Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-04 11:40:16 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 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 1.12.0 (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 | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: autonomics |
Version: 1.12.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings autonomics_1.12.0.tar.gz |
StartedAt: 2024-05-04 04:57:05 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 05:13:19 -0000 (Sat, 04 May 2024) |
EllapsedTime: 973.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: autonomics.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:autonomics.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘autonomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘autonomics’ version ‘1.12.0’ * 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 ... ERROR Running examples in ‘autonomics-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: .read_rnaseq_bams > ### Title: Read rnaseq counts/bams > ### Aliases: .read_rnaseq_bams .read_rnaseq_counts read_rnaseq_bams > ### read_rnaseq_counts > > ### ** Examples > > # read_rnaseq_bams > if (requireNamespace('Rsubread')){ + dir <- download_data('billing16.bam.zip') + object <- read_rnaseq_bams(dir, paired = TRUE, genome = 'hg38') + object <- read_rnaseq_bams(dir, paired = TRUE, genome = 'hg38', plot = TRUE) + } Loading required namespace: Rsubread unzip Warning in unzip(filepath, exdir = substr(filepath, 1, nchar(filepath) - : error 1 in extracting from zip file NCBI RefSeq annotation for hg38 (build 38.2) is used. Error in (function (files, annot.inbuilt = "mm39", annot.ext = NULL, isGTFAnnotationFile = FALSE, : No read files provided! Calls: read_rnaseq_bams ... .read_rnaseq_bams -> count_reads -> do.call -> <Anonymous> Execution halted * 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 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log’ for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 191.877 2.771 193.884
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.001 | 0.000 | 0.000 | |
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 | 0.000 | 0.000 | 0.001 | |
abstract_fit | 1.798 | 0.040 | 1.847 | |
add_adjusted_pvalues | 0.797 | 0.051 | 0.855 | |
add_assay_means | 0.651 | 0.020 | 0.673 | |
add_facetvars | 3.174 | 0.188 | 3.365 | |
add_opentargets_by_uniprot | 0.558 | 0.020 | 0.584 | |
add_psp | 0.701 | 0.016 | 0.721 | |
add_smiles | 0.655 | 0.008 | 0.660 | |
analysis | 0.536 | 0.004 | 0.540 | |
analyze | 17.572 | 0.084 | 17.683 | |
annotate_maxquant | 1.144 | 0.020 | 1.168 | |
annotate_uniprot_rest | 0.079 | 0.020 | 4.935 | |
assert_is_valid_sumexp | 0.784 | 0.107 | 0.891 | |
bin | 0.562 | 0.008 | 0.575 | |
biplot | 5.149 | 0.072 | 5.229 | |
biplot_corrections | 4.426 | 0.004 | 4.436 | |
biplot_covariates | 7.145 | 0.024 | 7.182 | |
block2lme | 0.003 | 0.000 | 0.004 | |
center | 2.798 | 0.067 | 2.870 | |
code | 6.813 | 0.024 | 6.847 | |
coefs | 1.033 | 0.004 | 1.036 | |
collapsed_entrezg_to_symbol | 0 | 0 | 0 | |
contrast_subgroup_cols | 0.841 | 0.004 | 0.844 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.588 | 0.000 | 0.590 | |
counts2cpm | 0.555 | 0.000 | 0.557 | |
counts2tpm | 0.516 | 0.004 | 0.522 | |
cpm | 0.561 | 0.000 | 0.563 | |
create_design | 1.015 | 0.004 | 1.018 | |
default_formula | 21.541 | 0.535 | 21.931 | |
default_geom | 0.708 | 0.024 | 0.731 | |
default_sfile | 0.000 | 0.002 | 0.001 | |
demultiplex | 0.018 | 0.001 | 0.019 | |
dequantify | 0.003 | 0.000 | 0.003 | |
dot-merge | 0.021 | 0.000 | 0.021 | |
dot-plot_survival | 5.327 | 0.127 | 5.465 | |
dot-read_maxquant_proteingroups | 0.134 | 0.004 | 0.138 | |
download_contaminants | 0.028 | 0.000 | 5.266 | |
download_data | 0.001 | 0.000 | 0.000 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.005 | 0.000 | 0.004 | |
enrichment | 1.622 | 0.044 | 1.669 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.000 | |
explore_transformations | 4.842 | 0.044 | 4.895 | |
extract_coef_features | 6.890 | 0.052 | 6.952 | |
extract_rectangle | 0.146 | 0.012 | 0.158 | |
fdata | 0.789 | 0.000 | 0.790 | |
fdr2p | 1.293 | 0.000 | 1.293 | |
filter_exprs_replicated_in_some_subgroup | 1.456 | 0.020 | 1.473 | |
filter_features | 0.757 | 0.016 | 0.771 | |
filter_medoid | 1.093 | 0.020 | 1.114 | |
filter_samples | 0.828 | 0.004 | 0.830 | |
fit | 17.162 | 0.088 | 17.221 | |
fit_lmx | 5.955 | 0.128 | 6.077 | |
fitcoefs | 1.115 | 0.012 | 1.125 | |
fits | 1.028 | 0.012 | 1.038 | |
fitvars | 1.511 | 0.008 | 1.519 | |
fix_xlgenes | 0.002 | 0.000 | 0.003 | |
flevels | 0.601 | 0.044 | 0.647 | |
fnames | 0.652 | 0.127 | 0.783 | |
formula2str | 0.000 | 0.000 | 0.001 | |
fvalues | 0.596 | 0.016 | 0.614 | |
fvars | 0.568 | 0.004 | 0.573 | |
genome_to_orgdb | 0 | 0 | 0 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.736 | 0.040 | 0.777 | |
guess_maxquant_quantity | 0.007 | 0.000 | 0.007 | |
guess_sep | 0.694 | 0.004 | 0.696 | |
has_multiple_levels | 0.073 | 0.000 | 0.074 | |
hdlproteins | 0.051 | 0.028 | 0.089 | |
impute | 4.195 | 0.008 | 4.212 | |
invert_subgroups | 0.933 | 0.004 | 0.938 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_diann_report | 0.553 | 0.032 | 0.749 | |
is_fastadt | 0.087 | 0.000 | 0.087 | |
is_file | 0.001 | 0.000 | 0.001 | |
is_fraction | 0.000 | 0.002 | 0.002 | |
is_imputed | 1.029 | 0.085 | 1.115 | |
is_positive_number | 0.003 | 0.000 | 0.003 | |
is_scalar_subset | 0.498 | 0.132 | 0.630 | |
is_sig | 1.683 | 0.068 | 1.754 | |
is_valid_formula | 0.069 | 0.012 | 0.081 | |
keep_connected_blocks | 0.739 | 0.020 | 0.757 | |
keep_connected_features | 1.027 | 0.024 | 1.047 | |
keep_replicated_features | 1.130 | 0.004 | 1.131 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.000 | |
log2counts | 0.568 | 0.000 | 0.569 | |
log2cpm | 0.607 | 0.000 | 0.609 | |
log2diffs | 0.474 | 0.000 | 0.475 | |
log2proteins | 0.472 | 0.004 | 0.477 | |
log2sites | 0.467 | 0.008 | 0.475 | |
log2tpm | 0.545 | 0.000 | 0.546 | |
log2transform | 5.268 | 0.127 | 5.407 | |
logical2factor | 0.001 | 0.000 | 0.001 | |
make_alpha_palette | 0.788 | 0.012 | 0.799 | |
make_colors | 0.010 | 0.000 | 0.011 | |
make_volcano_dt | 1.199 | 0.000 | 1.201 | |
map_fvalues | 0.568 | 0.000 | 0.570 | |
matrix2sumexp | 1.399 | 0.008 | 1.407 | |
merge_sample_file | 0.644 | 0.000 | 0.646 | |
merge_sdata | 0.772 | 0.012 | 0.782 | |
message_df | 0.003 | 0.000 | 0.002 | |
modelvar | 2.339 | 0.016 | 2.353 | |
order_on_p | 1.384 | 0.016 | 1.400 | |
pca | 4.271 | 0.016 | 4.293 | |
pg_to_canonical | 0.008 | 0.000 | 0.008 | |
plot_contrast_venn | 2.675 | 0.004 | 2.673 | |
plot_contrastogram | 3.269 | 0.060 | 3.330 | |
plot_data | 1.808 | 0.016 | 1.824 | |
plot_densities | 12.826 | 0.152 | 13.008 | |
plot_design | 0.877 | 0.000 | 0.879 | |
plot_exprs | 29.191 | 0.191 | 29.436 | |
plot_exprs_per_coef | 27.752 | 0.112 | 27.910 | |
plot_fit_summary | 2.570 | 0.016 | 2.585 | |
plot_heatmap | 2.405 | 0.016 | 2.426 | |
plot_matrix | 0.755 | 0.012 | 0.765 | |
plot_sample_nas | 8.663 | 0.020 | 8.698 | |
plot_subgroup_points | 6.494 | 0.028 | 6.532 | |
plot_summary | 17.085 | 0.056 | 17.167 | |
plot_venn | 0.015 | 0.000 | 0.015 | |
plot_venn_heatmap | 0.045 | 0.004 | 0.050 | |
plot_violins | 5.366 | 0.024 | 5.397 | |
plot_volcano | 14.076 | 0.139 | 14.241 | |
preprocess_rnaseq_counts | 0.551 | 0.004 | 0.557 | |
pull_columns | 0.003 | 0.001 | 0.003 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.011 | 0.000 | 0.011 | |
read_diann_proteingroups | 137.036 | 1.324 | 135.195 | |
read_fragpipe | 8.048 | 0.076 | 7.967 | |
read_maxquant_phosphosites | 2.196 | 0.016 | 2.216 | |
read_maxquant_proteingroups | 1.800 | 0.008 | 1.811 | |
read_metabolon | 17.285 | 0.060 | 17.375 | |
read_msigdt | 0.001 | 0.000 | 0.001 | |
read_olink | 1.723 | 0.028 | 1.741 | |
read_rectangles | 0.218 | 0.008 | 0.227 | |