Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:36:17 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 112/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.12.0 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.12.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings autonomics_1.12.0.tar.gz |
StartedAt: 2024-05-03 20:47:35 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 21:03:54 -0400 (Fri, 03 May 2024) |
EllapsedTime: 979.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: autonomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings autonomics_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * 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 ‘1.12.0’ * 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 ... NOTE checkRd: (-1) dequantify.Rd:24: Lost braces; missing escapes or markup? 24 | Encode {channel} as suffix. | ^ * 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 91.786 4.867 91.965 read_rnaseq_counts 26.838 1.021 27.622 plot_exprs 19.349 0.311 19.533 rm_diann_contaminants 18.729 0.316 18.987 plot_exprs_per_coef 18.695 0.256 18.839 default_formula 14.516 0.379 14.450 fit 12.973 0.537 12.337 analyze 12.246 0.100 12.261 read_somascan 11.558 0.008 11.501 read_metabolon 11.444 0.112 11.435 plot_summary 10.955 0.132 11.004 plot_volcano 8.873 0.056 8.873 plot_densities 8.090 0.264 8.274 plot_sample_nas 6.828 0.127 6.908 read_fragpipe 6.441 0.236 6.391 biplot_covariates 5.252 0.020 5.251 extract_coef_features 4.682 0.396 5.056 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’ for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 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 126.751 4.656 129.060
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0 | 0 | 0 | |
CONTAMINANTSURL | 0 | 0 | 0 | |
FITSEP | 0 | 0 | 0 | |
LINMOD_ENGINES | 0.001 | 0.000 | 0.001 | |
MAXQUANT_PATTERNS | 0.001 | 0.000 | 0.000 | |
TAXON_TO_ORGNAME | 0.001 | 0.000 | 0.000 | |
TESTS | 0 | 0 | 0 | |
abstract_fit | 1.267 | 0.051 | 1.296 | |
add_adjusted_pvalues | 0.575 | 0.048 | 0.623 | |
add_assay_means | 1.013 | 0.036 | 1.049 | |
add_facetvars | 1.525 | 0.080 | 1.584 | |
add_opentargets_by_uniprot | 0.396 | 0.015 | 0.414 | |
add_psp | 0.511 | 0.012 | 0.524 | |
add_smiles | 0.491 | 0.012 | 0.483 | |
analysis | 0.405 | 0.004 | 0.409 | |
analyze | 12.246 | 0.100 | 12.261 | |
annotate_maxquant | 0.834 | 0.020 | 0.854 | |
annotate_uniprot_rest | 0.413 | 0.008 | 2.567 | |
assert_is_valid_sumexp | 0.713 | 0.036 | 0.728 | |
bin | 1.247 | 0.048 | 1.295 | |
biplot | 3.465 | 0.052 | 3.497 | |
biplot_corrections | 3.247 | 0.019 | 3.245 | |
biplot_covariates | 5.252 | 0.020 | 5.251 | |
block2lme | 0.002 | 0.002 | 0.004 | |
center | 1.374 | 0.014 | 1.389 | |
code | 4.657 | 0.028 | 4.663 | |
coefs | 0.691 | 0.052 | 0.721 | |
collapsed_entrezg_to_symbol | 0 | 0 | 0 | |
contrast_subgroup_cols | 0.593 | 0.020 | 0.592 | |
count_in | 0.002 | 0.000 | 0.001 | |
counts | 0.428 | 0.000 | 0.427 | |
counts2cpm | 0.380 | 0.000 | 0.379 | |
counts2tpm | 0.332 | 0.000 | 0.332 | |
cpm | 0.381 | 0.000 | 0.380 | |
create_design | 0.671 | 0.024 | 0.674 | |
default_formula | 14.516 | 0.379 | 14.450 | |
default_geom | 0.501 | 0.009 | 0.489 | |
default_sfile | 0.002 | 0.000 | 0.001 | |
demultiplex | 0.014 | 0.000 | 0.013 | |
dequantify | 0.003 | 0.000 | 0.002 | |
dot-merge | 0.015 | 0.000 | 0.016 | |
dot-plot_survival | 3.989 | 0.171 | 4.161 | |
dot-read_maxquant_proteingroups | 0.123 | 0.000 | 0.123 | |
download_contaminants | 0.188 | 0.008 | 2.576 | |
download_data | 0.000 | 0.002 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.000 | 0.001 | |
dt2mat | 0.003 | 0.004 | 0.007 | |
enrichment | 1.191 | 0.084 | 1.276 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
explore_transformations | 3.418 | 0.212 | 3.630 | |
extract_coef_features | 4.682 | 0.396 | 5.056 | |
extract_rectangle | 0.099 | 0.031 | 0.131 | |
fdata | 0.548 | 0.052 | 0.600 | |
fdr2p | 0.893 | 0.075 | 0.948 | |
filter_exprs_replicated_in_some_subgroup | 1.070 | 0.073 | 1.030 | |
filter_features | 0.542 | 0.016 | 0.520 | |
filter_medoid | 0.730 | 0.024 | 0.754 | |
filter_samples | 0.549 | 0.036 | 0.547 | |
fit | 12.973 | 0.537 | 12.337 | |
fit_lmx | 4.334 | 0.096 | 4.217 | |
fitcoefs | 0.785 | 0.044 | 0.790 | |
fits | 0.695 | 0.019 | 0.694 | |
fitvars | 1.004 | 0.044 | 1.028 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.421 | 0.015 | 0.436 | |
fnames | 0.465 | 0.005 | 0.468 | |
formula2str | 0.000 | 0.000 | 0.001 | |
fvalues | 0.415 | 0.008 | 0.423 | |
fvars | 0.392 | 0.000 | 0.391 | |
genome_to_orgdb | 0.001 | 0.000 | 0.000 | |
group_by_level | 0.002 | 0.000 | 0.001 | |
guess_fitsep | 0.487 | 0.003 | 0.491 | |
guess_maxquant_quantity | 0.006 | 0.001 | 0.006 | |
guess_sep | 0.493 | 0.016 | 0.486 | |
has_multiple_levels | 0.048 | 0.004 | 0.051 | |
hdlproteins | 0.054 | 0.036 | 0.092 | |
impute | 3.020 | 0.056 | 3.075 | |
invert_subgroups | 0.688 | 0.024 | 0.712 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_diann_report | 0.441 | 0.063 | 0.461 | |
is_fastadt | 0.058 | 0.008 | 0.066 | |
is_file | 0.001 | 0.000 | 0.001 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.729 | 0.056 | 0.785 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.359 | 0.032 | 0.391 | |
is_sig | 1.284 | 0.116 | 1.401 | |
is_valid_formula | 0.044 | 0.004 | 0.048 | |
keep_connected_blocks | 0.566 | 0.048 | 0.574 | |
keep_connected_features | 0.817 | 0.104 | 0.847 | |
keep_replicated_features | 0.913 | 0.052 | 0.867 | |
label2index | 0.000 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.395 | 0.036 | 0.432 | |
log2cpm | 0.433 | 0.068 | 0.501 | |
log2diffs | 0.358 | 0.032 | 0.390 | |
log2proteins | 0.351 | 0.036 | 0.387 | |
log2sites | 0.356 | 0.040 | 0.396 | |
log2tpm | 0.396 | 0.032 | 0.428 | |
log2transform | 3.687 | 0.224 | 3.912 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.589 | 0.036 | 0.603 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.853 | 0.040 | 0.893 | |
map_fvalues | 0.401 | 0.028 | 0.430 | |
matrix2sumexp | 0.965 | 0.048 | 0.990 | |
merge_sample_file | 0.454 | 0.016 | 0.469 | |
merge_sdata | 0.551 | 0.041 | 0.569 | |
message_df | 0.003 | 0.000 | 0.003 | |
modelvar | 1.612 | 0.044 | 1.599 | |
order_on_p | 0.892 | 0.060 | 0.931 | |
pca | 2.857 | 0.104 | 2.940 | |
pg_to_canonical | 0.006 | 0.000 | 0.006 | |
plot_contrast_venn | 1.830 | 0.044 | 1.797 | |
plot_contrastogram | 2.378 | 0.108 | 2.371 | |
plot_data | 1.191 | 0.040 | 1.210 | |
plot_densities | 8.090 | 0.264 | 8.274 | |
plot_design | 0.615 | 0.028 | 0.643 | |
plot_exprs | 19.349 | 0.311 | 19.533 | |
plot_exprs_per_coef | 18.695 | 0.256 | 18.839 | |
plot_fit_summary | 1.773 | 0.028 | 1.744 | |
plot_heatmap | 1.635 | 0.051 | 1.688 | |
plot_matrix | 0.501 | 0.008 | 0.488 | |
plot_sample_nas | 6.828 | 0.127 | 6.908 | |
plot_subgroup_points | 3.999 | 0.029 | 3.988 | |
plot_summary | 10.955 | 0.132 | 11.004 | |
plot_venn | 0.012 | 0.004 | 0.016 | |
plot_venn_heatmap | 0.034 | 0.004 | 0.039 | |
plot_violins | 3.412 | 0.064 | 3.455 | |
plot_volcano | 8.873 | 0.056 | 8.873 | |
preprocess_rnaseq_counts | 0.342 | 0.000 | 0.342 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.067 | 0.004 | 1.254 | |
read_diann_proteingroups | 91.786 | 4.867 | 91.965 | |
read_fragpipe | 6.441 | 0.236 | 6.391 | |
read_maxquant_phosphosites | 1.561 | 0.008 | 1.568 | |
read_maxquant_proteingroups | 1.268 | 0.012 | 1.280 | |
read_metabolon | 11.444 | 0.112 | 11.435 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.262 | 0.072 | 1.284 | |
read_rectangles | 0.181 | 0.004 | 0.185 | |
read_rnaseq_counts | 26.838 | 1.021 | 27.622 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 11.558 | 0.008 | 11.501 | |
read_uniprotdt | 0.266 | 0.015 | 0.282 | |
reset_fit | 4.045 | 0.020 | 3.968 | |
rm_diann_contaminants | 18.729 | 0.316 | 18.987 | |
rm_missing_in_some_samples | 0.520 | 0.008 | 0.506 | |
rm_unmatched_samples | 0.529 | 0.004 | 0.534 | |
scaledlibsizes | 0.358 | 0.004 | 0.362 | |
scoremat | 1.011 | 0.016 | 1.005 | |
slevels | 0.443 | 0.000 | 0.444 | |
snames | 0.410 | 0.004 | 0.414 | |
split_extract_fixed | 0.548 | 0.012 | 0.539 | |
split_samples | 1.192 | 0.004 | 1.175 | |
stri_any_regex | 0.001 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.340 | 0.000 | 0.341 | |
subgroup_matrix | 0.537 | 0.008 | 0.522 | |
subtract_baseline | 4.346 | 0.012 | 4.304 | |
sumexp_to_longdt | 1.843 | 0.052 | 1.840 | |
sumexp_to_tsv | 0.500 | 0.008 | 0.508 | |
sumexplist_to_longdt | 1.610 | 0.008 | 1.619 | |
summarize_fit | 1.555 | 0.016 | 1.483 | |
svalues | 0.423 | 0.000 | 0.423 | |
svars | 0.400 | 0.008 | 0.408 | |
systematic_nas | 0.727 | 0.016 | 0.744 | |
tag_features | 1.123 | 0.032 | 1.156 | |
tag_hdlproteins | 0.540 | 0.008 | 0.548 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.511 | 0.000 | 0.510 | |
uncollapse | 0.006 | 0.003 | 0.010 | |
values | 0.413 | 0.004 | 0.417 | |
varlevels_dont_clash | 0.018 | 0.000 | 0.018 | |
venn_detects | 0.546 | 0.004 | 0.551 | |
weights | 0.374 | 0.000 | 0.374 | |
write_xl | 0.829 | 0.012 | 0.802 | |
zero_to_na | 0.002 | 0.000 | 0.002 | |