Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-15 21:53 -0400 (Tue, 15 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 |
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 | |||||||||
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: 2024-10-13 21:12:28 -0400 (Sun, 13 Oct 2024) |
EndedAt: 2024-10-13 21:28:13 -0400 (Sun, 13 Oct 2024) |
EllapsedTime: 944.7 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_1.12.1.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 90.603 3.852 89.891 read_rnaseq_counts 26.842 2.234 28.773 rm_diann_contaminants 20.416 0.560 20.960 plot_exprs 19.174 0.064 19.147 plot_exprs_per_coef 18.085 0.120 18.120 default_formula 15.423 0.421 15.448 fit 12.313 0.103 11.266 analyze 11.660 0.156 11.697 read_somascan 11.364 0.367 11.664 read_metabolon 11.124 0.180 11.180 plot_summary 11.217 0.024 11.086 plot_volcano 8.864 0.060 8.850 plot_densities 7.877 0.071 7.849 plot_sample_nas 5.843 0.053 5.817 read_fragpipe 5.268 0.048 5.030 * 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 130.998 4.068 132.677
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 | 0.000 | |
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 | 1.210 | 0.042 | 1.229 | |
add_adjusted_pvalues | 0.535 | 0.025 | 0.560 | |
add_assay_means | 0.428 | 0.023 | 0.452 | |
add_facetvars | 2.099 | 0.080 | 2.158 | |
add_opentargets_by_uniprot | 0.379 | 0.012 | 0.393 | |
add_psp | 0.491 | 0.012 | 0.504 | |
add_smiles | 0.487 | 0.008 | 0.464 | |
analysis | 0.387 | 0.000 | 0.387 | |
analyze | 11.660 | 0.156 | 11.697 | |
annotate_maxquant | 0.828 | 0.032 | 0.859 | |
annotate_uniprot_rest | 0.432 | 0.004 | 2.544 | |
assert_is_valid_sumexp | 0.570 | 0.012 | 0.562 | |
bin | 0.390 | 0.012 | 0.403 | |
biplot | 3.438 | 0.080 | 3.497 | |
biplot_corrections | 2.942 | 0.020 | 2.924 | |
biplot_covariates | 4.806 | 0.024 | 4.792 | |
block2lme | 0.003 | 0.000 | 0.004 | |
center | 2.089 | 0.072 | 2.161 | |
code | 4.569 | 0.056 | 4.594 | |
coefs | 0.681 | 0.020 | 0.678 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.000 | |
contrast_subgroup_cols | 0.577 | 0.012 | 0.566 | |
count_in | 0.002 | 0.000 | 0.001 | |
counts | 0.393 | 0.004 | 0.396 | |
counts2cpm | 0.362 | 0.000 | 0.361 | |
counts2tpm | 0.336 | 0.000 | 0.336 | |
cpm | 0.354 | 0.000 | 0.354 | |
create_design | 0.674 | 0.024 | 0.676 | |
default_formula | 15.423 | 0.421 | 15.448 | |
default_geom | 0.489 | 0.008 | 0.473 | |
default_sfile | 0.001 | 0.000 | 0.001 | |
demultiplex | 0.014 | 0.000 | 0.014 | |
dequantify | 0.000 | 0.003 | 0.002 | |
dot-merge | 0.018 | 0.001 | 0.019 | |
dot-plot_survival | 3.776 | 0.268 | 4.045 | |
dot-read_maxquant_proteingroups | 0.108 | 0.004 | 0.112 | |
download_contaminants | 0.144 | 0.004 | 2.902 | |
download_data | 0.001 | 0.000 | 0.000 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.004 | 0.000 | 0.004 | |
enrichment | 1.108 | 0.012 | 1.122 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.001 | |
explore_transformations | 3.277 | 0.092 | 3.370 | |
extract_coef_features | 4.429 | 0.020 | 4.429 | |
extract_rectangle | 0.109 | 0.012 | 0.122 | |
fdata | 0.561 | 0.016 | 0.578 | |
fdr2p | 0.935 | 0.048 | 0.947 | |
filter_exprs_replicated_in_some_subgroup | 0.968 | 0.007 | 0.916 | |
filter_features | 0.505 | 0.017 | 0.501 | |
filter_medoid | 0.715 | 0.008 | 0.724 | |
filter_samples | 0.514 | 0.008 | 0.486 | |
fit | 12.313 | 0.103 | 11.266 | |
fit_lmx | 4.341 | 0.016 | 4.004 | |
fitcoefs | 0.756 | 0.008 | 0.726 | |
fits | 0.745 | 0.024 | 0.730 | |
fitvars | 0.996 | 0.016 | 0.974 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.401 | 0.000 | 0.400 | |
fnames | 0.460 | 0.008 | 0.468 | |
formula2str | 0 | 0 | 0 | |
fvalues | 0.393 | 0.003 | 0.396 | |
fvars | 0.386 | 0.000 | 0.387 | |
genome_to_orgdb | 0.000 | 0.000 | 0.001 | |
group_by_level | 0.001 | 0.000 | 0.002 | |
guess_fitsep | 0.444 | 0.004 | 0.449 | |
guess_maxquant_quantity | 0.006 | 0.000 | 0.006 | |
guess_sep | 0.511 | 0.024 | 0.498 | |
has_multiple_levels | 0.050 | 0.000 | 0.051 | |
hdlproteins | 0.037 | 0.032 | 0.072 | |
impute | 2.798 | 0.012 | 2.809 | |
invert_subgroups | 0.817 | 0.020 | 0.837 | |
is_collapsed_subset | 0.000 | 0.001 | 0.001 | |
is_diann_report | 0.396 | 0.035 | 0.390 | |
is_fastadt | 0.065 | 0.004 | 0.069 | |
is_file | 0.001 | 0.000 | 0.000 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 0.660 | 0.008 | 0.668 | |
is_positive_number | 0.002 | 0.000 | 0.001 | |
is_scalar_subset | 0.307 | 0.007 | 0.314 | |
is_sig | 1.110 | 0.012 | 1.121 | |
is_valid_formula | 0.038 | 0.000 | 0.038 | |
keep_connected_blocks | 0.481 | 0.016 | 0.470 | |
keep_connected_features | 0.703 | 0.004 | 0.668 | |
keep_replicated_features | 0.786 | 0.004 | 0.726 | |
label2index | 0.000 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
log2counts | 0.369 | 0.000 | 0.370 | |
log2cpm | 0.374 | 0.000 | 0.375 | |
log2diffs | 0.315 | 0.000 | 0.316 | |
log2proteins | 0.314 | 0.000 | 0.314 | |
log2sites | 0.313 | 0.007 | 0.320 | |
log2tpm | 0.364 | 0.004 | 0.368 | |
log2transform | 3.446 | 0.068 | 3.514 | |
logical2factor | 0.001 | 0.000 | 0.001 | |
make_alpha_palette | 0.538 | 0.012 | 0.526 | |
make_colors | 0.01 | 0.00 | 0.01 | |
make_volcano_dt | 0.779 | 0.000 | 0.779 | |
map_fvalues | 0.388 | 0.008 | 0.397 | |
matrix2sumexp | 0.917 | 0.000 | 0.894 | |
merge_sample_file | 0.430 | 0.012 | 0.443 | |
merge_sdata | 0.559 | 0.020 | 0.556 | |
message_df | 0.002 | 0.000 | 0.002 | |
modelvar | 1.514 | 0.040 | 1.495 | |
order_on_p | 0.900 | 0.032 | 0.910 | |
pca | 2.690 | 0.064 | 2.731 | |
pg_to_canonical | 0.006 | 0.000 | 0.006 | |
plot_contrast_venn | 1.753 | 0.012 | 1.685 | |
plot_contrastogram | 2.108 | 0.032 | 2.067 | |
plot_data | 1.161 | 0.012 | 1.142 | |
plot_densities | 7.877 | 0.071 | 7.849 | |
plot_design | 0.589 | 0.000 | 0.589 | |
plot_exprs | 19.174 | 0.064 | 19.147 | |
plot_exprs_per_coef | 18.085 | 0.120 | 18.120 | |
plot_fit_summary | 1.773 | 0.016 | 1.691 | |
plot_heatmap | 1.666 | 0.004 | 1.671 | |
plot_matrix | 0.533 | 0.031 | 0.543 | |
plot_sample_nas | 5.843 | 0.053 | 5.817 | |
plot_subgroup_points | 4.349 | 0.028 | 4.296 | |
plot_summary | 11.217 | 0.024 | 11.086 | |
plot_venn | 0.017 | 0.000 | 0.016 | |
plot_venn_heatmap | 0.038 | 0.000 | 0.038 | |
plot_violins | 4.686 | 0.140 | 4.787 | |
plot_volcano | 8.864 | 0.060 | 8.850 | |
preprocess_rnaseq_counts | 0.327 | 0.004 | 0.332 | |
pull_columns | 0.002 | 0.000 | 0.002 | |
read_affymetrix | 0.001 | 0.000 | 0.000 | |
read_contaminants | 0.083 | 0.004 | 1.335 | |
read_diann_proteingroups | 90.603 | 3.852 | 89.891 | |
read_fragpipe | 5.268 | 0.048 | 5.030 | |
read_maxquant_phosphosites | 1.445 | 0.012 | 1.457 | |
read_maxquant_proteingroups | 1.214 | 0.044 | 1.258 | |
read_metabolon | 11.124 | 0.180 | 11.180 | |
read_msigdt | 0.000 | 0.001 | 0.001 | |
read_olink | 1.086 | 0.014 | 1.029 | |
read_rectangles | 0.167 | 0.004 | 0.171 | |
read_rnaseq_counts | 26.842 | 2.234 | 28.773 | |
read_salmon | 0.000 | 0.001 | 0.000 | |
read_somascan | 11.364 | 0.367 | 11.664 | |
read_uniprotdt | 0.281 | 0.016 | 0.297 | |
reset_fit | 4.073 | 0.072 | 4.038 | |
rm_diann_contaminants | 20.416 | 0.560 | 20.960 | |
rm_missing_in_some_samples | 0.514 | 0.032 | 0.516 | |
rm_unmatched_samples | 0.565 | 0.012 | 0.576 | |
scaledlibsizes | 0.358 | 0.016 | 0.374 | |
scoremat | 1.006 | 0.036 | 1.005 | |
slevels | 0.402 | 0.004 | 0.407 | |
snames | 0.405 | 0.007 | 0.413 | |
split_extract_fixed | 0.516 | 0.013 | 0.506 | |
split_samples | 1.136 | 0.051 | 1.145 | |
stri_any_regex | 0.001 | 0.001 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.339 | 0.011 | 0.351 | |
subgroup_matrix | 0.610 | 0.009 | 0.580 | |
subtract_baseline | 3.978 | 0.012 | 3.933 | |
sumexp_to_longdt | 1.745 | 0.059 | 1.721 | |
sumexp_to_tsv | 0.501 | 0.012 | 0.513 | |
sumexplist_to_longdt | 1.452 | 0.032 | 1.484 | |
summarize_fit | 1.394 | 0.016 | 1.348 | |
svalues | 0.437 | 0.004 | 0.441 | |
svars | 0.416 | 0.008 | 0.423 | |
systematic_nas | 0.54 | 0.00 | 0.54 | |
tag_features | 0.893 | 0.024 | 0.916 | |
tag_hdlproteins | 0.488 | 0.044 | 0.532 | |
taxon2org | 0.001 | 0.000 | 0.001 | |
tpm | 0.338 | 0.012 | 0.350 | |
uncollapse | 0.006 | 0.004 | 0.010 | |
values | 0.400 | 0.012 | 0.412 | |
varlevels_dont_clash | 0.013 | 0.008 | 0.021 | |
venn_detects | 0.581 | 0.008 | 0.589 | |
weights | 0.34 | 0.00 | 0.34 | |
write_xl | 0.634 | 0.032 | 0.644 | |
zero_to_na | 0.002 | 0.000 | 0.002 | |