Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the animalcules package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/animalcules.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 51/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
animalcules 1.15.0 (landing page) Yue Zhao
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: animalcules |
Version: 1.15.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings animalcules_1.15.0.tar.gz |
StartedAt: 2023-02-27 20:14:17 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 20:20:18 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 360.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: animalcules.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings animalcules_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/animalcules.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘animalcules/DESCRIPTION’ ... OK * this is package ‘animalcules’ version ‘1.15.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘animalcules’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’ Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’ Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’ See ‘/home/biocbuild/bbs-3.17-bioc/meat/animalcules.Rcheck/00install.out’ for details. * 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 ... NOTE alpha_div_boxplot: no visible binding for global variable ‘richness’ differential_abundance: no visible binding for global variable ‘padj’ differential_abundance: no visible binding for global variable ‘pValue’ differential_abundance: no visible binding for global variable ‘log2FoldChange’ diversities_help: no visible binding for global variable ‘x’ find_biomarker: no visible binding for global variable ‘rowname’ find_biomarker: no visible binding for global variable ‘importance’ find_biomarker: no visible binding for global variable ‘.’ find_biomarker: no visible binding for global variable ‘Overall’ find_biomarker: no visible binding for global variable ‘y’ find_biomarker: no visible binding for global variable ‘m’ find_biomarker: no visible binding for global variable ‘d’ relabu_barplot: no visible binding for global variable ‘.’ relabu_boxplot: no visible binding for global variable ‘.’ relabu_heatmap: no visible binding for global variable ‘.’ upsample_counts: no visible binding for global variable ‘.’ Undefined global functions or variables: . Overall d importance log2FoldChange m pValue padj richness rowname x y * 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 dimred_tsne 8.253 0.236 8.489 differential_abundance 6.773 0.216 6.989 find_biomarker 5.403 0.132 5.534 * 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 ... ‘animalcules.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/animalcules.Rcheck/00check.log’ for details.
animalcules.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL animalcules ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘animalcules’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’ Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’ Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’ Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’ Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’ Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’ Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’ ** testing if installed package keeps a record of temporary installation path * DONE (animalcules)
animalcules.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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(animalcules) Warning messages: 1: replacing previous import 'SummarizedExperiment::rownames' by 'biomformat::rownames' when loading 'animalcules' 2: replacing previous import 'SummarizedExperiment::colnames' by 'biomformat::colnames' when loading 'animalcules' 3: replacing previous import 'ape::where' by 'dplyr::where' when loading 'animalcules' > > test_check("animalcules") [ FAIL 0 | WARN 7 | SKIP 0 | PASS 38 ] [ FAIL 0 | WARN 7 | SKIP 0 | PASS 38 ] > > proc.time() user system elapsed 35.808 1.522 38.821
animalcules.Rcheck/animalcules-Ex.timings
name | user | system | elapsed | |
alpha_div_boxplot | 0.747 | 0.036 | 0.794 | |
alpha_div_test | 0.005 | 0.000 | 0.004 | |
counts_to_logcpm | 0.001 | 0.000 | 0.001 | |
counts_to_relabu | 0.003 | 0.000 | 0.002 | |
df_char_to_factor | 0.001 | 0.000 | 0.001 | |
differential_abundance | 6.773 | 0.216 | 6.989 | |
dimred_pca | 0.210 | 0.044 | 0.254 | |
dimred_pcoa | 0.174 | 0.012 | 0.186 | |
dimred_tsne | 8.253 | 0.236 | 8.489 | |
dimred_umap | 0.545 | 0.027 | 0.572 | |
diversities | 0 | 0 | 0 | |
diversities_help | 0 | 0 | 0 | |
diversity_beta_boxplot | 0.334 | 0.008 | 0.342 | |
diversity_beta_heatmap | 0.273 | 0.008 | 0.280 | |
diversity_beta_test | 0.127 | 0.000 | 0.128 | |
do_alpha_div_test | 0.089 | 0.004 | 0.092 | |
filter_categorize | 0.345 | 0.024 | 0.369 | |
filter_summary_bar_density | 0.375 | 0.024 | 0.399 | |
filter_summary_pie_box | 0.278 | 0.024 | 0.303 | |
find_biomarker | 5.403 | 0.132 | 5.534 | |
find_taxon_mat | 0.261 | 0.022 | 2.871 | |
find_taxonomy | 0.031 | 0.001 | 0.811 | |
find_taxonomy_300 | 0.031 | 0.000 | 0.866 | |
gini_simpson | 0 | 0 | 0 | |
grep_tid | 0 | 0 | 0 | |
inverse_simpson | 0 | 0 | 0 | |
is_categorical | 0 | 0 | 0 | |
is_integer0 | 0.001 | 0.000 | 0.000 | |
is_integer1 | 0.000 | 0.000 | 0.001 | |
mae_pick_organisms | 0.120 | 0.004 | 0.125 | |
mae_pick_samples | 0.094 | 0.000 | 0.093 | |
pct2str | 0 | 0 | 0 | |
percent | 0 | 0 | 0 | |
relabu_barplot | 2.464 | 0.187 | 2.651 | |
relabu_boxplot | 0.127 | 0.016 | 0.143 | |
relabu_heatmap | 0.156 | 0.024 | 0.180 | |
run_animalcules | 0 | 0 | 0 | |
shannon | 0.000 | 0.000 | 0.001 | |
simpson_index | 0 | 0 | 0 | |
upsample_counts | 0.012 | 0.004 | 0.017 | |