Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:36:32 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 111/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.10.2 (landing page) Aditya Bhagwat
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.1 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. |
Package: autonomics |
Version: 1.10.2 |
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings autonomics_1.10.2.tar.gz |
StartedAt: 2024-03-27 22:28:27 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 22:38:57 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 630.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: autonomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings autonomics_1.10.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/autonomics.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * 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 '1.10.2' * 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 R 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_rnaseq_counts 18.36 0.58 18.79 is_sig 14.20 0.25 14.35 pca 11.78 0.19 12.05 filter_medoid 11.18 0.47 11.59 explore_imputations 10.99 0.28 11.42 fit_limma 10.18 0.25 10.36 read_rectangles 9.72 0.57 10.50 read_somascan 9.53 0.19 9.70 plot_detections 8.74 0.36 8.95 read_metabolon 8.46 0.17 8.72 summarize_fit 7.81 0.29 7.92 biplot_covariates 6.86 0.26 7.19 plot_features 5.59 0.14 5.86 subtract_baseline 5.08 0.24 5.39 biplot_corrections 5.11 0.09 5.34 analyze 4.74 0.23 5.02 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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-3.18-bioc/meat/autonomics.Rcheck/00check.log' for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'autonomics' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '/' ** 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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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 object is masked from 'package:stats': biplot > > test_check("autonomics") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 103 ] > > proc.time() user system elapsed 116.18 5.59 121.12
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0 | 0 | 0 | |
MAXQUANT_PATTERNS_PEPCOUNTS | 0 | 0 | 0 | |
MAXQUANT_PATTERNS_QUANTITY | 0 | 0 | 0 | |
TESTS | 0 | 0 | 0 | |
add_smiles | 1.98 | 0.15 | 2.36 | |
analysis | 1.87 | 0.10 | 1.95 | |
analyze | 4.74 | 0.23 | 5.02 | |
assert_is_valid_sumexp | 1.66 | 0.30 | 2.14 | |
biplot | 2.77 | 0.27 | 3.13 | |
biplot_corrections | 5.11 | 0.09 | 5.34 | |
biplot_covariates | 6.86 | 0.26 | 7.19 | |
center | 2.20 | 0.21 | 2.39 | |
contrast_subgroup_cols | 0.75 | 0.12 | 0.92 | |
contrastdefs | 1.81 | 0.08 | 1.74 | |
counts | 1.55 | 0.09 | 1.67 | |
counts2cpm | 2.09 | 0.13 | 2.18 | |
counts2tpm | 1.35 | 0.06 | 1.36 | |
cpm | 1.31 | 0.19 | 1.46 | |
create_design | 2.48 | 0.16 | 2.59 | |
create_sfile | 1.19 | 0.12 | 1.22 | |
default_formula | 0.84 | 0.03 | 0.92 | |
default_sfile | 0.26 | 0.00 | 0.26 | |
download_data | 1.68 | 0.36 | 2.32 | |
download_gtf | 0 | 0 | 0 | |
dt2mat | 0.01 | 0.00 | 0.01 | |
explore_imputations | 10.99 | 0.28 | 11.42 | |
explore_transformations | 4.18 | 0.33 | 4.44 | |
extract_features | 1.21 | 0.09 | 1.20 | |
extract_rectangle | 0.75 | 0.22 | 1.03 | |
fdata | 1.00 | 0.13 | 1.00 | |
filter_exprs_replicated_in_some_subgroup | 1.57 | 0.20 | 1.84 | |
filter_features | 1.07 | 0.16 | 1.27 | |
filter_medoid | 11.18 | 0.47 | 11.59 | |
filter_replicated | 1.23 | 0.18 | 1.30 | |
filter_samples | 0.94 | 0.07 | 1.06 | |
fit_limma | 10.18 | 0.25 | 10.36 | |
flevels | 1.33 | 0.11 | 1.31 | |
fnames | 1.23 | 0.07 | 1.17 | |
formula2str | 0 | 0 | 0 | |
fvalues | 1.14 | 0.08 | 1.13 | |
fvars | 0.96 | 0.10 | 0.93 | |
guess_maxquant_quantity | 2.07 | 0.20 | 2.18 | |
guess_sep | 0 | 0 | 0 | |
halfnormimpute | 1.35 | 0.09 | 1.43 | |
impute_systematic_nondetects | 2.45 | 0.19 | 2.55 | |
invert | 1.66 | 0.11 | 1.64 | |
is_imputed | 0.97 | 0.08 | 0.92 | |
is_sig | 14.20 | 0.25 | 14.35 | |
limma | 1.80 | 0.15 | 1.79 | |
log2counts | 1.47 | 0.08 | 1.50 | |
log2countsratios | 1.31 | 0.08 | 1.39 | |
log2cpm | 1.81 | 0.14 | 1.93 | |
log2cpmratios | 1.61 | 0.09 | 1.67 | |
log2tpm | 1.58 | 0.09 | 1.64 | |
log2tpmratios | 1.92 | 0.08 | 1.93 | |
log2transform | 3.77 | 0.17 | 3.84 | |
make_volcano_dt | 2.05 | 0.16 | 2.15 | |
matrix2sumexp | 1.56 | 0.14 | 1.72 | |
merge_sdata | 0.72 | 0.24 | 1.03 | |
merge_sfile | 1.59 | 0.21 | 1.83 | |
message_df | 0 | 0 | 0 | |
occupancies | 1.50 | 0.14 | 1.50 | |
pca | 11.78 | 0.19 | 12.05 | |
plot_boxplots | 3.74 | 0.22 | 4.04 | |
plot_contrastogram | 1.59 | 0.16 | 1.88 | |
plot_data | 1.53 | 0.22 | 1.83 | |
plot_densities | 2.25 | 0.04 | 2.39 | |
plot_detections | 8.74 | 0.36 | 8.95 | |
plot_features | 5.59 | 0.14 | 5.86 | |
plot_venn | 4.85 | 0.08 | 4.90 | |
plot_violins | 4.48 | 0.15 | 4.75 | |
plot_volcano | 3.08 | 0.21 | 3.16 | |
preprocess_rnaseq_counts | 2.67 | 0.09 | 2.75 | |
proteingroups | 1.25 | 0.08 | 1.23 | |
read_affymetrix | 1.32 | 0.17 | 1.50 | |
read_metabolon | 8.46 | 0.17 | 8.72 | |
read_proteingroups | 4.13 | 0.24 | 4.17 | |
read_rectangles | 9.72 | 0.57 | 10.50 | |
read_rnaseq_counts | 18.36 | 0.58 | 18.79 | |
read_somascan | 9.53 | 0.19 | 9.70 | |
rm_singleton_samples | 0.70 | 0.03 | 0.73 | |
scaledlibsizes | 1.65 | 0.13 | 1.76 | |
sdata | 1.13 | 0.11 | 1.13 | |
slevels | 1.09 | 0.06 | 1.06 | |
snames | 1.30 | 0.14 | 1.28 | |
split_by_svar | 1.18 | 0.08 | 1.16 | |
split_extract | 0.77 | 0.07 | 0.93 | |
standardize_maxquant_snames | 0 | 0 | 0 | |
subgroup_matrix | 0.92 | 0.08 | 1.12 | |
subtract_baseline | 5.08 | 0.24 | 5.39 | |
sumexp2mae | 2.10 | 0.14 | 2.29 | |
sumexp_to_long_dt | 4.50 | 0.43 | 4.86 | |
summarize_fit | 7.81 | 0.29 | 7.92 | |
svalues | 1.06 | 0.16 | 1.10 | |
svars | 1.14 | 0.12 | 1.15 | |
tpm | 1.59 | 0.03 | 1.61 | |
values | 1.25 | 0.15 | 1.31 | |
venn_detects | 1.36 | 0.03 | 1.24 | |
weights | 1.94 | 0.22 | 1.84 | |
zero_to_na | 0.03 | 0.00 | 0.03 | |