 | |
is_valid_formula | 0.037 | 0.004 | 0.040 | |
keep_connected_blocks | 0.553 | 0.004 | 0.517 | |
keep_connected_features | 0.747 | 0.012 | 0.668 | |
keep_replicated_features | 0.887 | 0.008 | 0.775 | |
label2index | 0.000 | 0.000 | 0.001 | |
list2mat | 0.000 | 0.001 | 0.001 | |
log2counts | 0.413 | 0.021 | 0.434 | |
log2cpm | 0.388 | 0.000 | 0.388 | |
log2diffs | 0.329 | 0.004 | 0.333 | |
log2proteins | 0.325 | 0.000 | 0.324 | |
log2sites | 0.312 | 0.004 | 0.316 | |
log2tpm | 0.385 | 0.000 | 0.385 | |
log2transform | 3.505 | 0.052 | 3.557 | |
logical2factor | 0.001 | 0.000 | 0.001 | |
make_alpha_palette | 0.591 | 0.012 | 0.581 | |
make_colors | 0.009 | 0.000 | 0.011 | |
make_volcano_dt | 0.822 | 0.020 | 0.843 | |
map_fvalues | 0.397 | 0.012 | 0.409 | |
matrix2sumexp | 0.946 | 0.020 | 0.944 | |
merge_sample_file | 0.468 | 0.004 | 0.472 | |
merge_sdata | 0.570 | 0.016 | 0.566 | |
message_df | 0.002 | 0.000 | 0.002 | |
modelvar | 3.459 | 0.028 | 3.383 | |
order_on_p | 0.893 | 0.008 | 0.879 | |
pca | 2.745 | 0.012 | 2.738 | |
pg_to_canonical | 0.002 | 0.004 | 0.006 | |
plot_contrast_venn | 2.270 | 0.020 | 2.212 | |
plot_contrastogram | 2.979 | 0.048 | 2.924 | |
plot_data | 1.157 | 0.024 | 1.152 | |
plot_densities | 8.025 | 0.160 | 8.112 | |
plot_design | 0.609 | 0.004 | 0.613 | |
plot_exprs | 23.159 | 0.176 | 23.201 | |
plot_exprs_per_coef | 23.762 | 0.184 | 23.861 | |
plot_fit_summary | 1.735 | 0.008 | 1.689 | |
plot_heatmap | 1.632 | 0.027 | 1.659 | |
plot_matrix | 0.502 | 0.020 | 0.500 | |
plot_sample_nas | 5.411 | 0.100 | 5.466 | |
plot_subgroup_points | 4.132 | 0.024 | 4.118 | |
plot_summary | 11.797 | 0.104 | 11.819 | |
plot_venn | 0.016 | 0.000 | 0.016 | |
plot_venn_heatmap | 0.019 | 0.000 | 0.019 | |
plot_violins | 3.403 | 0.029 | 3.410 | |
plot_volcano | 9.339 | 0.040 | 9.329 | |
preprocess_rnaseq_counts | 0.328 | 0.004 | 0.332 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0.001 | 0.000 | 0.000 | |
read_contaminants | 0.108 | 0.008 | 1.385 | |
read_diann_proteingroups | 88.397 | 3.288 | 87.215 | |
read_fragpipe | 6.396 | 0.160 | 6.287 | |
read_maxquant_phosphosites | 1.531 | 0.016 | 1.547 | |
read_maxquant_proteingroups | 1.206 | 0.016 | 1.222 | |
read_metabolon | 11.900 | 0.097 | 11.918 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.349 | 0.020 | 1.330 | |
read_rectangles | 0.162 | 0.008 | 0.171 | |
read_rnaseq_counts | 27.676 | 1.036 | 28.520 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 12.131 | 0.148 | 12.228 | |
read_uniprotdt | 0.274 | 0.004 | 0.278 | |
reset_fit | 4.568 | 0.036 | 4.511 | |
rm_diann_contaminants | 17.852 | 0.164 | 18.094 | |
rm_missing_in_some_samples | 0.482 | 0.024 | 0.487 | |
rm_unmatched_samples | 0.505 | 0.004 | 0.508 | |
scaledlibsizes | 0.397 | 0.008 | 0.405 | |
scoremat | 0.898 | 0.024 | 0.903 | |
slevels | 0.393 | 0.004 | 0.398 | |
snames | 0.443 | 0.008 | 0.452 | |
split_extract_fixed | 0.480 | 0.004 | 0.464 | |
split_samples | 1.151 | 0.000 | 1.114 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.336 | 0.000 | 0.336 | |
subgroup_matrix | 0.503 | 0.012 | 0.495 | |
subtract_baseline | 4.238 | 0.052 | 4.242 | |
sumexp_to_longdt | 1.821 | 0.033 | 1.802 | |
sumexp_to_tsv | 0.478 | 0.000 | 0.478 | |
sumexplist_to_longdt | 1.623 | 0.048 | 1.671 | |
summarize_fit | 1.607 | 0.015 | 1.558 | |
svalues | 0.393 | 0.000 | 0.392 | |
svars | 0.396 | 0.000 | 0.397 | |
systematic_nas | 0.503 | 0.000 | 0.503 | |
tag_features | 1.030 | 0.007 | 1.038 | |
tag_hdlproteins | 0.498 | 0.012 | 0.510 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.372 | 0.005 | 0.377 | |
uncollapse | 0.01 | 0.00 | 0.01 | |
values | 0.479 | 0.031 | 0.511 | |
varlevels_dont_clash | 0.018 | 0.001 | 0.018 | |
venn_detects | 0.510 | 0.004 | 0.515 | |
weights | 0.362 | 0.003 | 0.367 | |
write_xl | 0.657 | 0.004 | 0.640 | |
zero_to_na | 0.002 | 0.000 | 0.002 | |