Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 115/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.13.21 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.13.21 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings autonomics_1.13.21.tar.gz |
StartedAt: 2024-08-20 22:24:21 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 22:42:31 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 1090.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: autonomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings autonomics_1.13.21.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'autonomics/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'autonomics' version '1.13.21' * 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 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 ... OK * 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 136.66 5.58 139.69 read_rnaseq_counts 36.00 1.92 37.87 rm_diann_contaminants 30.28 1.02 31.00 plot_exprs 29.80 0.43 30.29 plot_exprs_per_coef 28.18 0.44 28.64 default_formula 17.45 0.42 17.83 read_metabolon 15.71 0.22 15.99 fit 15.39 0.31 15.78 read_somascan 15.39 0.11 15.50 plot_summary 15.16 0.28 15.49 analyze 14.83 0.33 15.21 plot_volcano 12.47 0.26 12.78 read_fragpipe 9.61 0.27 9.78 ftype 8.61 0.42 9.14 plot_densities 8.52 0.24 8.82 fcluster 7.64 0.17 7.84 plot_sample_nas 7.51 0.08 7.64 code 7.30 0.16 7.47 extract_coef_features 6.84 0.16 7.16 plot_subgroup_points 6.03 0.19 6.23 biplot_covariates 5.83 0.22 6.16 reset_fit 5.83 0.11 6.00 fit_lmx 5.64 0.11 5.83 dot-plot_survival 4.61 0.95 5.93 plot_violins 5.12 0.19 5.37 subtract_baseline 5.19 0.11 5.36 pca 5.00 0.23 5.35 biplot 4.94 0.11 5.14 * 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: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck/00check.log' for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 The following object is masked from 'package:base': beta > > test_check("autonomics") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 159 ] > > proc.time() user system elapsed 185.23 14.17 208.34
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0 | 0 | 0 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
CONTAMINANTSURL | 0 | 0 | 0 | |
FITSEP | 0 | 0 | 0 | |
LINMOD_ENGINES | 0 | 0 | 0 | |
MAXQUANT_PATTERNS | 0 | 0 | 0 | |
TAXON_TO_ORGNAME | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
X | 2.15 | 0.11 | 2.39 | |
abstract_fit | 1.80 | 0.04 | 1.95 | |
add_adjusted_pvalues | 0.53 | 0.00 | 0.58 | |
add_assay_means | 0.41 | 0.05 | 0.45 | |
add_facetvars | 2.75 | 0.06 | 2.88 | |
add_opentargets_by_uniprot | 0.37 | 0.03 | 0.42 | |
add_psp | 0.49 | 0.07 | 0.59 | |
add_smiles | 0.67 | 0.07 | 0.86 | |
analysis | 0.47 | 0.02 | 0.49 | |
analyze | 14.83 | 0.33 | 15.21 | |
annotate_maxquant | 1.18 | 0.05 | 1.25 | |
annotate_uniprot_rest | 0.04 | 0.02 | 1.71 | |
assert_is_valid_sumexp | 0.62 | 0.12 | 0.83 | |
bin | 0.59 | 0.02 | 0.63 | |
biplot | 4.94 | 0.11 | 5.14 | |
biplot_corrections | 3.80 | 0.18 | 4.03 | |
biplot_covariates | 5.83 | 0.22 | 6.16 | |
block2lme | 0.00 | 0.02 | 0.01 | |
center | 1.82 | 0.09 | 1.94 | |
code | 7.30 | 0.16 | 7.47 | |
coefs | 0.83 | 0.08 | 0.98 | |
collapsed_entrezg_to_symbol | 0 | 0 | 0 | |
contrast_subgroup_cols | 0.67 | 0.12 | 0.85 | |
count_in | 0 | 0 | 0 | |
counts | 0.60 | 0.02 | 0.62 | |
counts2cpm | 0.48 | 0.00 | 0.49 | |
counts2tpm | 1.41 | 0.00 | 1.40 | |
cpm | 0.54 | 0.01 | 0.58 | |
create_design | 0.85 | 0.11 | 1.02 | |
default_coefs | 0.89 | 0.08 | 1.06 | |
default_formula | 17.45 | 0.42 | 17.83 | |
default_geom | 0.61 | 0.13 | 0.76 | |
default_sfile | 0.02 | 0.00 | 0.02 | |
demultiplex | 0.01 | 0.00 | 0.01 | |
dequantify | 0 | 0 | 0 | |
dequantify_compounddiscoverer | 0 | 0 | 0 | |
dot-merge | 0.02 | 0.00 | 0.02 | |
dot-plot_survival | 4.61 | 0.95 | 5.93 | |
dot-read_maxquant_proteingroups | 0.12 | 0.03 | 0.15 | |
download_contaminants | 0.03 | 0.00 | 1.13 | |
download_data | 0.00 | 0.02 | 0.01 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0 | 0 | 0 | |
enrichment | 1.67 | 0.17 | 1.86 | |
entrezg_to_symbol | 0 | 0 | 0 | |
explore_transformations | 4.52 | 0.15 | 4.69 | |
extract_coef_features | 6.84 | 0.16 | 7.16 | |
extract_rectangle | 0.16 | 0.06 | 0.37 | |
fcluster | 7.64 | 0.17 | 7.84 | |
fcor | 1.16 | 0.04 | 1.19 | |
fdata | 0.70 | 0.03 | 0.74 | |
fdr2p | 1.12 | 0.12 | 1.32 | |
filter_exprs_replicated_in_some_subgroup | 1.27 | 0.11 | 1.46 | |
filter_features | 0.75 | 0.13 | 0.92 | |
filter_medoid | 0.98 | 0.04 | 1.05 | |
filter_samples | 0.66 | 0.10 | 0.86 | |
fit | 15.39 | 0.31 | 15.78 | |
fit_lmx | 5.64 | 0.11 | 5.83 | |
fitcoefs | 0.78 | 0.05 | 0.95 | |
fits | 0.85 | 0.11 | 1.01 | |
fitvars | 1.56 | 0.07 | 1.71 | |
fix_xlgenes | 0 | 0 | 0 | |
flevels | 0.62 | 0.05 | 0.67 | |
fnames | 0.63 | 0.00 | 0.64 | |
formula2str | 0 | 0 | 0 | |
ftype | 8.61 | 0.42 | 9.14 | |
fvalues | 0.58 | 0.02 | 0.61 | |
fvars | 0.43 | 0.03 | 0.52 | |
genome_to_orgdb | 0.02 | 0.00 | 0.01 | |
group_by_level | 0 | 0 | 0 | |
guess_compounddiscoverer_quantity | 0 | 0 | 0 | |
guess_fitsep | 0.61 | 0.01 | 0.63 | |
guess_maxquant_quantity | 0 | 0 | 0 | |
guess_sep | 0.64 | 0.05 | 0.86 | |
has_multiple_levels | 0.10 | 0.00 | 0.09 | |
hdlproteins | 0.09 | 0.02 | 0.16 | |
impute | 3.66 | 0.08 | 3.79 | |
invert_subgroups | 0.96 | 0.03 | 1.00 | |
is_collapsed_subset | 0 | 0 | 0 | |
is_correlation_matrix | 0.02 | 0.00 | 0.02 | |
is_diann_report | 0.34 | 0.09 | 0.53 | |
is_fastadt | 0.07 | 0.00 | 0.06 | |
is_file | 0.00 | 0.02 | 0.02 | |
is_fraction | 0 | 0 | 0 | |
is_imputed | 1.07 | 0.03 | 1.12 | |
is_positive_number | 0 | 0 | 0 | |
is_scalar_subset | 0.49 | 0.03 | 0.53 | |
is_sig | 1.69 | 0.03 | 1.74 | |
is_valid_formula | 0.06 | 0.00 | 0.06 | |
keep_connected_blocks | 0.59 | 0.11 | 0.83 | |
keep_connected_features | 0.75 | 0.09 | 0.92 | |
keep_replicated_features | 1.00 | 0.14 | 1.24 | |
label2index | 0 | 0 | 0 | |
list2mat | 0 | 0 | 0 | |
log2counts | 0.5 | 0.0 | 0.5 | |
log2cpm | 0.46 | 0.02 | 0.46 | |
log2diffs | 0.39 | 0.00 | 0.41 | |
log2proteins | 0.37 | 0.01 | 0.41 | |
log2sites | 0.5 | 0.0 | 0.5 | |
log2tpm | 0.45 | 0.00 | 0.45 | |
log2transform | 4.83 | 0.11 | 4.97 | |
logical2factor | 0 | 0 | 0 | |
make_alpha_palette | 0.74 | 0.13 | 0.97 | |
make_colors | 0 | 0 | 0 | |
make_volcano_dt | 1.20 | 0.02 | 1.24 | |
map_fvalues | 0.52 | 0.00 | 0.51 | |
matrix2sumexp | 1.23 | 0.09 | 1.38 | |
merge_sample_file | 0.73 | 0.02 | 0.76 | |
merge_sdata | 0.82 | 0.08 | 0.99 | |
message_df | 0 | 0 | 0 | |
modelvar | 4.45 | 0.19 | 4.73 | |
order_on_p | 1.19 | 0.14 | 1.39 | |
pca | 5.00 | 0.23 | 5.35 | |
pg_to_canonical | 0.01 | 0.00 | 0.01 | |
plot_contrast_venn | 2.55 | 0.14 | 2.71 | |
plot_contrastogram | 3.62 | 0.16 | 3.89 | |
plot_data | 1.50 | 0.09 | 1.68 | |
plot_densities | 8.52 | 0.24 | 8.82 | |
plot_design | 0.83 | 0.00 | 0.86 | |
plot_exprs | 29.80 | 0.43 | 30.29 | |
plot_exprs_per_coef | 28.18 | 0.44 | 28.64 | |
plot_fit_summary | 2.42 | 0.09 | 2.63 | |
plot_heatmap | 1.82 | 0.04 | 1.86 | |
plot_matrix | 0.58 | 0.07 | 0.72 | |
plot_sample_nas | 7.51 | 0.08 | 7.64 | |
plot_subgroup_points | 6.03 | 0.19 | 6.23 | |
plot_summary | 15.16 | 0.28 | 15.49 | |
plot_venn | 0.01 | 0.00 | 0.01 | |
plot_venn_heatmap | 0.02 | 0.00 | 0.02 | |
plot_violins | 5.12 | 0.19 | 5.37 | |
plot_volcano | 12.47 | 0.26 | 12.78 | |
preprocess_rnaseq_counts | 0.49 | 0.00 | 0.50 | |
pull_columns | 0 | 0 | 0 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.01 | 0.00 | 0.39 | |
read_diann_proteingroups | 136.66 | 5.58 | 139.69 | |
read_fragpipe | 9.61 | 0.27 | 9.78 | |
read_maxquant_phosphosites | 1.89 | 0.08 | 2.05 | |
read_maxquant_proteingroups | 1.42 | 0.06 | 1.50 | |
read_metabolon | 15.71 | 0.22 | 15.99 | |
read_msigdt | 0 | 0 | 0 | |
read_olink | 1.75 | 0.07 | 1.93 | |
read_rectangles | 0.31 | 0.05 | 0.38 | |
read_rnaseq_counts | 36.00 | 1.92 | 37.87 | |
read_salmon | 0 | 0 | 0 | |
read_somascan | 15.39 | 0.11 | 15.50 | |
read_uniprotdt | 0.28 | 0.03 | 0.32 | |
reset_fit | 5.83 | 0.11 | 6.00 | |
rm_diann_contaminants | 30.28 | 1.02 | 31.00 | |
rm_missing_in_some_samples | 0.62 | 0.11 | 0.84 | |
rm_unmatched_samples | 0.74 | 0.01 | 0.73 | |
scaledlibsizes | 0.42 | 0.02 | 0.44 | |
scoremat | 1.28 | 0.06 | 1.47 | |
slevels | 0.58 | 0.00 | 0.61 | |
snames | 0.41 | 0.05 | 0.47 | |
split_extract_fixed | 0.72 | 0.08 | 0.89 | |
split_samples | 1.21 | 0.14 | 1.42 | |
stri_any_regex | 0 | 0 | 0 | |
stri_detect_fixed_in_collapsed | 0.53 | 0.01 | 0.56 | |
subgroup_matrix | 0.81 | 0.07 | 0.95 | |
subtract_baseline | 5.19 | 0.11 | 5.36 | |
sumexp_to_longdt | 2.25 | 0.10 | 2.52 | |
sumexp_to_tsv | 0.47 | 0.05 | 0.53 | |
sumexplist_to_longdt | 2.02 | 0.03 | 2.06 | |
summarize_fit | 2.04 | 0.08 | 2.14 | |
svalues | 0.44 | 0.02 | 0.47 | |
svars | 0.50 | 0.01 | 0.51 | |
systematic_nas | 0.69 | 0.03 | 0.74 | |
tag_features | 0.92 | 0.02 | 0.94 | |
tag_hdlproteins | 0.61 | 0.03 | 0.67 | |
taxon2org | 0 | 0 | 0 | |
tpm | 0.61 | 0.02 | 0.64 | |
uncollapse | 0.02 | 0.00 | 0.02 | |
values | 0.48 | 0.01 | 0.50 | |
varlevels_dont_clash | 0.03 | 0.00 | 0.03 | |
venn_detects | 0.77 | 0.02 | 0.79 | |
weights | 0.41 | 0.01 | 0.43 | |
write_xl | 0.98 | 0.13 | 1.18 | |
zero_to_na | 0.02 | 0.00 | 0.02 | |