Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-11 20:38 -0400 (Fri, 11 Oct 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" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 1.12.1 (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 12.7.5 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: 2024-10-09 20:43:04 -0400 (Wed, 09 Oct 2024) |
EndedAt: 2024-10-09 20:58:14 -0400 (Wed, 09 Oct 2024) |
EllapsedTime: 910.6 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 22.04.5 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 89.475 1.173 85.801 read_rnaseq_counts 27.275 0.971 27.923 plot_exprs 19.415 0.060 19.375 rm_diann_contaminants 18.819 0.331 19.085 plot_exprs_per_coef 18.333 0.112 18.337 default_formula 15.416 0.384 15.478 fit 12.235 0.091 11.443 analyze 11.701 0.144 11.697 read_somascan 11.526 0.020 11.452 read_metabolon 11.447 0.084 11.444 plot_summary 11.308 0.028 11.223 plot_volcano 9.983 0.132 10.059 plot_densities 7.808 0.048 7.738 plot_sample_nas 5.968 0.052 5.947 read_fragpipe 5.331 0.048 5.123 * 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 130.163 4.230 131.353
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.001 | 0.000 | 0.000 | |
CONTAMINANTSURL | 0.001 | 0.000 | 0.000 | |
FITSEP | 0.001 | 0.000 | 0.000 | |
LINMOD_ENGINES | 0.000 | 0.000 | 0.001 | |
MAXQUANT_PATTERNS | 0.000 | 0.000 | 0.001 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
abstract_fit | 1.216 | 0.036 | 1.227 | |
add_adjusted_pvalues | 0.532 | 0.019 | 0.552 | |
add_assay_means | 0.431 | 0.008 | 0.439 | |
add_facetvars | 2.059 | 0.100 | 2.138 | |
add_opentargets_by_uniprot | 0.370 | 0.020 | 0.391 | |
add_psp | 0.483 | 0.016 | 0.500 | |
add_smiles | 0.449 | 0.012 | 0.441 | |
analysis | 0.378 | 0.004 | 0.382 | |
analyze | 11.701 | 0.144 | 11.697 | |
annotate_maxquant | 0.890 | 0.012 | 0.903 | |
annotate_uniprot_rest | 0.423 | 0.012 | 2.664 | |
assert_is_valid_sumexp | 0.636 | 0.004 | 0.621 | |
bin | 0.387 | 0.016 | 0.403 | |
biplot | 3.475 | 0.052 | 3.494 | |
biplot_corrections | 2.857 | 0.028 | 2.847 | |
biplot_covariates | 4.738 | 0.024 | 4.742 | |
block2lme | 0.000 | 0.003 | 0.003 | |
center | 2.046 | 0.080 | 2.125 | |
code | 4.528 | 0.084 | 4.576 | |
coefs | 0.687 | 0.012 | 0.679 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.593 | 0.012 | 0.585 | |
count_in | 0.001 | 0.000 | 0.002 | |
counts | 0.405 | 0.004 | 0.410 | |
counts2cpm | 0.387 | 0.000 | 0.388 | |
counts2tpm | 0.325 | 0.004 | 0.329 | |
cpm | 0.356 | 0.000 | 0.356 | |
create_design | 0.704 | 0.020 | 0.704 | |
default_formula | 15.416 | 0.384 | 15.478 | |
default_geom | 0.528 | 0.008 | 0.514 | |
default_sfile | 0.002 | 0.000 | 0.002 | |
demultiplex | 0.010 | 0.004 | 0.014 | |
dequantify | 0.000 | 0.002 | 0.002 | |
dot-merge | 0.018 | 0.001 | 0.019 | |
dot-plot_survival | 4.376 | 0.164 | 4.541 | |
dot-read_maxquant_proteingroups | 0.113 | 0.003 | 0.116 | |
download_contaminants | 0.204 | 0.000 | 2.552 | |
download_data | 0.002 | 0.000 | 0.002 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.001 | 0.000 | 0.001 | |
dt2mat | 0.006 | 0.000 | 0.006 | |
enrichment | 1.106 | 0.000 | 1.107 | |
entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
explore_transformations | 3.169 | 0.124 | 3.293 | |
extract_coef_features | 4.336 | 0.012 | 4.327 | |
extract_rectangle | 0.094 | 0.021 | 0.116 | |
fdata | 0.557 | 0.011 | 0.567 | |
fdr2p | 0.912 | 0.040 | 0.914 | |
filter_exprs_replicated_in_some_subgroup | 1.081 | 0.008 | 0.964 | |
filter_features | 0.563 | 0.004 | 0.528 | |
filter_medoid | 0.761 | 0.012 | 0.773 | |
filter_samples | 0.575 | 0.004 | 0.544 | |
fit | 12.235 | 0.091 | 11.443 | |
fit_lmx | 4.188 | 0.020 | 4.026 | |
fitcoefs | 0.752 | 0.011 | 0.742 | |
fits | 0.731 | 0.017 | 0.711 | |
fitvars | 0.998 | 0.015 | 0.992 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.413 | 0.000 | 0.414 | |
fnames | 0.466 | 0.000 | 0.466 | |
formula2str | 0 | 0 | 0 | |
fvalues | 0.415 | 0.000 | 0.415 | |
fvars | 0.409 | 0.004 | 0.412 | |
genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
group_by_level | 0.002 | 0.000 | 0.002 | |
guess_fitsep | 0.493 | 0.008 | 0.501 | |
guess_maxquant_quantity | 0.006 | 0.000 | 0.006 | |
guess_sep | 0.538 | 0.011 | 0.529 | |
has_multiple_levels | 0.053 | 0.000 | 0.054 | |
hdlproteins | 0.040 | 0.036 | 0.078 | |
impute | 2.947 | 0.032 | 2.979 | |
invert_subgroups | 0.815 | 0.036 | 0.851 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_diann_report | 0.339 | 0.056 | 0.370 | |
is_fastadt | 0.056 | 0.012 | 0.068 | |
is_file | 0.000 | 0.000 | 0.001 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.680 | 0.008 | 0.687 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.319 | 0.001 | 0.320 | |
is_sig | 1.125 | 0.006 | 1.132 | |
is_valid_formula | 0.039 | 0.000 | 0.040 | |
keep_connected_blocks | 0.503 | 0.016 | 0.480 | |
keep_connected_features | 0.734 | 0.012 | 0.675 | |
keep_replicated_features | 0.805 | 0.024 | 0.759 | |
label2index | 0.000 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.375 | 0.000 | 0.374 | |
log2cpm | 0.365 | 0.004 | 0.368 | |
log2diffs | 0.310 | 0.004 | 0.315 | |
log2proteins | 0.307 | 0.004 | 0.311 | |
log2sites | 0.330 | 0.000 | 0.329 | |
log2tpm | 0.382 | 0.008 | 0.389 | |
log2transform | 3.453 | 0.072 | 3.525 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.571 | 0.016 | 0.565 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.845 | 0.008 | 0.853 | |
map_fvalues | 0.412 | 0.000 | 0.412 | |
matrix2sumexp | 0.949 | 0.024 | 0.943 | |
merge_sample_file | 0.443 | 0.012 | 0.455 | |
merge_sdata | 0.537 | 0.024 | 0.540 | |
message_df | 0.003 | 0.000 | 0.003 | |
modelvar | 1.594 | 0.068 | 1.605 | |
order_on_p | 0.888 | 0.040 | 0.890 | |
pca | 2.793 | 0.020 | 2.775 | |
pg_to_canonical | 0.006 | 0.000 | 0.005 | |
plot_contrast_venn | 1.819 | 0.012 | 1.689 | |
plot_contrastogram | 2.135 | 0.048 | 2.103 | |
plot_data | 1.158 | 0.008 | 1.132 | |
plot_densities | 7.808 | 0.048 | 7.738 | |
plot_design | 0.705 | 0.004 | 0.709 | |
plot_exprs | 19.415 | 0.060 | 19.375 | |
plot_exprs_per_coef | 18.333 | 0.112 | 18.337 | |
plot_fit_summary | 1.868 | 0.020 | 1.780 | |
plot_heatmap | 1.730 | 0.000 | 1.731 | |
plot_matrix | 0.516 | 0.008 | 0.502 | |
plot_sample_nas | 5.968 | 0.052 | 5.947 | |
plot_subgroup_points | 4.136 | 0.020 | 4.104 | |
plot_summary | 11.308 | 0.028 | 11.223 | |
plot_venn | 0.016 | 0.000 | 0.016 | |
plot_venn_heatmap | 0.039 | 0.000 | 0.039 | |
plot_violins | 3.508 | 0.060 | 3.547 | |
plot_volcano | 9.983 | 0.132 | 10.059 | |
preprocess_rnaseq_counts | 0.330 | 0.000 | 0.329 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.119 | 0.008 | 1.292 | |
read_diann_proteingroups | 89.475 | 1.173 | 85.801 | |
read_fragpipe | 5.331 | 0.048 | 5.123 | |
read_maxquant_phosphosites | 1.506 | 0.012 | 1.519 | |
read_maxquant_proteingroups | 1.204 | 0.012 | 1.216 | |
read_metabolon | 11.447 | 0.084 | 11.444 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.296 | 0.044 | 1.239 | |
read_rectangles | 0.174 | 0.008 | 0.182 | |
read_rnaseq_counts | 27.275 | 0.971 | 27.923 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 11.526 | 0.020 | 11.452 | |
read_uniprotdt | 0.285 | 0.008 | 0.293 | |
reset_fit | 4.126 | 0.036 | 3.999 | |
rm_diann_contaminants | 18.819 | 0.331 | 19.085 | |
rm_missing_in_some_samples | 0.538 | 0.016 | 0.533 | |
rm_unmatched_samples | 0.505 | 0.004 | 0.509 | |
scaledlibsizes | 0.343 | 0.004 | 0.347 | |
scoremat | 0.972 | 0.037 | 0.987 | |
slevels | 0.392 | 0.000 | 0.391 | |
snames | 0.399 | 0.004 | 0.404 | |
split_extract_fixed | 0.510 | 0.024 | 0.497 | |
split_samples | 1.147 | 0.020 | 1.130 | |
stri_any_regex | 0.000 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.335 | 0.008 | 0.342 | |
subgroup_matrix | 0.558 | 0.016 | 0.550 | |
subtract_baseline | 4.096 | 0.020 | 4.025 | |
sumexp_to_longdt | 1.957 | 0.068 | 1.917 | |
sumexp_to_tsv | 0.467 | 0.004 | 0.470 | |
sumexplist_to_longdt | 1.534 | 0.004 | 1.538 | |
summarize_fit | 1.512 | 0.020 | 1.439 | |
svalues | 0.398 | 0.004 | 0.402 | |
svars | 0.387 | 0.004 | 0.390 | |
systematic_nas | 0.519 | 0.008 | 0.527 | |
tag_features | 0.892 | 0.048 | 0.940 | |
tag_hdlproteins | 0.534 | 0.012 | 0.545 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.391 | 0.000 | 0.390 | |
uncollapse | 0.011 | 0.000 | 0.011 | |
values | 0.498 | 0.004 | 0.501 | |
varlevels_dont_clash | 0.020 | 0.000 | 0.019 | |
venn_detects | 0.524 | 0.000 | 0.524 | |
weights | 0.355 | 0.007 | 0.361 | |
write_xl | 0.727 | 0.008 | 0.715 | |
zero_to_na | 0.002 | 0.000 | 0.002 | |