Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:38 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 1.12.1 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | 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: 1.12.1 |
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_1.12.1.tar.gz |
StartedAt: 2024-07-07 20:41:08 -0400 (Sun, 07 Jul 2024) |
EndedAt: 2024-07-07 20:55:41 -0400 (Sun, 07 Jul 2024) |
EllapsedTime: 872.9 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_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-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 ‘1.12.1’ * 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 87.334 1.264 84.229 read_rnaseq_counts 26.172 1.051 26.995 plot_exprs 19.101 0.064 19.075 rm_diann_contaminants 18.442 0.275 18.727 plot_exprs_per_coef 16.967 0.096 16.977 default_formula 13.886 0.253 13.744 fit 11.889 0.056 11.265 analyze 11.355 0.153 11.389 read_metabolon 11.097 0.084 11.066 read_somascan 11.143 0.015 11.108 plot_summary 10.787 0.040 10.723 plot_volcano 8.909 0.056 8.861 plot_densities 8.667 0.123 8.697 plot_sample_nas 5.547 0.056 5.548 read_fragpipe 5.123 0.004 4.830 * 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 4.4.1 (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 124.688 3.837 126.052
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0 | 0 | 0 | |
CONTAMINANTSURL | 0.000 | 0.000 | 0.001 | |
FITSEP | 0.001 | 0.000 | 0.001 | |
LINMOD_ENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0.000 | 0.000 | 0.001 | |
abstract_fit | 1.206 | 0.027 | 1.212 | |
add_adjusted_pvalues | 0.542 | 0.020 | 0.563 | |
add_assay_means | 0.433 | 0.016 | 0.448 | |
add_facetvars | 2.059 | 0.096 | 2.136 | |
add_opentargets_by_uniprot | 0.401 | 0.012 | 0.420 | |
add_psp | 0.498 | 0.016 | 0.514 | |
add_smiles | 0.455 | 0.012 | 0.446 | |
analysis | 0.369 | 0.008 | 0.377 | |
analyze | 11.355 | 0.153 | 11.389 | |
annotate_maxquant | 0.802 | 0.040 | 0.843 | |
annotate_uniprot_rest | 0.310 | 0.008 | 2.296 | |
assert_is_valid_sumexp | 0.562 | 0.012 | 0.553 | |
bin | 0.371 | 0.000 | 0.372 | |
biplot | 3.436 | 0.048 | 3.448 | |
biplot_corrections | 2.919 | 0.016 | 2.914 | |
biplot_covariates | 4.786 | 0.028 | 4.794 | |
block2lme | 0.000 | 0.003 | 0.003 | |
center | 2.119 | 0.112 | 2.231 | |
code | 4.503 | 0.054 | 4.521 | |
coefs | 0.677 | 0.036 | 0.684 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.551 | 0.016 | 0.541 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.372 | 0.004 | 0.377 | |
counts2cpm | 0.385 | 0.000 | 0.384 | |
counts2tpm | 0.33 | 0.00 | 0.33 | |
cpm | 0.353 | 0.000 | 0.353 | |
create_design | 0.670 | 0.016 | 0.667 | |
default_formula | 13.886 | 0.253 | 13.744 | |
default_geom | 0.496 | 0.012 | 0.482 | |
default_sfile | 0.001 | 0.000 | 0.002 | |
demultiplex | 0.013 | 0.000 | 0.013 | |
dequantify | 0.002 | 0.000 | 0.002 | |
dot-merge | 0.015 | 0.000 | 0.015 | |
dot-plot_survival | 3.958 | 0.156 | 4.115 | |
dot-read_maxquant_proteingroups | 0.124 | 0.004 | 0.128 | |
download_contaminants | 0.146 | 0.008 | 2.956 | |
download_data | 0.001 | 0.000 | 0.001 | |
download_gtf | 0.000 | 0.000 | 0.001 | |
download_mcclain21 | 0.000 | 0.001 | 0.000 | |
dt2mat | 0.003 | 0.005 | 0.007 | |
enrichment | 1.105 | 0.088 | 1.194 | |
entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
explore_transformations | 3.203 | 0.116 | 3.320 | |
extract_coef_features | 4.470 | 0.100 | 4.543 | |
extract_rectangle | 0.104 | 0.012 | 0.116 | |
fdata | 0.527 | 0.016 | 0.542 | |
fdr2p | 0.858 | 0.020 | 0.858 | |
filter_exprs_replicated_in_some_subgroup | 0.978 | 0.012 | 0.937 | |
filter_features | 0.525 | 0.032 | 0.519 | |
filter_medoid | 0.728 | 0.020 | 0.749 | |
filter_samples | 0.560 | 0.003 | 0.525 | |
fit | 11.889 | 0.056 | 11.265 | |
fit_lmx | 4.317 | 0.021 | 4.173 | |
fitcoefs | 0.786 | 0.003 | 0.769 | |
fits | 0.740 | 0.012 | 0.729 | |
fitvars | 0.986 | 0.004 | 0.962 | |
fix_xlgenes | 0.001 | 0.000 | 0.002 | |
flevels | 0.420 | 0.004 | 0.424 | |
fnames | 0.446 | 0.008 | 0.453 | |
formula2str | 0 | 0 | 0 | |
fvalues | 0.421 | 0.020 | 0.440 | |
fvars | 0.414 | 0.012 | 0.426 | |
genome_to_orgdb | 0.000 | 0.000 | 0.001 | |
group_by_level | 0.000 | 0.001 | 0.002 | |
guess_fitsep | 0.49 | 0.01 | 0.50 | |
guess_maxquant_quantity | 0.002 | 0.004 | 0.006 | |
guess_sep | 0.499 | 0.008 | 0.486 | |
has_multiple_levels | 0.049 | 0.004 | 0.053 | |
hdlproteins | 0.041 | 0.032 | 0.075 | |
impute | 2.903 | 0.004 | 2.907 | |
invert_subgroups | 0.666 | 0.004 | 0.670 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_diann_report | 0.496 | 0.040 | 0.491 | |
is_fastadt | 0.073 | 0.000 | 0.073 | |
is_file | 0.000 | 0.000 | 0.001 | |
is_fraction | 0.002 | 0.000 | 0.001 | |
is_imputed | 0.701 | 0.000 | 0.701 | |
is_positive_number | 0.001 | 0.000 | 0.002 | |
is_scalar_subset | 0.33 | 0.00 | 0.33 | |
is_sig | 1.122 | 0.024 | 1.146 | |
is_valid_formula | 0.039 | 0.000 | 0.039 | |
keep_connected_blocks | 0.489 | 0.012 | 0.475 | |
keep_connected_features | 0.702 | 0.048 | 0.710 | |
keep_replicated_features | 0.766 | 0.021 | 0.721 | |
label2index | 0.000 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.363 | 0.000 | 0.363 | |
log2cpm | 0.38 | 0.00 | 0.38 | |
log2diffs | 0.319 | 0.007 | 0.327 | |
log2proteins | 0.337 | 0.000 | 0.337 | |
log2sites | 0.337 | 0.000 | 0.338 | |
log2tpm | 0.370 | 0.000 | 0.369 | |
log2transform | 3.500 | 0.032 | 3.532 | |
logical2factor | 0.002 | 0.000 | 0.001 | |
make_alpha_palette | 0.551 | 0.032 | 0.562 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.814 | 0.023 | 0.838 | |
map_fvalues | 0.388 | 0.004 | 0.393 | |
matrix2sumexp | 0.923 | 0.016 | 0.919 | |
merge_sample_file | 0.442 | 0.012 | 0.453 | |
merge_sdata | 0.545 | 0.016 | 0.540 | |
message_df | 0.000 | 0.002 | 0.002 | |
modelvar | 1.542 | 0.017 | 1.503 | |
order_on_p | 0.896 | 0.008 | 0.882 | |
pca | 2.729 | 0.064 | 2.772 | |
pg_to_canonical | 0.006 | 0.000 | 0.006 | |
plot_contrast_venn | 1.751 | 0.005 | 1.683 | |
plot_contrastogram | 2.096 | 0.008 | 2.029 | |
plot_data | 1.156 | 0.012 | 1.148 | |
plot_densities | 8.667 | 0.123 | 8.697 | |
plot_design | 0.59 | 0.00 | 0.59 | |
plot_exprs | 19.101 | 0.064 | 19.075 | |
plot_exprs_per_coef | 16.967 | 0.096 | 16.977 | |
plot_fit_summary | 1.659 | 0.004 | 1.607 | |
plot_heatmap | 1.514 | 0.008 | 1.522 | |
plot_matrix | 0.491 | 0.008 | 0.463 | |
plot_sample_nas | 5.547 | 0.056 | 5.548 | |
plot_subgroup_points | 4.078 | 0.028 | 4.052 | |
plot_summary | 10.787 | 0.040 | 10.723 | |
plot_venn | 0.016 | 0.000 | 0.017 | |
plot_venn_heatmap | 0.036 | 0.000 | 0.036 | |
plot_violins | 3.473 | 0.016 | 3.451 | |
plot_volcano | 8.909 | 0.056 | 8.861 | |
preprocess_rnaseq_counts | 0.354 | 0.000 | 0.353 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.116 | 0.004 | 1.266 | |
read_diann_proteingroups | 87.334 | 1.264 | 84.229 | |
read_fragpipe | 5.123 | 0.004 | 4.830 | |
read_maxquant_phosphosites | 1.465 | 0.004 | 1.468 | |
read_maxquant_proteingroups | 1.191 | 0.016 | 1.207 | |
read_metabolon | 11.097 | 0.084 | 11.066 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.206 | 0.024 | 1.185 | |
read_rectangles | 0.158 | 0.012 | 0.170 | |
read_rnaseq_counts | 26.172 | 1.051 | 26.995 | |
read_salmon | 0.001 | 0.000 | 0.001 | |
read_somascan | 11.143 | 0.015 | 11.108 | |
read_uniprotdt | 0.269 | 0.008 | 0.276 | |
reset_fit | 3.872 | 0.024 | 3.805 | |
rm_diann_contaminants | 18.442 | 0.275 | 18.727 | |
rm_missing_in_some_samples | 0.497 | 0.013 | 0.489 | |
rm_unmatched_samples | 0.517 | 0.000 | 0.517 | |
scaledlibsizes | 0.403 | 0.004 | 0.407 | |
scoremat | 0.895 | 0.012 | 0.886 | |
slevels | 0.391 | 0.000 | 0.391 | |
snames | 0.439 | 0.000 | 0.439 | |
split_extract_fixed | 0.472 | 0.012 | 0.464 | |
split_samples | 1.140 | 0.036 | 1.151 | |
stri_any_regex | 0.001 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.330 | 0.016 | 0.346 | |
subgroup_matrix | 0.506 | 0.020 | 0.489 | |
subtract_baseline | 4.082 | 0.024 | 4.016 | |
sumexp_to_longdt | 1.798 | 0.052 | 1.775 | |
sumexp_to_tsv | 0.463 | 0.004 | 0.467 | |
sumexplist_to_longdt | 1.546 | 0.024 | 1.570 | |
summarize_fit | 1.448 | 0.012 | 1.399 | |
svalues | 0.387 | 0.003 | 0.391 | |
svars | 0.392 | 0.005 | 0.396 | |
systematic_nas | 0.503 | 0.000 | 0.504 | |
tag_features | 0.850 | 0.052 | 0.901 | |
tag_hdlproteins | 0.496 | 0.012 | 0.508 | |
taxon2org | 0.000 | 0.001 | 0.001 | |
tpm | 0.361 | 0.005 | 0.367 | |
uncollapse | 0.011 | 0.001 | 0.010 | |
values | 0.467 | 0.003 | 0.471 | |
varlevels_dont_clash | 0.017 | 0.001 | 0.017 | |
venn_detects | 0.512 | 0.000 | 0.512 | |
weights | 0.367 | 0.000 | 0.367 | |
write_xl | 0.695 | 0.024 | 0.699 | |
zero_to_na | 0.002 | 0.000 | 0.002 | |