Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the autonomics package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 102/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
autonomics 1.0.1 (landing page) Aditya Bhagwat
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: autonomics |
Version: 1.0.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings autonomics_1.0.1.tar.gz |
StartedAt: 2021-10-14 16:24:39 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:38:28 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 829.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: autonomics.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings autonomics_1.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘autonomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘autonomics’ version ‘1.0.1’ * 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 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 ... WARNING Undocumented code objects: ‘translate’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 23.352 0.770 24.209 is_sig 21.763 0.074 21.849 filter_medoid 19.520 0.701 20.234 pca 17.110 0.154 17.278 explore_imputations 15.431 0.215 15.659 plot_detections 14.436 0.329 14.777 read_somascan 13.629 0.258 13.903 fit_limma 13.398 0.110 13.533 read_rectangles 11.745 0.322 12.123 biplot_covariates 10.876 0.110 10.993 summarize_fit 10.506 0.293 10.809 read_metabolon 10.107 0.138 10.258 explore_transformations 7.908 0.173 8.095 plot_venn 7.921 0.111 8.047 sumexp_to_long_dt 7.014 0.190 7.207 subtract_baseline 6.988 0.089 7.087 analyze 6.767 0.186 6.959 plot_violins 6.739 0.118 6.875 read_proteingroups 6.691 0.082 6.790 log2transform 6.645 0.127 6.781 plot_features 6.584 0.064 6.655 plot_boxplots 6.319 0.073 6.398 biplot_corrections 5.461 0.144 5.608 * 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.13-bioc/meat/autonomics.Rcheck/00check.log’ for details.
autonomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL autonomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 102 ] > > proc.time() user system elapsed 173.772 3.887 177.918
autonomics.Rcheck/autonomics-Ex.timings
name | user | system | elapsed | |
AUTONOMICS_DATASETS | 0.000 | 0.001 | 0.001 | |
MAXQUANT_PATTERNS_PEPCOUNTS | 0.000 | 0.000 | 0.001 | |
MAXQUANT_PATTERNS_QUANTITY | 0.001 | 0.001 | 0.001 | |
TESTS | 0.001 | 0.000 | 0.000 | |
add_smiles | 3.347 | 0.146 | 4.076 | |
analysis | 1.876 | 0.127 | 2.054 | |
analyze | 6.767 | 0.186 | 6.959 | |
assert_is_valid_sumexp | 2.495 | 0.149 | 2.653 | |
biplot | 3.559 | 0.097 | 3.658 | |
biplot_corrections | 5.461 | 0.144 | 5.608 | |
biplot_covariates | 10.876 | 0.110 | 10.993 | |
center | 3.042 | 0.074 | 3.164 | |
contrast_subgroup_cols | 1.060 | 0.043 | 1.106 | |
contrastdefs | 3.332 | 0.055 | 3.390 | |
counts | 2.717 | 0.110 | 2.882 | |
counts2cpm | 2.847 | 0.125 | 2.974 | |
counts2tpm | 1.226 | 0.021 | 1.248 | |
cpm | 3.016 | 0.165 | 3.182 | |
create_design | 3.904 | 0.222 | 4.130 | |
create_sfile | 2.225 | 0.052 | 2.279 | |
default_formula | 0.868 | 0.039 | 0.907 | |
default_sfile | 0.366 | 0.005 | 0.372 | |
download_data | 3.228 | 0.180 | 3.425 | |
download_gtf | 0.000 | 0.001 | 0.001 | |
dt2mat | 0.003 | 0.000 | 0.004 | |
explore_imputations | 15.431 | 0.215 | 15.659 | |
explore_transformations | 7.908 | 0.173 | 8.095 | |
extract_features | 1.778 | 0.048 | 1.828 | |
extract_rectangle | 1.296 | 0.068 | 1.363 | |
fdata | 1.803 | 0.048 | 1.851 | |
filter_exprs_replicated_in_some_subgroup | 1.874 | 0.088 | 1.963 | |
filter_features | 1.186 | 0.064 | 1.250 | |
filter_medoid | 19.520 | 0.701 | 20.234 | |
filter_replicated | 1.970 | 0.065 | 2.037 | |
filter_samples | 1.155 | 0.065 | 1.224 | |
fit_limma | 13.398 | 0.110 | 13.533 | |
flevels | 1.767 | 0.048 | 1.827 | |
fnames | 1.586 | 0.033 | 1.621 | |
formula2str | 0.000 | 0.001 | 0.000 | |
fvalues | 1.548 | 0.039 | 1.587 | |
fvars | 1.919 | 0.054 | 1.975 | |
guess_maxquant_quantity | 3.198 | 0.077 | 3.280 | |
guess_sep | 0.000 | 0.000 | 0.001 | |
halfnormimpute | 1.379 | 0.034 | 1.414 | |
impute_systematic_nondetects | 4.116 | 0.119 | 4.241 | |
invert | 2.869 | 0.066 | 2.937 | |
is_imputed | 1.741 | 0.049 | 1.791 | |
is_sig | 21.763 | 0.074 | 21.849 | |
limma | 3.638 | 0.062 | 3.703 | |
log2counts | 3.156 | 0.118 | 3.277 | |
log2countsratios | 2.388 | 0.178 | 2.568 | |
log2cpm | 2.779 | 0.091 | 2.873 | |
log2cpmratios | 3.362 | 0.133 | 3.500 | |
log2tpm | 2.538 | 0.122 | 2.684 | |
log2tpmratios | 2.88 | 0.06 | 2.94 | |
log2transform | 6.645 | 0.127 | 6.781 | |
make_volcano_dt | 3.478 | 0.058 | 3.541 | |
matrix2sumexp | 2.561 | 0.085 | 2.656 | |
merge_sdata | 1.222 | 0.050 | 1.272 | |
merge_sfile | 2.547 | 0.150 | 2.779 | |
message_df | 0.004 | 0.001 | 0.004 | |
occupancies | 2.458 | 0.077 | 2.542 | |
pca | 17.110 | 0.154 | 17.278 | |
plot_boxplots | 6.319 | 0.073 | 6.398 | |
plot_contrastogram | 1.756 | 0.049 | 1.808 | |
plot_data | 2.546 | 0.075 | 2.625 | |
plot_densities | 4.066 | 0.084 | 4.154 | |
plot_detections | 14.436 | 0.329 | 14.777 | |
plot_features | 6.584 | 0.064 | 6.655 | |
plot_venn | 7.921 | 0.111 | 8.047 | |
plot_violins | 6.739 | 0.118 | 6.875 | |
plot_volcano | 3.779 | 0.073 | 3.856 | |
preprocess_rnaseq_counts | 3.216 | 0.130 | 3.349 | |
proteingroups | 2.087 | 0.052 | 2.141 | |
read_affymetrix | 1.287 | 0.121 | 1.415 | |
read_metabolon | 10.107 | 0.138 | 10.258 | |
read_proteingroups | 6.691 | 0.082 | 6.790 | |
read_rectangles | 11.745 | 0.322 | 12.123 | |
read_rnaseq_counts | 23.352 | 0.770 | 24.209 | |
read_somascan | 13.629 | 0.258 | 13.903 | |
rm_singleton_samples | 1.360 | 0.030 | 1.392 | |
scaledlibsizes | 2.239 | 0.160 | 2.401 | |
sdata | 1.747 | 0.045 | 1.793 | |
slevels | 1.649 | 0.039 | 1.690 | |
snames | 1.691 | 0.046 | 1.738 | |
split_by_svar | 1.411 | 0.050 | 1.463 | |
split_extract | 1.211 | 0.068 | 1.281 | |
standardize_maxquant_snames | 0.004 | 0.001 | 0.006 | |
subgroup_matrix | 1.218 | 0.051 | 1.271 | |
subtract_baseline | 6.988 | 0.089 | 7.087 | |
sumexp2mae | 3.018 | 0.088 | 3.107 | |
sumexp_to_long_dt | 7.014 | 0.190 | 7.207 | |
summarize_fit | 10.506 | 0.293 | 10.809 | |
svalues | 1.907 | 0.059 | 1.967 | |
svars | 1.628 | 0.051 | 1.680 | |
tpm | 2.501 | 0.111 | 2.615 | |
values | 1.877 | 0.080 | 1.966 | |
venn_detects | 1.742 | 0.050 | 1.794 | |
weights | 3.000 | 0.112 | 3.115 | |
zero_to_na | 0.026 | 0.003 | 0.027 | |