Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-05 11:43 -0400 (Sat, 05 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 116/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.13.21 (landing page) Aditya Bhagwat
| teran2 | Linux (Ubuntu 24.04.1 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 | OK | 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: /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_1.13.21.tar.gz |
StartedAt: 2024-10-04 19:28:18 -0400 (Fri, 04 Oct 2024) |
EndedAt: 2024-10-04 19:33:02 -0400 (Fri, 04 Oct 2024) |
EllapsedTime: 283.3 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_1.13.21.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * 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 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 ... 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 37.964 1.434 29.667 read_rnaseq_counts 11.681 0.774 9.539 plot_exprs 9.208 0.146 6.761 plot_exprs_per_coef 8.987 0.171 6.764 rm_diann_contaminants 7.972 0.267 6.697 default_formula 6.707 0.178 5.160 fit 6.500 0.161 3.801 read_somascan 5.210 0.079 4.091 analyze 5.084 0.104 3.690 * 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 ‘/Users/biocbuild/bbs-3.20-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-arm64/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: aarch64-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 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 60.588 3.183 51.444
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.000 | 0.001 | |
COMPOUNDDISCOVERER_PATTERNS | 0 | 0 | 0 | |
CONTAMINANTSURL | 0.000 | 0.000 | 0.001 | |
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 | 0.697 | 0.031 | 0.515 | |
abstract_fit | 0.948 | 0.047 | 0.617 | |
add_adjusted_pvalues | 0.197 | 0.006 | 0.184 | |
add_assay_means | 0.107 | 0.002 | 0.109 | |
add_facetvars | 0.753 | 0.026 | 0.565 | |
add_opentargets_by_uniprot | 0.130 | 0.001 | 0.131 | |
add_psp | 0.159 | 0.004 | 0.164 | |
add_smiles | 0.176 | 0.015 | 0.157 | |
analysis | 0.233 | 0.007 | 0.120 | |
analyze | 5.084 | 0.104 | 3.690 | |
annotate_maxquant | 0.313 | 0.009 | 0.324 | |
annotate_uniprot_rest | 0.028 | 0.006 | 2.058 | |
assert_is_valid_sumexp | 0.196 | 0.015 | 0.167 | |
bin | 0.577 | 0.015 | 0.425 | |
biplot | 1.166 | 0.026 | 0.983 | |
biplot_corrections | 1.070 | 0.025 | 0.885 | |
biplot_covariates | 1.658 | 0.032 | 1.481 | |
block2lme | 0.001 | 0.000 | 0.002 | |
center | 0.435 | 0.007 | 0.442 | |
code | 2.069 | 0.030 | 1.887 | |
coefs | 0.341 | 0.022 | 0.246 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.000 | |
contrast_subgroup_cols | 0.332 | 0.021 | 0.192 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.245 | 0.007 | 0.127 | |
counts2cpm | 0.491 | 0.002 | 0.483 | |
counts2tpm | 0.104 | 0.000 | 0.104 | |
cpm | 0.114 | 0.001 | 0.115 | |
create_design | 0.304 | 0.020 | 0.223 | |
default_coefs | 0.425 | 0.023 | 0.226 | |
default_formula | 6.707 | 0.178 | 5.160 | |
default_geom | 0.339 | 0.024 | 0.183 | |
default_sfile | 0.002 | 0.000 | 0.000 | |
demultiplex | 0.007 | 0.001 | 0.003 | |
dequantify | 0.002 | 0.000 | 0.000 | |
dequantify_compounddiscoverer | 0.001 | 0.000 | 0.001 | |
dot-merge | 0.013 | 0.001 | 0.007 | |
dot-plot_survival | 1.881 | 0.101 | 1.845 | |
dot-read_maxquant_proteingroups | 0.047 | 0.001 | 0.049 | |
download_contaminants | 0.030 | 0.004 | 2.736 | |
download_data | 0 | 0 | 0 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0.000 | 0.000 | 0.001 | |
dt2mat | 0.001 | 0.000 | 0.001 | |
enrichment | 0.384 | 0.026 | 0.410 | |
entrezg_to_symbol | 0 | 0 | 0 | |
explore_transformations | 1.009 | 0.026 | 1.036 | |
extract_coef_features | 1.629 | 0.026 | 1.443 | |
extract_rectangle | 0.043 | 0.014 | 0.056 | |
fcluster | 2.370 | 0.048 | 1.793 | |
fcor | 0.332 | 0.010 | 0.342 | |
fdata | 0.169 | 0.003 | 0.172 | |
fdr2p | 0.424 | 0.020 | 0.290 | |
filter_exprs_replicated_in_some_subgroup | 0.496 | 0.025 | 0.292 | |
filter_features | 0.334 | 0.020 | 0.177 | |
filter_medoid | 0.375 | 0.010 | 0.222 | |
filter_samples | 0.200 | 0.015 | 0.169 | |
fit | 6.500 | 0.161 | 3.801 | |
fit_lmx | 2.276 | 0.062 | 1.260 | |
fitcoefs | 0.342 | 0.018 | 0.243 | |
fits | 0.419 | 0.021 | 0.243 | |
fitvars | 0.589 | 0.027 | 0.315 | |
fix_xlgenes | 0.001 | 0.000 | 0.000 | |
flevels | 0.158 | 0.002 | 0.140 | |
fnames | 0.136 | 0.001 | 0.138 | |
formula2str | 0 | 0 | 0 | |
ftype | 3.144 | 0.150 | 2.217 | |
fvalues | 0.263 | 0.007 | 0.135 | |
fvars | 0.160 | 0.003 | 0.125 | |
genome_to_orgdb | 0 | 0 | 0 | |
group_by_level | 0.000 | 0.000 | 0.001 | |
guess_compounddiscoverer_quantity | 0.001 | 0.000 | 0.000 | |
guess_fitsep | 0.133 | 0.001 | 0.134 | |
guess_maxquant_quantity | 0.001 | 0.001 | 0.002 | |
guess_sep | 0.185 | 0.015 | 0.161 | |
has_multiple_levels | 0.062 | 0.002 | 0.032 | |
hdlproteins | 0.053 | 0.011 | 0.035 | |
impute | 0.990 | 0.011 | 0.914 | |
invert_subgroups | 0.188 | 0.002 | 0.189 | |
is_collapsed_subset | 0.000 | 0.000 | 0.001 | |
is_correlation_matrix | 0.001 | 0.000 | 0.000 | |
is_diann_report | 0.260 | 0.022 | 0.162 | |
is_fastadt | 0.065 | 0.002 | 0.034 | |
is_file | 0.001 | 0.000 | 0.000 | |
is_fraction | 0.003 | 0.000 | 0.001 | |
is_imputed | 0.354 | 0.010 | 0.224 | |
is_positive_number | 0.000 | 0.000 | 0.001 | |
is_scalar_subset | 0.103 | 0.001 | 0.104 | |
is_sig | 0.469 | 0.003 | 0.471 | |
is_valid_formula | 0.013 | 0.000 | 0.013 | |
keep_connected_blocks | 0.193 | 0.017 | 0.167 | |
keep_connected_features | 0.464 | 0.028 | 0.246 | |
keep_replicated_features | 0.490 | 0.028 | 0.260 | |
label2index | 0.000 | 0.001 | 0.000 | |
list2mat | 0.000 | 0.000 | 0.001 | |
log2counts | 0.223 | 0.006 | 0.114 | |
log2cpm | 0.184 | 0.004 | 0.110 | |
log2diffs | 0.163 | 0.015 | 0.178 | |
log2proteins | 0.101 | 0.001 | 0.102 | |
log2sites | 0.102 | 0.004 | 0.106 | |
log2tpm | 0.116 | 0.011 | 0.128 | |
log2transform | 1.135 | 0.020 | 1.166 | |
logical2factor | 0.001 | 0.000 | 0.001 | |
make_alpha_palette | 0.205 | 0.016 | 0.173 | |
make_colors | 0.009 | 0.001 | 0.005 | |
make_volcano_dt | 0.422 | 0.010 | 0.273 | |
map_fvalues | 0.120 | 0.002 | 0.122 | |
matrix2sumexp | 0.471 | 0.023 | 0.312 | |
merge_sample_file | 0.173 | 0.004 | 0.148 | |
merge_sdata | 0.229 | 0.027 | 0.197 | |
message_df | 0.002 | 0.000 | 0.001 | |
modelvar | 1.622 | 0.048 | 1.045 | |
order_on_p | 0.445 | 0.025 | 0.300 | |
pca | 1.108 | 0.039 | 0.890 | |
pg_to_canonical | 0.002 | 0.000 | 0.001 | |
plot_contrast_venn | 1.041 | 0.041 | 0.687 | |
plot_contrastogram | 1.436 | 0.076 | 1.048 | |
plot_data | 0.713 | 0.029 | 0.407 | |
plot_densities | 4.111 | 0.160 | 3.089 | |
plot_design | 0.295 | 0.007 | 0.203 | |
plot_exprs | 9.208 | 0.146 | 6.761 | |
plot_exprs_per_coef | 8.987 | 0.171 | 6.764 | |
plot_fit_summary | 0.876 | 0.034 | 0.560 | |
plot_heatmap | 0.506 | 0.003 | 0.508 | |
plot_matrix | 0.192 | 0.023 | 0.177 | |
plot_sample_nas | 2.523 | 0.044 | 1.722 | |
plot_subgroup_points | 2.011 | 0.050 | 1.312 | |
plot_summary | 4.867 | 0.080 | 3.524 | |
plot_venn | 0.009 | 0.001 | 0.009 | |
plot_venn_heatmap | 0.007 | 0.000 | 0.007 | |
plot_violins | 1.295 | 0.037 | 1.120 | |
plot_volcano | 3.355 | 0.049 | 2.944 | |
preprocess_rnaseq_counts | 0.124 | 0.001 | 0.125 | |
pull_columns | 0.000 | 0.000 | 0.001 | |
read_affymetrix | 0.000 | 0.000 | 0.001 | |
read_contaminants | 0.014 | 0.001 | 0.989 | |
read_diann_proteingroups | 37.964 | 1.434 | 29.667 | |
read_fragpipe | 3.607 | 0.176 | 2.684 | |
read_maxquant_phosphosites | 0.601 | 0.016 | 0.482 | |
read_maxquant_proteingroups | 0.381 | 0.005 | 0.386 | |
read_metabolon | 4.868 | 0.130 | 3.594 | |
read_msigdt | 0 | 0 | 0 | |
read_olink | 0.669 | 0.032 | 0.442 | |
read_rectangles | 0.059 | 0.008 | 0.067 | |
read_rnaseq_counts | 11.681 | 0.774 | 9.539 | |
read_salmon | 0.000 | 0.001 | 0.000 | |
read_somascan | 5.210 | 0.079 | 4.091 | |
read_uniprotdt | 0.097 | 0.007 | 0.106 | |
reset_fit | 2.126 | 0.057 | 1.382 | |
rm_diann_contaminants | 7.972 | 0.267 | 6.697 | |
rm_missing_in_some_samples | 0.188 | 0.015 | 0.162 | |
rm_unmatched_samples | 0.332 | 0.014 | 0.175 | |
scaledlibsizes | 0.102 | 0.001 | 0.102 | |
scoremat | 0.483 | 0.022 | 0.313 | |
slevels | 0.143 | 0.003 | 0.126 | |
snames | 0.124 | 0.002 | 0.127 | |
split_extract_fixed | 0.186 | 0.014 | 0.160 | |
split_samples | 0.689 | 0.029 | 0.362 | |
stri_any_regex | 0.000 | 0.000 | 0.001 | |
stri_detect_fixed_in_collapsed | 0.107 | 0.001 | 0.108 | |
subgroup_matrix | 0.239 | 0.017 | 0.190 | |
subtract_baseline | 1.818 | 0.068 | 1.412 | |
sumexp_to_longdt | 1.017 | 0.062 | 0.604 | |
sumexp_to_tsv | 0.148 | 0.003 | 0.150 | |
sumexplist_to_longdt | 0.491 | 0.006 | 0.495 | |
summarize_fit | 0.936 | 0.044 | 0.489 | |
svalues | 0.243 | 0.007 | 0.127 | |
svars | 0.145 | 0.002 | 0.148 | |
systematic_nas | 0.156 | 0.001 | 0.157 | |
tag_features | 0.309 | 0.010 | 0.318 | |
tag_hdlproteins | 0.196 | 0.019 | 0.215 | |
taxon2org | 0 | 0 | 0 | |
tpm | 0.113 | 0.001 | 0.114 | |
uncollapse | 0.004 | 0.000 | 0.004 | |
values | 0.134 | 0.003 | 0.136 | |
varlevels_dont_clash | 0.007 | 0.000 | 0.007 | |
venn_detects | 0.157 | 0.001 | 0.158 | |
weights | 0.142 | 0.000 | 0.144 | |
write_xl | 0.299 | 0.025 | 0.228 | |
zero_to_na | 0.001 | 0.001 | 0.000 | |