Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 950/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hipathia 3.5.0 (landing page) Marta R. Hidalgo
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the hipathia package: - 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 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: hipathia |
Version: 3.5.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hipathia.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings hipathia_3.5.0.tar.gz |
StartedAt: 2024-06-10 03:55:05 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 04:11:39 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 993.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hipathia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hipathia.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings hipathia_3.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'hipathia/DESCRIPTION' ... OK * this is package 'hipathia' version '3.5.0' * 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 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 4.4Mb * 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 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed quantify_terms 24.88 4.00 29.94 create_report 20.41 1.39 22.98 get_pathways_annotations 19.22 1.95 21.40 visualize_report 17.86 1.36 19.44 hipathia 17.92 1.17 19.67 load_pathways 17.55 1.22 19.66 normalize_data 17.20 1.20 18.72 normalize_paths 17.30 1.05 19.17 pathway_comparison_plot 16.97 1.30 18.42 get_path_names 16.62 1.23 17.98 save_results 16.28 1.16 17.86 node_color 15.93 1.19 17.24 get_pathways_list 15.52 1.03 16.64 get_pathways_summary 15.11 1.29 16.50 node_color_per_de 15.08 1.16 16.36 translate_data 14.69 1.25 16.11 get_node_names 14.78 1.11 16.00 * 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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck/00check.log' for details.
hipathia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL hipathia ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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, 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 object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 1 | SKIP 0 | PASS 119 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 119 ] > > proc.time() user system elapsed 221.92 29.21 254.37
hipathia.Rcheck/hipathia-Ex.timings
name | user | system | elapsed | |
DAcomp | 0.82 | 0.15 | 0.98 | |
DAoverview | 0.29 | 0.04 | 0.33 | |
DAreport | 0.64 | 0.07 | 2.90 | |
DAsummary | 1.14 | 0.10 | 1.24 | |
DAtop | 0.64 | 0.01 | 0.66 | |
create_report | 20.41 | 1.39 | 22.98 | |
define_colors | 0 | 0 | 0 | |
do_pca | 0.03 | 0.02 | 0.05 | |
do_wilcoxon | 0.06 | 0.01 | 0.07 | |
get_go_names | 2.97 | 0.91 | 4.02 | |
get_node_names | 14.78 | 1.11 | 16.00 | |
get_nodes_data | 0.00 | 0.02 | 0.02 | |
get_path_names | 16.62 | 1.23 | 17.98 | |
get_paths_data | 0.02 | 0.00 | 0.02 | |
get_pathways_annotations | 19.22 | 1.95 | 21.40 | |
get_pathways_list | 15.52 | 1.03 | 16.64 | |
get_pathways_summary | 15.11 | 1.29 | 16.50 | |
heatmap_plot | 0.14 | 0.03 | 0.18 | |
hhead | 0 | 0 | 0 | |
hipathia | 17.92 | 1.17 | 19.67 | |
load_pathways | 17.55 | 1.22 | 19.66 | |
multiple_pca_plot | 0.02 | 0.01 | 0.03 | |
node_color | 15.93 | 1.19 | 17.24 | |
node_color_per_de | 15.08 | 1.16 | 16.36 | |
normalize_data | 17.20 | 1.20 | 18.72 | |
normalize_paths | 17.30 | 1.05 | 19.17 | |
paths_to_go_ancestor | 0.22 | 0.04 | 0.27 | |
pathway_comparison_plot | 16.97 | 1.30 | 18.42 | |
pca_plot | 0.03 | 0.02 | 0.05 | |
plotVG | 1.00 | 0.07 | 1.10 | |
quantify_terms | 24.88 | 4.00 | 29.94 | |
save_results | 16.28 | 1.16 | 17.86 | |
top_pathways | 0.01 | 0.00 | 0.02 | |
translate_data | 14.69 | 1.25 | 16.11 | |
visualize_report | 17.86 | 1.36 | 19.44 | |