Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:49 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | 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: 1.12.0 |
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: 2024-05-31 01:18:23 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 01:34:21 -0400 (Fri, 31 May 2024) |
EllapsedTime: 957.7 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 (2024-04-24) * 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 88.090 3.148 86.822 read_rnaseq_counts 26.831 1.804 28.386 rm_diann_contaminants 20.062 0.872 20.847 plot_exprs 19.667 0.416 19.961 plot_exprs_per_coef 17.139 0.204 17.231 default_formula 13.974 0.548 14.062 read_somascan 12.010 0.352 12.310 fit 11.957 0.307 11.334 analyze 11.560 0.092 11.526 plot_summary 11.006 0.176 11.055 read_metabolon 11.015 0.056 10.987 plot_volcano 9.123 0.139 9.182 plot_densities 7.852 0.068 7.836 plot_sample_nas 5.552 0.004 5.492 read_fragpipe 5.211 0.044 4.954 * 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 (2024-04-24) -- "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 124.972 4.120 126.585
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0 | 0 | 0 | |
CONTAMINANTSURL | 0.001 | 0.000 | 0.000 | |
FITSEP | 0 | 0 | 0 | |
LINMOD_ENGINES | 0.000 | 0.000 | 0.001 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
abstract_fit | 1.225 | 0.032 | 1.235 | |
add_adjusted_pvalues | 0.535 | 0.056 | 0.591 | |
add_assay_means | 0.427 | 0.016 | 0.443 | |
add_facetvars | 2.048 | 0.083 | 2.111 | |
add_opentargets_by_uniprot | 0.381 | 0.008 | 0.391 | |
add_psp | 0.482 | 0.012 | 0.494 | |
add_smiles | 0.438 | 0.020 | 0.436 | |
analysis | 0.378 | 0.004 | 0.383 | |
analyze | 11.560 | 0.092 | 11.526 | |
annotate_maxquant | 0.824 | 0.040 | 0.864 | |
annotate_uniprot_rest | 0.338 | 0.008 | 2.578 | |
assert_is_valid_sumexp | 0.625 | 0.220 | 0.820 | |
bin | 0.406 | 0.024 | 0.430 | |
biplot | 3.547 | 0.356 | 3.881 | |
biplot_corrections | 2.932 | 0.104 | 3.015 | |
biplot_covariates | 4.847 | 0.083 | 4.895 | |
block2lme | 0.004 | 0.000 | 0.003 | |
center | 2.078 | 0.164 | 2.242 | |
code | 4.596 | 0.016 | 4.591 | |
coefs | 0.696 | 0.008 | 0.669 | |
collapsed_entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.558 | 0.008 | 0.547 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.383 | 0.008 | 0.391 | |
counts2cpm | 0.354 | 0.004 | 0.359 | |
counts2tpm | 0.341 | 0.004 | 0.344 | |
cpm | 0.356 | 0.016 | 0.373 | |
create_design | 0.696 | 0.012 | 0.671 | |
default_formula | 13.974 | 0.548 | 14.062 | |
default_geom | 0.505 | 0.012 | 0.496 | |
default_sfile | 0.001 | 0.001 | 0.002 | |
demultiplex | 0.011 | 0.003 | 0.013 | |
dequantify | 0.003 | 0.000 | 0.002 | |
dot-merge | 0.018 | 0.000 | 0.017 | |
dot-plot_survival | 4.101 | 0.259 | 4.361 | |
dot-read_maxquant_proteingroups | 0.120 | 0.004 | 0.124 | |
download_contaminants | 0.158 | 0.012 | 2.642 | |
download_data | 0.002 | 0.001 | 0.002 | |
download_gtf | 0.001 | 0.000 | 0.001 | |
download_mcclain21 | 0.001 | 0.000 | 0.001 | |
dt2mat | 0.010 | 0.000 | 0.009 | |
enrichment | 1.235 | 0.156 | 1.391 | |
entrezg_to_symbol | 0.000 | 0.000 | 0.001 | |
explore_transformations | 3.448 | 0.400 | 3.849 | |
extract_coef_features | 4.471 | 0.100 | 4.549 | |
extract_rectangle | 0.098 | 0.016 | 0.113 | |
fdata | 0.515 | 0.012 | 0.526 | |
fdr2p | 0.876 | 0.008 | 0.858 | |
filter_exprs_replicated_in_some_subgroup | 0.981 | 0.012 | 0.912 | |
filter_features | 0.493 | 0.011 | 0.485 | |
filter_medoid | 0.723 | 0.008 | 0.730 | |
filter_samples | 0.507 | 0.004 | 0.491 | |
fit | 11.957 | 0.307 | 11.334 | |
fit_lmx | 4.159 | 0.048 | 4.001 | |
fitcoefs | 0.760 | 0.068 | 0.806 | |
fits | 0.720 | 0.052 | 0.750 | |
fitvars | 1.034 | 0.020 | 1.034 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.407 | 0.008 | 0.415 | |
fnames | 0.451 | 0.000 | 0.452 | |
formula2str | 0.000 | 0.000 | 0.001 | |
fvalues | 0.412 | 0.008 | 0.421 | |
fvars | 0.415 | 0.004 | 0.419 | |
genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.45 | 0.00 | 0.45 | |
guess_maxquant_quantity | 0.002 | 0.004 | 0.006 | |
guess_sep | 0.497 | 0.012 | 0.487 | |
has_multiple_levels | 0.045 | 0.004 | 0.049 | |
hdlproteins | 0.046 | 0.024 | 0.072 | |
impute | 2.907 | 0.016 | 2.924 | |
invert_subgroups | 0.593 | 0.004 | 0.598 | |
is_collapsed_subset | 0.001 | 0.000 | 0.001 | |
is_diann_report | 0.514 | 0.061 | 0.514 | |
is_fastadt | 0.054 | 0.004 | 0.059 | |
is_file | 0.000 | 0.000 | 0.001 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.693 | 0.008 | 0.701 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.312 | 0.004 | 0.315 | |
is_sig | 1.111 | 0.016 | 1.126 | |
is_valid_formula | 0.033 | 0.008 | 0.041 | |
keep_connected_blocks | 0.530 | 0.072 | 0.576 | |
keep_connected_features | 0.718 | 0.028 | 0.708 | |
keep_replicated_features | 0.868 | 0.056 | 0.858 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.000 | 0.000 | 0.001 | |
log2counts | 0.382 | 0.012 | 0.394 | |
log2cpm | 0.373 | 0.008 | 0.381 | |
log2diffs | 0.311 | 0.024 | 0.335 | |
log2proteins | 0.314 | 0.012 | 0.326 | |
log2sites | 0.414 | 0.020 | 0.434 | |
log2tpm | 0.359 | 0.000 | 0.359 | |
log2transform | 3.504 | 0.008 | 3.512 | |
logical2factor | 0.001 | 0.000 | 0.002 | |
make_alpha_palette | 0.537 | 0.004 | 0.518 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.827 | 0.004 | 0.832 | |
map_fvalues | 0.387 | 0.004 | 0.391 | |
matrix2sumexp | 0.887 | 0.012 | 0.879 | |
merge_sample_file | 0.456 | 0.004 | 0.461 | |
merge_sdata | 0.519 | 0.039 | 0.539 | |
message_df | 0.000 | 0.002 | 0.002 | |
modelvar | 1.559 | 0.020 | 1.526 | |
order_on_p | 0.849 | 0.020 | 0.849 | |
pca | 2.763 | 0.172 | 2.900 | |
pg_to_canonical | 0.005 | 0.000 | 0.006 | |
plot_contrast_venn | 1.848 | 0.028 | 1.732 | |
plot_contrastogram | 2.197 | 0.020 | 2.133 | |
plot_data | 1.207 | 0.004 | 1.189 | |
plot_densities | 7.852 | 0.068 | 7.836 | |
plot_design | 0.677 | 0.052 | 0.728 | |
plot_exprs | 19.667 | 0.416 | 19.961 | |
plot_exprs_per_coef | 17.139 | 0.204 | 17.231 | |
plot_fit_summary | 1.729 | 0.016 | 1.659 | |
plot_heatmap | 1.643 | 0.016 | 1.659 | |
plot_matrix | 0.480 | 0.020 | 0.479 | |
plot_sample_nas | 5.552 | 0.004 | 5.492 | |
plot_subgroup_points | 4.066 | 0.016 | 4.038 | |
plot_summary | 11.006 | 0.176 | 11.055 | |
plot_venn | 0.016 | 0.000 | 0.015 | |
plot_venn_heatmap | 0.036 | 0.000 | 0.036 | |
plot_violins | 3.456 | 0.024 | 3.456 | |
plot_volcano | 9.123 | 0.139 | 9.182 | |
preprocess_rnaseq_counts | 0.335 | 0.008 | 0.343 | |
pull_columns | 0.003 | 0.001 | 0.003 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.123 | 0.015 | 1.292 | |
read_diann_proteingroups | 88.090 | 3.148 | 86.822 | |
read_fragpipe | 5.211 | 0.044 | 4.954 | |
read_maxquant_phosphosites | 1.386 | 0.016 | 1.402 | |
read_maxquant_proteingroups | 1.193 | 0.000 | 1.193 | |
read_metabolon | 11.015 | 0.056 | 10.987 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.221 | 0.024 | 1.207 | |
read_rectangles | 0.165 | 0.008 | 0.173 | |
read_rnaseq_counts | 26.831 | 1.804 | 28.386 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 12.010 | 0.352 | 12.310 | |
read_uniprotdt | 0.282 | 0.008 | 0.290 | |
reset_fit | 4.130 | 0.063 | 4.060 | |
rm_diann_contaminants | 20.062 | 0.872 | 20.847 | |
rm_missing_in_some_samples | 0.525 | 0.024 | 0.519 | |
rm_unmatched_samples | 0.581 | 0.016 | 0.597 | |
scaledlibsizes | 0.347 | 0.004 | 0.351 | |
scoremat | 0.951 | 0.024 | 0.954 | |
slevels | 0.443 | 0.044 | 0.488 | |
snames | 0.410 | 0.012 | 0.421 | |
split_extract_fixed | 0.490 | 0.032 | 0.501 | |
split_samples | 1.383 | 0.096 | 1.442 | |
stri_any_regex | 0.001 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.338 | 0.020 | 0.358 | |
subgroup_matrix | 0.546 | 0.024 | 0.548 | |
subtract_baseline | 4.090 | 0.104 | 4.111 | |
sumexp_to_longdt | 1.798 | 0.044 | 1.732 | |
sumexp_to_tsv | 0.489 | 0.000 | 0.488 | |
sumexplist_to_longdt | 1.545 | 0.008 | 1.552 | |
summarize_fit | 1.449 | 0.037 | 1.427 | |
svalues | 0.396 | 0.015 | 0.412 | |
svars | 0.463 | 0.001 | 0.463 | |
systematic_nas | 0.523 | 0.000 | 0.522 | |
tag_features | 0.861 | 0.040 | 0.900 | |
tag_hdlproteins | 0.525 | 0.016 | 0.541 | |
taxon2org | 0.001 | 0.000 | 0.002 | |
tpm | 0.42 | 0.02 | 0.44 | |
uncollapse | 0.010 | 0.000 | 0.011 | |
values | 0.414 | 0.012 | 0.427 | |
varlevels_dont_clash | 0.018 | 0.000 | 0.018 | |
venn_detects | 0.539 | 0.039 | 0.579 | |
weights | 0.442 | 0.033 | 0.474 | |
write_xl | 0.655 | 0.027 | 0.662 | |
zero_to_na | 0.002 | 0.000 | 0.002 | |