Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:05 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 175/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bioCancer 1.34.0 (landing page) Karim Mezhoud
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the bioCancer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bioCancer.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: bioCancer |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bioCancer_1.34.0.tar.gz |
StartedAt: 2024-11-19 19:49:58 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 20:03:39 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 821.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: bioCancer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bioCancer_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/bioCancer.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bioCancer/DESCRIPTION’ ... OK * this is package ‘bioCancer’ version ‘1.34.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘bioCancer’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: app 3.3Mb extdata 2.6Mb * 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 ... OK * checking Rd files ... OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'bioCancer.Rd': ‘-package’ * 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 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/bioCancer.Rcheck/00check.log’ for details.
bioCancer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bioCancer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘bioCancer’ ... ** 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 (bioCancer)
bioCancer.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(bioCancer) Loading required package: radiant.data Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not Loading required package: ggplot2 Loading required package: lubridate Attaching package: 'lubridate' The following objects are masked from 'package:base': date, intersect, setdiff, union Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:magrittr': extract The following object is masked from 'package:testthat': matches Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Attaching package: 'radiant.data' The following objects are masked from 'package:lubridate': month, wday The following object is masked from 'package:ggplot2': diamonds The following object is masked from 'package:magrittr': set_attr The following object is masked from 'package:testthat': describe The following object is masked from 'package:base': date Loading required package: cBioPortalData Loading required package: AnVIL Loading required package: AnVILBase Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following object is masked from 'package:dplyr': count 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: BiocGenerics Attaching package: 'BiocGenerics' The following object is masked from 'package:radiant.data': normalize The following objects are masked from 'package:dplyr': combine, intersect, setdiff, union The following objects are masked from 'package:lubridate': intersect, setdiff, 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:dplyr': first, rename The following object is masked from 'package:tidyr': expand The following objects are masked from 'package:lubridate': second, second<- 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 objects are masked from 'package:dplyr': collapse, desc, slice The following object is masked from 'package:lubridate': %within% Loading required package: GenomeInfoDb Attaching package: 'GenomicRanges' The following object is masked from 'package:magrittr': subtract 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 Loading required package: XML > > test_check("bioCancer") getCancerStudies... OK getCaseLists (1/1) ... OK getClinicalData (1/1) ... OK getGeneticProfiles (1/1) ... OK getProfileData (1/1) ... OK ReactomeFI connection... OK [ FAIL 0 | WARN 1 | SKIP 2 | PASS 0 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test_funs.R:8:1', 'test_funs.R:20:1' [ FAIL 0 | WARN 1 | SKIP 2 | PASS 0 ] > > proc.time() user system elapsed 13.482 1.217 18.520
bioCancer.Rcheck/bioCancer-Ex.timings
name | user | system | elapsed | |
AnnotationFuncs | 0.167 | 0.013 | 0.288 | |
Edges_Diseases_obj | 0.001 | 0.000 | 0.002 | |
Mutation_obj | 0.070 | 0.010 | 0.524 | |
Node_Diseases_obj | 0.001 | 0.000 | 0.002 | |
Node_df_FreqIn | 0.000 | 0.001 | 0.001 | |
Node_obj_CNA_ProfData | 0.044 | 0.001 | 0.062 | |
Node_obj_FreqIn | 0 | 0 | 0 | |
Node_obj_Met_ProfData | 0.047 | 0.002 | 0.065 | |
Node_obj_mRNA_Classifier | 0.000 | 0.001 | 0.000 | |
Studies_obj | 0.004 | 0.001 | 0.005 | |
UnifyRowNames | 0.047 | 0.002 | 0.066 | |
attriColorGene | 0.050 | 0.006 | 0.074 | |
attriColorValue | 0.050 | 0.009 | 0.075 | |
attriColorVector | 0.047 | 0.007 | 0.099 | |
attriShape2Gene | 0 | 0 | 0 | |
attriShape2Node | 0 | 0 | 0 | |
bioCancer | 0.000 | 0.000 | 0.001 | |
checkDimensions | 0.050 | 0.008 | 0.092 | |
coffeewheel | 0 | 0 | 0 | |
coffeewheelOutput | 0.000 | 0.000 | 0.001 | |
displayTable | 0.047 | 0.008 | 0.099 | |
findPhantom | 0 | 0 | 0 | |
getEvidenceCodes | 0.001 | 0.001 | 0.000 | |
getFreqMutData | 0.047 | 0.008 | 0.080 | |
getGenesClassification | 0.105 | 0.005 | 0.154 | |
getListProfData | 0.044 | 0.001 | 0.100 | |
getList_Cases | 0.044 | 0.001 | 0.077 | |
getList_GenProfs | 0.043 | 0.001 | 0.063 | |
getOrthologs | 0 | 0 | 0 | |
getProfData | 0.044 | 0.002 | 0.091 | |
getSequensed_SampleSize | 0 | 0 | 0 | |
mapLists | 0.000 | 0.000 | 0.001 | |
metabologram | 0.000 | 0.001 | 0.000 | |
metabologramOutput | 0 | 0 | 0 | |
pickGO | 0.069 | 0.005 | 0.121 | |
pickRefSeq | 0.047 | 0.003 | 0.050 | |
reStrColorGene | 0.043 | 0.002 | 0.091 | |
reStrDimension | 0.044 | 0.001 | 0.274 | |
reStrDisease | 0.044 | 0.002 | 0.079 | |
removeNAs | 0 | 0 | 0 | |
renderCoffeewheel | 0 | 0 | 0 | |
renderMetabologram | 0 | 0 | 0 | |
returnTextAreaInput | 0 | 0 | 0 | |
translate | 0.084 | 0.004 | 0.089 | |
whichGeneList | 0.000 | 0.001 | 0.001 | |
widgetThumbnail | 0.000 | 0.000 | 0.001 | |