Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-09 11:40:34 -0400 (Thu, 09 May 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" | 4748 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
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: 2024-05-09 04:51:54 -0000 (Thu, 09 May 2024) |
EndedAt: 2024-05-09 05:08:08 -0000 (Thu, 09 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 192.222 2.599 194.111
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.000 | 0.001 | |
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 | |
abstract_fit | 1.845 | 0.040 | 1.895 | |
add_adjusted_pvalues | 0.814 | 0.024 | 0.843 | |
add_assay_means | 0.612 | 0.008 | 0.621 | |
add_facetvars | 3.075 | 0.095 | 3.173 | |
add_opentargets_by_uniprot | 0.580 | 0.004 | 0.590 | |
add_psp | 0.719 | 0.000 | 0.722 | |
add_smiles | 0.663 | 0.012 | 0.673 | |
analysis | 0.541 | 0.004 | 0.546 | |
analyze | 17.578 | 0.108 | 17.710 | |
annotate_maxquant | 1.154 | 0.008 | 1.166 | |
annotate_uniprot_rest | 0.086 | 0.012 | 5.219 | |
assert_is_valid_sumexp | 0.836 | 0.032 | 0.867 | |
bin | 0.567 | 0.008 | 0.576 | |
biplot | 5.126 | 0.040 | 5.173 | |
biplot_corrections | 4.599 | 0.080 | 4.683 | |
biplot_covariates | 7.341 | 0.047 | 7.401 | |
block2lme | 0.004 | 0.000 | 0.004 | |
center | 2.938 | 0.064 | 3.007 | |
code | 7.006 | 0.052 | 7.069 | |
coefs | 1.039 | 0.032 | 1.070 | |
collapsed_entrezg_to_symbol | 0.001 | 0.000 | 0.000 | |
contrast_subgroup_cols | 0.824 | 0.024 | 0.846 | |
count_in | 0.001 | 0.000 | 0.001 | |
counts | 0.581 | 0.000 | 0.583 | |
counts2cpm | 0.581 | 0.000 | 0.583 | |
counts2tpm | 0.522 | 0.000 | 0.523 | |
cpm | 0.572 | 0.004 | 0.577 | |
create_design | 1.009 | 0.012 | 1.019 | |
default_formula | 21.572 | 0.416 | 21.845 | |
default_geom | 0.714 | 0.027 | 0.740 | |
default_sfile | 0.002 | 0.000 | 0.002 | |
demultiplex | 0.021 | 0.000 | 0.021 | |
dequantify | 0.003 | 0.000 | 0.003 | |
dot-merge | 0.021 | 0.000 | 0.022 | |
dot-plot_survival | 5.508 | 0.164 | 5.684 | |
dot-read_maxquant_proteingroups | 0.138 | 0.004 | 0.142 | |
download_contaminants | 0.029 | 0.000 | 4.673 | |
download_data | 0.000 | 0.000 | 0.001 | |
download_gtf | 0 | 0 | 0 | |
download_mcclain21 | 0 | 0 | 0 | |
dt2mat | 0.005 | 0.000 | 0.004 | |
enrichment | 1.679 | 0.048 | 1.731 | |
entrezg_to_symbol | 0.001 | 0.000 | 0.000 | |
explore_transformations | 4.849 | 0.076 | 4.932 | |
extract_coef_features | 6.358 | 0.072 | 6.438 | |
extract_rectangle | 0.143 | 0.008 | 0.151 | |
fdata | 0.811 | 0.000 | 0.812 | |
fdr2p | 1.338 | 0.012 | 1.349 | |
filter_exprs_replicated_in_some_subgroup | 1.418 | 0.024 | 1.438 | |
filter_features | 0.722 | 0.012 | 0.732 | |
filter_medoid | 1.108 | 0.004 | 1.115 | |
filter_samples | 0.798 | 0.020 | 0.816 | |
fit | 17.284 | 0.080 | 17.330 | |
fit_lmx | 5.939 | 0.048 | 5.980 | |
fitcoefs | 1.073 | 0.004 | 1.076 | |
fits | 1.044 | 0.012 | 1.054 | |
fitvars | 1.536 | 0.012 | 1.548 | |
fix_xlgenes | 0.002 | 0.000 | 0.002 | |
flevels | 0.604 | 0.008 | 0.613 | |
fnames | 0.647 | 0.008 | 0.656 | |
formula2str | 0.001 | 0.000 | 0.000 | |
fvalues | 0.626 | 0.027 | 0.655 | |
fvars | 0.585 | 0.008 | 0.594 | |
genome_to_orgdb | 0 | 0 | 0 | |
group_by_level | 0.001 | 0.000 | 0.001 | |
guess_fitsep | 0.700 | 0.024 | 0.726 | |
guess_maxquant_quantity | 0.006 | 0.002 | 0.007 | |
guess_sep | 0.740 | 0.006 | 0.744 | |
has_multiple_levels | 0.072 | 0.000 | 0.072 | |
hdlproteins | 0.072 | 0.008 | 0.089 | |
impute | 4.307 | 0.028 | 4.343 | |
invert_subgroups | 0.966 | 0.024 | 0.991 | |
is_collapsed_subset | 0.001 | 0.000 | 0.000 | |
is_diann_report | 0.558 | 0.044 | 0.770 | |
is_fastadt | 0.089 | 0.004 | 0.093 | |
is_file | 0 | 0 | 0 | |
is_fraction | 0.002 | 0.000 | 0.002 | |
is_imputed | 1.086 | 0.016 | 1.104 | |
is_positive_number | 0.002 | 0.000 | 0.002 | |
is_scalar_subset | 0.495 | 0.004 | 0.500 | |
is_sig | 1.731 | 0.004 | 1.738 | |
is_valid_formula | 0.061 | 0.000 | 0.062 | |
keep_connected_blocks | 0.793 | 0.008 | 0.799 | |
keep_connected_features | 1.025 | 0.008 | 1.028 | |
keep_replicated_features | 1.121 | 0.008 | 1.124 | |
label2index | 0.001 | 0.000 | 0.001 | |
list2mat | 0.000 | 0.000 | 0.001 | |
log2counts | 0.607 | 0.000 | 0.608 | |
log2cpm | 0.575 | 0.000 | 0.576 | |
log2diffs | 0.483 | 0.004 | 0.488 | |
log2proteins | 0.474 | 0.004 | 0.479 | |
log2sites | 0.489 | 0.000 | 0.490 | |
log2tpm | 0.605 | 0.012 | 0.618 | |
log2transform | 5.203 | 0.068 | 5.280 | |
logical2factor | 0.002 | 0.000 | 0.002 | |
make_alpha_palette | 0.844 | 0.012 | 0.854 | |
make_colors | 0.010 | 0.000 | 0.009 | |
make_volcano_dt | 1.194 | 0.004 | 1.200 | |
map_fvalues | 0.555 | 0.000 | 0.556 | |
matrix2sumexp | 1.355 | 0.004 | 1.358 | |
merge_sample_file | 0.642 | 0.004 | 0.647 | |
merge_sdata | 0.769 | 0.004 | 0.771 | |
message_df | 0.002 | 0.000 | 0.003 | |
modelvar | 2.239 | 0.024 | 2.262 | |
order_on_p | 1.335 | 0.004 | 1.338 | |
pca | 4.185 | 0.012 | 4.202 | |
pg_to_canonical | 0.009 | 0.000 | 0.008 | |
plot_contrast_venn | 2.701 | 0.008 | 2.703 | |
plot_contrastogram | 3.370 | 0.028 | 3.405 | |
plot_data | 1.793 | 0.016 | 1.809 | |
plot_densities | 13.090 | 0.128 | 13.236 | |
plot_design | 0.935 | 0.012 | 0.948 | |
plot_exprs | 29.406 | 0.231 | 29.685 | |
plot_exprs_per_coef | 27.109 | 0.020 | 27.172 | |
plot_fit_summary | 2.696 | 0.016 | 2.711 | |
plot_heatmap | 2.499 | 0.028 | 2.532 | |
plot_matrix | 0.750 | 0.016 | 0.764 | |
plot_sample_nas | 8.584 | 0.036 | 8.640 | |
plot_subgroup_points | 6.458 | 0.032 | 6.497 | |
plot_summary | 17.531 | 0.104 | 17.658 | |
plot_venn | 0.016 | 0.000 | 0.016 | |
plot_venn_heatmap | 0.045 | 0.008 | 0.054 | |
plot_violins | 5.403 | 0.040 | 5.450 | |
plot_volcano | 13.825 | 0.019 | 13.861 | |
preprocess_rnaseq_counts | 0.532 | 0.004 | 0.537 | |
pull_columns | 0.003 | 0.000 | 0.003 | |
read_affymetrix | 0 | 0 | 0 | |
read_contaminants | 0.012 | 0.000 | 0.012 | |
read_diann_proteingroups | 139.148 | 1.415 | 137.364 | |
read_fragpipe | 9.486 | 0.048 | 9.371 | |
read_maxquant_phosphosites | 2.143 | 0.004 | 2.151 | |
read_maxquant_proteingroups | 1.774 | 0.027 | 1.805 | |
read_metabolon | 16.677 | 0.068 | 16.765 | |
read_msigdt | 0.002 | 0.000 | 0.001 | |
read_olink | 1.720 | 0.024 | 1.734 | |
read_rectangles | 0.208 | 0.016 | 0.224 | |