Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -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 1069/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
isomiRs 1.34.0 (landing page) Lorena Pantano
| 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 isomiRs package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/isomiRs.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: isomiRs |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings isomiRs_1.34.0.tar.gz |
StartedAt: 2024-11-19 23:21:25 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 23:28:45 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 439.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: isomiRs.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings isomiRs_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/isomiRs.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 ‘isomiRs/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘isomiRs’ 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 ... NOTE Found the following hidden files and directories: .travis.yml 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 ‘isomiRs’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 .clean_noise: no visible binding for global variable ‘total’ .clean_noise: no visible binding for global variable ‘hits’ .remove_gt_n_changes: no visible binding for global variable ‘changes’ isoAnnotate: no visible binding for global variable ‘pct’ isoCounts: no visible global function definition for ‘as.tibble’ isoPlot: no visible global function definition for ‘across’ isoPlot: no visible global function definition for ‘everything’ isoPlot: no visible binding for global variable ‘iso_sample’ isoPlotPosition: no visible global function definition for ‘across’ isoPlotPosition: no visible global function definition for ‘everything’ isoPlotPosition: no visible binding for global variable ‘iso_sample’ isoSelect.IsomirDataSeq: no visible global function definition for ‘across’ isoSelect.IsomirDataSeq: no visible global function definition for ‘everything’ mirna2targetscan: no visible binding for global variable ‘targetscan.Hs.egMIRNA’ mirna2targetscan: no visible binding for global variable ‘targetscan.Hs.egMIRBASE2FAMILY’ mirna2targetscan: no visible binding for global variable ‘targetscan.Hs.egTARGETS’ mirna2targetscan: no visible binding for global variable ‘targetscan.Hs.egTARGETSFULL’ mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egMIRNA’ mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egMIRBASE2FAMILY’ mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egTARGETS’ mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egTARGETSFULL’ isoSelect,IsomirDataSeq: no visible global function definition for ‘across’ isoSelect,IsomirDataSeq: no visible global function definition for ‘everything’ Undefined global functions or variables: across as.tibble changes everything hits iso_sample pct targetscan.Hs.egMIRBASE2FAMILY targetscan.Hs.egMIRNA targetscan.Hs.egTARGETS targetscan.Hs.egTARGETSFULL targetscan.Mm.egMIRBASE2FAMILY targetscan.Mm.egMIRNA targetscan.Mm.egTARGETS targetscan.Mm.egTARGETSFULL total * 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 isoNetwork 5.138 0.048 5.214 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/isomiRs.Rcheck/00check.log’ for details.
isomiRs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL isomiRs ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘isomiRs’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB Registered S3 method overwritten by 'GGally': method from +.gg ggplot2 ** 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 (isomiRs)
isomiRs.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(isomiRs) 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: BiocGenerics Attaching package: 'BiocGenerics' 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 object is masked from 'package:utils': findMatches 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 > > test_check("isomiRs") Dimmension of cor matrix: 20 20 Dimmension of cor matrix: 3 2 Dimmension of cor matrix: 3 2 Dimmension of cor matrix: 0 0 [ FAIL 0 | WARN 6 | SKIP 0 | PASS 25 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 25 ] > > proc.time() user system elapsed 13.227 0.683 13.947
isomiRs.Rcheck/isomiRs-Ex.timings
name | user | system | elapsed | |
IsomirDataSeq | 1.489 | 0.074 | 1.564 | |
IsomirDataSeqFromFiles | 1.103 | 0.020 | 1.111 | |
IsomirDataSeqFromMirtop | 0.610 | 0.007 | 0.616 | |
IsomirDataSeqFromRawData | 1.140 | 0.019 | 1.150 | |
counts | 0.079 | 0.012 | 0.091 | |
design | 0.139 | 0.012 | 0.151 | |
findTargets | 0.054 | 0.001 | 0.056 | |
isoAnnotate | 2.848 | 0.138 | 2.990 | |
isoCounts | 1.005 | 0.025 | 1.034 | |
isoDE | 3.336 | 0.038 | 3.378 | |
isoNetwork | 5.138 | 0.048 | 5.214 | |
isoNorm | 1.186 | 0.018 | 1.206 | |
isoPlot | 0.478 | 0.014 | 0.492 | |
isoPlotPosition | 0.273 | 0.008 | 0.282 | |
isoSelect | 0.112 | 0.006 | 0.118 | |
isoTop | 0.206 | 0.016 | 0.222 | |
mirna2targetscan | 1.210 | 0.053 | 1.287 | |