Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 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" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
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 | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | 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: 1.12.1 |
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: 2024-06-12 20:39:21 -0400 (Wed, 12 Jun 2024) |
EndedAt: 2024-06-12 20:54:11 -0400 (Wed, 12 Jun 2024) |
EllapsedTime: 890.8 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 4.4.0 (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 ‘1.12.1’ * 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 88.182 1.344 85.005 read_rnaseq_counts 28.334 2.598 30.667 rm_diann_contaminants 19.214 0.548 19.605 plot_exprs 18.696 0.232 18.801 plot_exprs_per_coef 17.579 0.160 17.584 default_formula 14.090 0.544 14.248 fit 12.333 0.400 11.941 read_somascan 12.034 0.316 12.273 analyze 12.033 0.096 12.049 read_metabolon 11.642 0.024 11.557 plot_summary 11.039 0.080 11.035 plot_volcano 8.998 0.048 8.993 plot_densities 8.860 0.184 8.978 plot_sample_nas 5.661 0.036 5.648 read_fragpipe 5.349 0.060 5.135 biplot_covariates 4.867 0.156 5.002 * 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 125.097 3.829 126.052
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.001 | 0.000 | 0.001 | |
CONTAMINANTSURL | 0 | 0 | 0 | |
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 | 1.234 | 0.016 | 1.227 | |
add_adjusted_pvalues | 0.538 | 0.020 | 0.559 | |
add_assay_means | 0.432 | 0.011 | 0.444 | |
add_facetvars | 2.140 | 0.064 | 2.182 | |
add_opentargets_by_uniprot | 0.395 | 0.003 | 0.401 | |
add_psp | 0.501 | 0.013 | 0.514 | |
add_smiles | 0.462 | 0.020 | 0.462 | |
analysis | 0.375 | 0.008 | 0.383 | |
analyze | 12.033 | 0.096 | 12.049 | |
annotate_maxquant | 0.870 | 0.028 | 0.898 | |
annotate_uniprot_rest | 0.381 | 0.027 | 2.732 | |
assert_is_valid_sumexp | 0.648 | 0.048 | 0.671 | |
bin | 0.381 | 0.024 | 0.405 | |
biplot | 3.486 | 0.212 | 3.664 | |
biplot_corrections | 3.036 | 0.096 | 3.111 | |
biplot_covariates | 4.867 | 0.156 | 5.002 | |
block2lme | 0.003 | 0.000 | 0.003 | |
center | 2.081 | 0.100 | 2.182 | |
code | 4.486 | 0.084 | 4.550 | |
coefs | 0.666 | 0.004 | 0.651 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
contrast_subgroup_cols | 0.544 | 0.025 | 0.549 | |
count_in | 0.000 | 0.001 | 0.001 | |
counts | 0.372 | 0.010 | 0.383 | |
counts2cpm | 0.356 | 0.008 | 0.364 | |
counts2tpm | 0.334 | 0.004 | 0.338 | |
cpm | 0.348 | 0.008 | 0.357 | |
create_design | 0.675 | 0.044 | 0.697 | |
default_formula | 14.090 | 0.544 | 14.248 | |
default_geom | 0.512 | 0.012 | 0.504 | |
default_sfile | 0.001 | 0.000 | 0.001 | |
demultiplex | 0.014 | 0.000 | 0.014 | |
dequantify | 0.001 | 0.002 | 0.002 | |
dot-merge | 0.016 | 0.001 | 0.018 | |
dot-plot_survival | 4.192 | 0.224 | 4.416 | |
dot-read_maxquant_proteingroups | 0.121 | 0.000 | 0.121 | |
download_contaminants | 0.17 | 0.02 | 2.17 | |
download_data | 0.001 | 0.000 | 0.000 | |
download_gtf | 0.001 | 0.000 | 0.000 | |
download_mcclain21 | 0.001 | 0.000 | 0.000 | |
dt2mat | 0.002 | 0.003 | 0.004 | |
enrichment | 1.119 | 0.124 | 1.244 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
explore_transformations | 3.479 | 0.357 | 3.836 | |
extract_coef_features | 4.589 | 0.344 | 4.896 | |
extract_rectangle | 0.102 | 0.016 | 0.118 | |
fdata | 0.516 | 0.020 | 0.537 | |
fdr2p | 0.827 | 0.052 | 0.858 | |
filter_exprs_replicated_in_some_subgroup | 1.010 | 0.056 | 1.010 | |
filter_features | 0.513 | 0.036 | 0.524 | |
filter_medoid | 0.726 | 0.068 | 0.794 | |
filter_samples | 0.505 | 0.024 | 0.496 | |
fit | 12.333 | 0.400 | 11.941 | |
fit_lmx | 4.218 | 0.040 | 4.072 | |
fitcoefs | 0.737 | 0.076 | 0.793 | |
fits | 0.700 | 0.020 | 0.699 | |
fitvars | 0.982 | 0.032 | 0.993 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.408 | 0.004 | 0.412 | |
fnames | 0.446 | 0.008 | 0.454 | |
formula2str | 0 | 0 | 0 | |
fvalues | 0.404 | 0.036 | 0.440 | |
fvars | 0.393 | 0.012 | 0.405 | |
genome_to_orgdb | 0.001 | 0.000 | 0.001 | |
group_by_level | 0.000 | 0.002 | 0.002 | |
guess_fitsep | 0.485 | 0.006 | 0.491 | |
guess_maxquant_quantity | 0.006 | 0.000 | 0.006 | |
guess_sep | 0.513 | 0.016 | 0.508 | |
has_multiple_levels | 0.046 | 0.012 | 0.057 | |
hdlproteins | 0.045 | 0.028 | 0.076 | |
impute | 3.010 | 0.044 | 3.054 | |
invert_subgroups | 0.709 | 0.016 | 0.724 | |
is_collapsed_subset | 0 | 0 | 0 | |
is_diann_report | 0.450 | 0.036 | 0.438 | |
is_fastadt | 0.063 | 0.000 | 0.062 | |
is_file | 0.001 | 0.000 | 0.000 | |
is_fraction | 0.001 | 0.000 | 0.002 | |
is_imputed | 0.729 | 0.004 | 0.733 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.377 | 0.020 | 0.397 | |
is_sig | 1.180 | 0.092 | 1.273 | |
is_valid_formula | 0.040 | 0.004 | 0.043 | |
keep_connected_blocks | 0.527 | 0.016 | 0.515 | |
keep_connected_features | 0.750 | 0.016 | 0.725 | |
keep_replicated_features | 0.846 | 0.039 | 0.826 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.408 | 0.012 | 0.420 | |
log2cpm | 0.378 | 0.004 | 0.382 | |
log2diffs | 0.320 | 0.000 | 0.321 | |
log2proteins | 0.314 | 0.016 | 0.330 | |
log2sites | 0.345 | 0.000 | 0.345 | |
log2tpm | 0.530 | 0.032 | 0.562 | |
log2transform | 3.396 | 0.016 | 3.412 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.534 | 0.024 | 0.538 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.772 | 0.008 | 0.780 | |
map_fvalues | 0.387 | 0.008 | 0.395 | |
matrix2sumexp | 0.928 | 0.024 | 0.932 | |
merge_sample_file | 0.438 | 0.016 | 0.453 | |
merge_sdata | 0.547 | 0.008 | 0.533 | |
message_df | 0.003 | 0.000 | 0.002 | |
modelvar | 1.584 | 0.036 | 1.565 | |
order_on_p | 0.896 | 0.015 | 0.890 | |
pca | 2.829 | 0.052 | 2.845 | |
pg_to_canonical | 0.006 | 0.000 | 0.006 | |
plot_contrast_venn | 1.873 | 0.072 | 1.865 | |
plot_contrastogram | 2.320 | 0.060 | 2.298 | |
plot_data | 1.295 | 0.016 | 1.291 | |
plot_densities | 8.860 | 0.184 | 8.978 | |
plot_design | 0.643 | 0.004 | 0.646 | |
plot_exprs | 18.696 | 0.232 | 18.801 | |
plot_exprs_per_coef | 17.579 | 0.160 | 17.584 | |
plot_fit_summary | 1.719 | 0.028 | 1.642 | |
plot_heatmap | 1.584 | 0.008 | 1.592 | |
plot_matrix | 0.508 | 0.008 | 0.478 | |
plot_sample_nas | 5.661 | 0.036 | 5.648 | |
plot_subgroup_points | 4.133 | 0.036 | 4.131 | |
plot_summary | 11.039 | 0.080 | 11.035 | |
plot_venn | 0.012 | 0.004 | 0.016 | |
plot_venn_heatmap | 0.033 | 0.004 | 0.038 | |
plot_violins | 3.520 | 0.068 | 3.569 | |
plot_volcano | 8.998 | 0.048 | 8.993 | |
preprocess_rnaseq_counts | 0.393 | 0.004 | 0.397 | |
pull_columns | 0.003 | 0.000 | 0.002 | |
read_affymetrix | 0.000 | 0.000 | 0.001 | |
read_contaminants | 0.122 | 0.004 | 1.296 | |
read_diann_proteingroups | 88.182 | 1.344 | 85.005 | |
read_fragpipe | 5.349 | 0.060 | 5.135 | |
read_maxquant_phosphosites | 1.551 | 0.004 | 1.555 | |
read_maxquant_proteingroups | 1.314 | 0.004 | 1.318 | |
read_metabolon | 11.642 | 0.024 | 11.557 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.297 | 0.056 | 1.307 | |
read_rectangles | 0.161 | 0.012 | 0.173 | |
read_rnaseq_counts | 28.334 | 2.598 | 30.667 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 12.034 | 0.316 | 12.273 | |
read_uniprotdt | 0.264 | 0.032 | 0.297 | |
reset_fit | 4.322 | 0.100 | 4.331 | |
rm_diann_contaminants | 19.214 | 0.548 | 19.605 | |
rm_missing_in_some_samples | 0.613 | 0.072 | 0.657 | |
rm_unmatched_samples | 0.572 | 0.076 | 0.647 | |
scaledlibsizes | 0.442 | 0.088 | 0.531 | |
scoremat | 1.008 | 0.108 | 1.095 | |
slevels | 0.506 | 0.076 | 0.582 | |
snames | 0.393 | 0.052 | 0.446 | |
split_extract_fixed | 0.532 | 0.052 | 0.562 | |
split_samples | 1.158 | 0.168 | 1.305 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.355 | 0.040 | 0.395 | |
subgroup_matrix | 0.541 | 0.048 | 0.568 | |
subtract_baseline | 4.183 | 0.372 | 4.496 | |
sumexp_to_longdt | 1.929 | 0.120 | 1.994 | |
sumexp_to_tsv | 0.492 | 0.036 | 0.528 | |
sumexplist_to_longdt | 1.579 | 0.076 | 1.654 | |
summarize_fit | 1.483 | 0.104 | 1.530 | |
svalues | 0.399 | 0.040 | 0.438 | |
svars | 0.453 | 0.032 | 0.484 | |
systematic_nas | 0.516 | 0.008 | 0.523 | |
tag_features | 0.833 | 0.044 | 0.877 | |
tag_hdlproteins | 0.496 | 0.032 | 0.528 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.404 | 0.028 | 0.431 | |
uncollapse | 0.007 | 0.004 | 0.011 | |
values | 0.439 | 0.032 | 0.472 | |
varlevels_dont_clash | 0.020 | 0.007 | 0.028 | |
venn_detects | 0.529 | 0.060 | 0.589 | |
weights | 0.572 | 0.084 | 0.657 | |
write_xl | 0.676 | 0.016 | 0.672 | |
zero_to_na | 0.000 | 0.002 | 0.002 | |