Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:05 -0400 (Wed, 24 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" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.12.1.tar.gz |
StartedAt: 2024-07-22 00:51:01 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 01:30:04 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 2343.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: autonomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 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 229.647 3.325 286.553 read_rnaseq_counts 63.150 2.986 81.051 plot_exprs 52.765 0.353 64.638 plot_exprs_per_coef 48.310 0.339 59.574 rm_diann_contaminants 46.430 0.602 61.123 default_formula 36.491 0.868 45.364 analyze 32.171 0.303 40.117 read_somascan 31.568 0.205 41.522 plot_summary 31.124 0.224 38.447 read_metabolon 30.972 0.315 39.181 fit 30.547 0.392 38.752 plot_volcano 24.543 0.214 29.516 plot_densities 20.927 0.454 26.789 plot_sample_nas 15.240 0.115 19.029 read_fragpipe 14.778 0.349 19.287 code 13.232 0.187 16.131 biplot_covariates 13.108 0.188 16.758 extract_coef_features 12.678 0.302 16.031 reset_fit 11.948 0.251 15.497 plot_subgroup_points 11.387 0.132 14.303 fit_lmx 11.050 0.137 14.116 subtract_baseline 11.015 0.159 13.779 biplot 10.004 0.168 12.662 plot_violins 9.651 0.132 12.068 log2transform 9.001 0.099 11.597 dot-plot_survival 8.374 0.725 11.403 explore_transformations 8.538 0.106 10.769 biplot_corrections 8.107 0.138 10.313 impute 7.655 0.086 9.670 pca 7.464 0.129 9.678 plot_contrastogram 5.797 0.233 7.581 plot_contrast_venn 4.770 0.094 6.093 sumexp_to_longdt 4.652 0.188 6.044 plot_fit_summary 4.652 0.094 5.777 plot_heatmap 4.455 0.073 5.501 add_facetvars 4.234 0.174 5.372 modelvar 4.154 0.100 5.388 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’ for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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-apple-darwin20 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 280.393 11.710 450.650
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.002 | |
CONTAMINANTSURL | 0.000 | 0.001 | 0.000 | |
FITSEP | 0.001 | 0.000 | 0.001 | |
LINMOD_ENGINES | 0.000 | 0.001 | 0.001 | |
MAXQUANT_PATTERNS | 0.000 | 0.001 | 0.001 | |
TAXON_TO_ORGNAME | 0.001 | 0.001 | 0.001 | |
TESTS | 0.000 | 0.000 | 0.001 | |
abstract_fit | 3.198 | 0.154 | 4.215 | |
add_adjusted_pvalues | 1.384 | 0.040 | 1.752 | |
add_assay_means | 1.674 | 0.018 | 2.107 | |
add_facetvars | 4.234 | 0.174 | 5.372 | |
add_opentargets_by_uniprot | 1.000 | 0.017 | 1.266 | |
add_psp | 1.250 | 0.032 | 1.595 | |
add_smiles | 1.259 | 0.082 | 1.668 | |
analysis | 0.946 | 0.013 | 1.190 | |
analyze | 32.171 | 0.303 | 40.117 | |
annotate_maxquant | 1.950 | 0.070 | 2.618 | |
annotate_uniprot_rest | 0.142 | 0.021 | 1.667 | |
assert_is_valid_sumexp | 1.444 | 0.073 | 1.832 | |
bin | 0.981 | 0.024 | 1.229 | |
biplot | 10.004 | 0.168 | 12.662 | |
biplot_corrections | 8.107 | 0.138 | 10.313 | |
biplot_covariates | 13.108 | 0.188 | 16.758 | |
block2lme | 0.006 | 0.002 | 0.008 | |
center | 3.569 | 0.048 | 4.409 | |
code | 13.232 | 0.187 | 16.131 | |
coefs | 1.889 | 0.084 | 2.297 | |
collapsed_entrezg_to_symbol | 0.001 | 0.001 | 0.003 | |
contrast_subgroup_cols | 1.559 | 0.083 | 2.021 | |
count_in | 0.002 | 0.002 | 0.005 | |
counts | 1.067 | 0.013 | 1.303 | |
counts2cpm | 1.004 | 0.012 | 1.235 | |
counts2tpm | 0.960 | 0.010 | 1.181 | |
cpm | 1.014 | 0.009 | 1.214 | |
create_design | 1.904 | 0.092 | 2.425 | |
default_formula | 36.491 | 0.868 | 45.364 | |
default_geom | 1.390 | 0.085 | 1.770 | |
default_sfile | 0.003 | 0.001 | 0.005 | |
demultiplex | 0.037 | 0.003 | 0.050 | |
dequantify | 0.004 | 0.001 | 0.007 | |
dot-merge | 0.032 | 0.004 | 0.049 | |
dot-plot_survival | 8.374 | 0.725 | 11.403 | |
dot-read_maxquant_proteingroups | 0.203 | 0.010 | 0.258 | |
download_contaminants | 0.077 | 0.012 | 2.976 | |
download_data | 0.001 | 0.002 | 0.004 | |
download_gtf | 0.000 | 0.000 | 0.001 | |
download_mcclain21 | 0.001 | 0.001 | 0.001 | |
dt2mat | 0.007 | 0.001 | 0.008 | |
enrichment | 3.075 | 0.138 | 3.976 | |
entrezg_to_symbol | 0.001 | 0.001 | 0.002 | |
explore_transformations | 8.538 | 0.106 | 10.769 | |
extract_coef_features | 12.678 | 0.302 | 16.031 | |
extract_rectangle | 0.292 | 0.074 | 0.467 | |
fdata | 1.394 | 0.030 | 1.755 | |
fdr2p | 2.457 | 0.100 | 3.268 | |
filter_exprs_replicated_in_some_subgroup | 2.661 | 0.097 | 3.584 | |
filter_features | 1.419 | 0.078 | 1.861 | |
filter_medoid | 2.045 | 0.051 | 2.663 | |
filter_samples | 1.397 | 0.082 | 1.814 | |
fit | 30.547 | 0.392 | 38.752 | |
fit_lmx | 11.050 | 0.137 | 14.116 | |
fitcoefs | 2.052 | 0.081 | 2.733 | |
fits | 1.917 | 0.080 | 2.506 | |
fitvars | 2.717 | 0.093 | 3.523 | |
fix_xlgenes | 0.003 | 0.000 | 0.003 | |
flevels | 1.039 | 0.013 | 1.319 | |
fnames | 1.124 | 0.013 | 1.419 | |
formula2str | 0.000 | 0.001 | 0.000 | |
fvalues | 1.036 | 0.011 | 1.298 | |
fvars | 1.023 | 0.013 | 1.267 | |
genome_to_orgdb | 0.001 | 0.000 | 0.002 | |
group_by_level | 0.002 | 0.001 | 0.003 | |
guess_fitsep | 1.230 | 0.014 | 1.557 | |
guess_maxquant_quantity | 0.011 | 0.002 | 0.018 | |
guess_sep | 1.374 | 0.076 | 1.839 | |
has_multiple_levels | 0.137 | 0.005 | 0.177 | |
hdlproteins | 0.085 | 0.064 | 0.181 | |
impute | 7.655 | 0.086 | 9.670 | |
invert_subgroups | 1.664 | 0.015 | 2.147 | |
is_collapsed_subset | 0.001 | 0.000 | 0.002 | |
is_diann_report | 0.376 | 0.077 | 0.635 | |
is_fastadt | 0.145 | 0.003 | 0.194 | |
is_file | 0.001 | 0.002 | 0.002 | |
is_fraction | 0.003 | 0.001 | 0.012 | |
is_imputed | 1.826 | 0.018 | 2.277 | |
is_positive_number | 0.004 | 0.002 | 0.008 | |
is_scalar_subset | 0.836 | 0.011 | 1.045 | |
is_sig | 2.997 | 0.026 | 3.891 | |
is_valid_formula | 0.108 | 0.003 | 0.148 | |
keep_connected_blocks | 1.398 | 0.080 | 1.915 | |
keep_connected_features | 1.842 | 0.084 | 2.577 | |
keep_replicated_features | 2.109 | 0.085 | 2.772 | |
label2index | 0.001 | 0.001 | 0.003 | |
list2mat | 0.001 | 0.001 | 0.002 | |
log2counts | 1.017 | 0.008 | 1.288 | |
log2cpm | 0.999 | 0.009 | 1.250 | |
log2diffs | 0.854 | 0.011 | 1.095 | |
log2proteins | 0.830 | 0.011 | 1.057 | |
log2sites | 0.938 | 0.014 | 1.182 | |
log2tpm | 0.992 | 0.008 | 1.195 | |
log2transform | 9.001 | 0.099 | 11.597 | |
logical2factor | 0.003 | 0.001 | 0.004 | |
make_alpha_palette | 1.438 | 0.076 | 1.893 | |
make_colors | 0.016 | 0.003 | 0.022 | |
make_volcano_dt | 2.212 | 0.024 | 2.797 | |
map_fvalues | 0.988 | 0.016 | 1.258 | |
matrix2sumexp | 2.425 | 0.084 | 3.160 | |
merge_sample_file | 1.172 | 0.020 | 1.496 | |
merge_sdata | 1.465 | 0.125 | 1.987 | |
message_df | 0.005 | 0.001 | 0.008 | |
modelvar | 4.154 | 0.100 | 5.388 | |
order_on_p | 2.332 | 0.087 | 3.052 | |
pca | 7.464 | 0.129 | 9.678 | |
pg_to_canonical | 0.015 | 0.001 | 0.019 | |
plot_contrast_venn | 4.770 | 0.094 | 6.093 | |
plot_contrastogram | 5.797 | 0.233 | 7.581 | |
plot_data | 3.210 | 0.098 | 4.174 | |
plot_densities | 20.927 | 0.454 | 26.789 | |
plot_design | 1.566 | 0.020 | 1.975 | |
plot_exprs | 52.765 | 0.353 | 64.638 | |
plot_exprs_per_coef | 48.310 | 0.339 | 59.574 | |
plot_fit_summary | 4.652 | 0.094 | 5.777 | |
plot_heatmap | 4.455 | 0.073 | 5.501 | |
plot_matrix | 1.296 | 0.073 | 1.633 | |
plot_sample_nas | 15.240 | 0.115 | 19.029 | |
plot_subgroup_points | 11.387 | 0.132 | 14.303 | |
plot_summary | 31.124 | 0.224 | 38.447 | |
plot_venn | 0.025 | 0.002 | 0.037 | |
plot_venn_heatmap | 0.075 | 0.007 | 0.098 | |
plot_violins | 9.651 | 0.132 | 12.068 | |
plot_volcano | 24.543 | 0.214 | 29.516 | |
preprocess_rnaseq_counts | 0.989 | 0.009 | 1.181 | |
pull_columns | 0.005 | 0.001 | 0.006 | |
read_affymetrix | 0.000 | 0.001 | 0.001 | |
read_contaminants | 0.039 | 0.005 | 1.062 | |
read_diann_proteingroups | 229.647 | 3.325 | 286.553 | |
read_fragpipe | 14.778 | 0.349 | 19.287 | |
read_maxquant_phosphosites | 3.585 | 0.057 | 4.540 | |
read_maxquant_proteingroups | 3.039 | 0.045 | 3.764 | |
read_metabolon | 30.972 | 0.315 | 39.181 | |
read_msigdt | 0.002 | 0.000 | 0.003 | |
read_olink | 2.893 | 0.100 | 3.897 | |
read_rectangles | 0.419 | 0.040 | 0.588 | |
read_rnaseq_counts | 63.150 | 2.986 | 81.051 | |
read_salmon | 0.000 | 0.000 | 0.001 | |
read_somascan | 31.568 | 0.205 | 41.522 | |
read_uniprotdt | 0.572 | 0.044 | 0.853 | |
reset_fit | 11.948 | 0.251 | 15.497 | |
rm_diann_contaminants | 46.430 | 0.602 | 61.123 | |
rm_missing_in_some_samples | 1.312 | 0.080 | 1.660 | |
rm_unmatched_samples | 1.516 | 0.052 | 1.879 | |
scaledlibsizes | 0.968 | 0.015 | 1.235 | |
scoremat | 2.680 | 0.097 | 3.515 | |
slevels | 0.966 | 0.021 | 1.239 | |
snames | 0.988 | 0.017 | 1.255 | |
split_extract_fixed | 1.301 | 0.078 | 1.754 | |
split_samples | 3.030 | 0.095 | 3.815 | |
stri_any_regex | 0.001 | 0.001 | 0.004 | |
stri_detect_fixed_in_collapsed | 0.866 | 0.011 | 1.061 | |
subgroup_matrix | 1.444 | 0.089 | 1.861 | |
subtract_baseline | 11.015 | 0.159 | 13.779 | |
sumexp_to_longdt | 4.652 | 0.188 | 6.044 | |
sumexp_to_tsv | 1.295 | 0.015 | 1.627 | |
sumexplist_to_longdt | 4.050 | 0.124 | 4.993 | |
summarize_fit | 3.746 | 0.115 | 4.858 | |
svalues | 1.077 | 0.020 | 1.419 | |
svars | 0.992 | 0.015 | 1.302 | |
systematic_nas | 1.377 | 0.024 | 1.831 | |
tag_features | 2.347 | 0.066 | 3.095 | |
tag_hdlproteins | 1.249 | 0.101 | 1.739 | |
taxon2org | 0.001 | 0.001 | 0.002 | |
tpm | 0.989 | 0.008 | 1.281 | |
uncollapse | 0.021 | 0.001 | 0.027 | |
values | 1.021 | 0.014 | 1.298 | |
varlevels_dont_clash | 0.034 | 0.002 | 0.047 | |
venn_detects | 1.485 | 0.024 | 1.875 | |
weights | 0.989 | 0.011 | 1.277 | |
write_xl | 1.814 | 0.104 | 2.939 | |
zero_to_na | 0.004 | 0.005 | 0.013 | |