Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:42 -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 hipathia package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hipathia.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 904/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hipathia 2.99.3 (landing page) Marta R. Hidalgo
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: hipathia |
Version: 2.99.3 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings hipathia_2.99.3.tar.gz |
StartedAt: 2023-02-28 05:45:37 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 06:11:38 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1561.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hipathia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings hipathia_2.99.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/hipathia.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 ‘hipathia/DESCRIPTION’ ... OK * this is package ‘hipathia’ version ‘2.99.3’ * 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 ‘hipathia’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: data 4.1Mb extdata 4.5Mb * 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 DAreport: no visible binding for global variable ‘ID’ DAreport: no visible binding for global variable ‘FDRp.value’ DAtop : <anonymous>: no visible binding for global variable ‘FDRp.value’ DAtop : <anonymous>: no visible binding for global variable ‘statistic’ DAtop : <anonymous>: no visible binding for global variable ‘p.value’ DAtop : <anonymous>: no visible binding for global variable ‘name’ DAtop : <anonymous>: no visible binding for global variable ‘logPV’ DAtop : <anonymous>: no visible binding for global variable ‘feature’ DAtop: no visible binding for global variable ‘name’ DAtop: no visible binding for global variable ‘logPV’ DAtop: no visible binding for global variable ‘direction’ get_edges_df: no visible binding for global variable ‘from’ get_edges_df: no visible binding for global variable ‘to’ nsig_plot: no visible binding for global variable ‘total’ nsig_plot: no visible binding for global variable ‘UPs’ nsig_plot: no visible binding for global variable ‘DOWNs’ nsig_plot: no visible binding for global variable ‘feature’ nsig_plot: no visible binding for global variable ‘UP’ nsig_plot: no visible binding for global variable ‘DOWN’ nsig_plot: no visible binding for global variable ‘Not’ nsig_plot: no visible binding for global variable ‘value’ nsig_plot: no visible binding for global variable ‘variable’ prepare_DAedges: no visible binding for global variable ‘to’ prepare_DAedges: no visible binding for global variable ‘functional’ prepare_DAedges: no visible binding for global variable ‘status’ prepare_DAedges: no visible binding for global variable ‘type’ prepare_DAnodes : <anonymous>: no visible binding for global variable ‘ID’ prepare_DAnodes : <anonymous>: no visible binding for global variable ‘FDRp.value’ prepare_DAnodes : <anonymous>: no visible binding for global variable ‘statistic’ prepare_DAnodes : <anonymous>: no visible binding for global variable ‘p.value’ prepare_edges: no visible binding for global variable ‘to’ prepare_edges: no visible binding for global variable ‘functional’ summary_plot: no visible binding for global variable ‘total’ summary_plot: no visible binding for global variable ‘UPs’ summary_plot: no visible binding for global variable ‘DOWNs’ summary_plot: no visible binding for global variable ‘name’ summary_plot: no visible binding for global variable ‘UP’ summary_plot: no visible binding for global variable ‘DOWN’ summary_plot: no visible binding for global variable ‘Not’ summary_plot: no visible binding for global variable ‘value’ summary_plot: no visible binding for global variable ‘variable’ summary_plot: no visible binding for global variable ‘UP.nodes’ summary_plot: no visible binding for global variable ‘DOWN.nodes’ summary_plot: no visible binding for global variable ‘nodes’ summary_plot: no visible binding for global variable ‘ratio.sigs’ summary_plot: no visible binding for global variable ‘ratio.UPs’ summary_plot: no visible binding for global variable ‘ratio.DOWNs’ Undefined global functions or variables: DOWN DOWN.nodes DOWNs FDRp.value ID Not UP UP.nodes UPs direction feature from functional logPV name nodes p.value ratio.DOWNs ratio.UPs ratio.sigs statistic status to total type value variable * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed quantify_terms 35.600 1.039 48.213 create_report 27.568 1.304 33.255 get_pathways_annotations 27.032 1.636 34.224 normalize_data 24.962 0.428 28.520 hipathia 24.581 0.596 28.076 pathway_comparison_plot 24.249 0.332 27.390 get_pathways_summary 23.585 0.833 27.332 get_node_names 23.294 1.100 26.691 load_pathways 23.782 0.500 27.058 visualize_report 23.293 0.668 26.841 translate_data 23.123 0.705 27.372 save_results 22.515 0.929 25.827 get_pathways_list 22.381 0.983 25.772 node_color 22.684 0.340 25.947 normalize_paths 21.848 0.412 25.447 get_path_names 21.583 0.628 25.060 node_color_per_de 20.652 0.451 23.964 get_go_names 4.923 0.272 8.037 * 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 ... ‘hipathia-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/hipathia.Rcheck/00check.log’ for details.
hipathia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL hipathia ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘hipathia’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (hipathia)
hipathia.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(hipathia) Loading required package: igraph Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: AnnotationHub Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:igraph': normalize, path, union The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: BiocFileCache Loading required package: dbplyr Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians The following object is masked from 'package:AnnotationHub': cache > > test_check("hipathia") Computing pathway... hsa03320 - PPAR signaling pathway hsa04012 - ErbB signaling pathway Computing pathway... hsa03320 - PPAR signaling pathway hsa04012 - ErbB signaling pathway translated ids = 3184 (1) untranslated ids = 3 (0.00094) multihit ids = 0 (0) [ FAIL 0 | WARN 0 | SKIP 0 | PASS 119 ] > > proc.time() user system elapsed 308.639 11.937 379.143
hipathia.Rcheck/hipathia-Ex.timings
name | user | system | elapsed | |
DAcomp | 1.788 | 0.096 | 1.883 | |
DAoverview | 0.475 | 0.012 | 0.486 | |
DAreport | 0.601 | 0.032 | 0.670 | |
DAsummary | 1.052 | 0.096 | 1.148 | |
DAtop | 0.812 | 0.031 | 0.843 | |
create_report | 27.568 | 1.304 | 33.255 | |
define_colors | 0.001 | 0.000 | 0.001 | |
do_pca | 0.030 | 0.012 | 0.042 | |
do_wilcoxon | 0.092 | 0.000 | 0.092 | |
get_go_names | 4.923 | 0.272 | 8.037 | |
get_node_names | 23.294 | 1.100 | 26.691 | |
get_nodes_data | 0.001 | 0.004 | 0.005 | |
get_path_names | 21.583 | 0.628 | 25.060 | |
get_paths_data | 0.005 | 0.000 | 0.005 | |
get_pathways_annotations | 27.032 | 1.636 | 34.224 | |
get_pathways_list | 22.381 | 0.983 | 25.772 | |
get_pathways_summary | 23.585 | 0.833 | 27.332 | |
heatmap_plot | 0.254 | 0.008 | 0.262 | |
hhead | 0.001 | 0.000 | 0.001 | |
hipathia | 24.581 | 0.596 | 28.076 | |
load_pathways | 23.782 | 0.500 | 27.058 | |
multiple_pca_plot | 0.030 | 0.000 | 0.031 | |
node_color | 22.684 | 0.340 | 25.947 | |
node_color_per_de | 20.652 | 0.451 | 23.964 | |
normalize_data | 24.962 | 0.428 | 28.520 | |
normalize_paths | 21.848 | 0.412 | 25.447 | |
paths_to_go_ancestor | 0.306 | 0.000 | 0.306 | |
pathway_comparison_plot | 24.249 | 0.332 | 27.390 | |
pca_plot | 0.022 | 0.000 | 0.022 | |
plotVG | 3.182 | 0.035 | 3.219 | |
quantify_terms | 35.600 | 1.039 | 48.213 | |
save_results | 22.515 | 0.929 | 25.827 | |
top_pathways | 0.009 | 0.003 | 0.012 | |
translate_data | 23.123 | 0.705 | 27.372 | |
visualize_report | 23.293 | 0.668 | 26.841 | |