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 15:42 -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 1365/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NanoStringNCTools 1.13.0 (landing page) Maddy Griswold
| 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 NanoStringNCTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoStringNCTools.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: NanoStringNCTools |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoStringNCTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoStringNCTools_1.13.0.tar.gz |
StartedAt: 2024-06-10 07:04:33 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 07:09:09 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 276.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NanoStringNCTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoStringNCTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoStringNCTools_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/NanoStringNCTools.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NanoStringNCTools/DESCRIPTION’ ... OK * this is package ‘NanoStringNCTools’ version ‘1.13.0’ * 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 ‘NanoStringNCTools’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 autoplot.NanoStringRccSet : <anonymous>: warning in switch(x[2], A = qcCutoffs[["BindingDensity"]][["maximumBD"]], B = qcCutoffs[["BindingDensity"]][["maximumBD"]], C = qcCutoffs[["BindingDensity"]][["maximumBD"]], D = qcCutoffs[["BindingDensity"]][["maximumBD"]], E = qcCutoffs[["BindingDensity"]][["maximumBD"]], G = qcCutoffs[["BindingDensity"]][["maximumBD"]], H = qcCutoffs[["BindingDensity"]][["maximumBD"]], P = qcCutoffs[["BindingDensity"]][["maximumBDSprint"]], default = qcCutoffs[["BindingDensity"]][["maximumBD"]]): partial argument match of 'E' to 'EXPR' setQCFlags,NanoStringRccSet : <anonymous>: warning in switch(x[2], A = maxBindDen, B = maxBindDen, C = maxBindDen, D = maxBindDen, E = maxBindDen, G = maxBindDen, H = maxBindDen, P = maxBindDenSprint, default = maxBindDen): partial argument match of 'E' to 'EXPR' autoplot.NanoStringRccSet: no visible binding for global variable ‘xend’ autoplot.NanoStringRccSet: no visible binding for global variable ‘passingThreshold’ autoplot.NanoStringRccSet: no visible binding for global variable ‘GeomMean’ autoplot.NanoStringRccSet: no visible binding for global variable ‘h’ autoplot.NanoStringRccSet: no visible binding for global variable ‘label’ Undefined global functions or variables: GeomMean h label passingThreshold xend * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.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/NanoStringNCTools.Rcheck/00check.log’ for details.
NanoStringNCTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NanoStringNCTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘NanoStringNCTools’ ... ** using staged installation ** R ** 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 (NanoStringNCTools)
NanoStringNCTools.Rcheck/tests/run_unitTests.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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. > require("NanoStringNCTools") || stop("unable to load NanoStringNCTools package") Loading required package: NanoStringNCTools Loading required package: Biobase 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, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: S4Vectors Loading required package: stats4 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: ggplot2 [1] TRUE > BiocGenerics:::testPackage("NanoStringNCTools") RUNIT TEST PROTOCOL -- Mon Jun 10 07:08:51 2024 *********************************************** Number of test functions: 52 Number of errors: 0 Number of failures: 0 1 Test Suite : NanoStringNCTools RUnit Tests - 52 test functions, 0 errors, 0 failures Number of test functions: 52 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 24.663 0.686 27.175
NanoStringNCTools.Rcheck/NanoStringNCTools-Ex.timings
name | user | system | elapsed | |
NanoStringRccSet-autoplot | 0.928 | 0.034 | 1.117 | |
NanoStringRccSet-class | 2.582 | 0.484 | 3.457 | |
SignatureSet | 0.053 | 0.002 | 0.063 | |
geom_beeswarm_interactive | 0.653 | 0.012 | 0.754 | |
log2t | 0.001 | 0.001 | 0.002 | |
normalize | 0.576 | 0.010 | 0.659 | |
readNanoStringRccSet | 1.791 | 0.026 | 2.025 | |
readRccFile | 0.111 | 0.004 | 0.122 | |
readRlfFile | 0.099 | 0.002 | 0.116 | |
sScale | 0.005 | 0.002 | 0.009 | |
setQCFlags | 1.323 | 0.013 | 1.513 | |
writeNanoStringRccSet | 0.940 | 0.025 | 1.101 | |