Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1392/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringNCTools 1.14.0  (landing page)
Maddy Griswold
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/NanoStringNCTools
git_branch: RELEASE_3_20
git_last_commit: cdd61d5
git_last_commit_date: 2024-10-29 10:54:57 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for NanoStringNCTools on merida1

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.

raw results


Summary

Package: NanoStringNCTools
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2024-12-20 06:47:38 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:51:40 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 241.9 seconds
RetCode: 0
Status:   OK  
CheckDir: NanoStringNCTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/NanoStringNCTools.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘NanoStringNCTools/DESCRIPTION’ ... OK
* this is package ‘NanoStringNCTools’ version ‘1.14.0’
* 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.


Installation output

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)

Tests output

NanoStringNCTools.Rcheck/tests/run_unitTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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, saveRDS, 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 -- Fri Dec 20 06:51:22 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 
 23.345   0.638  24.434 

Example timings

NanoStringNCTools.Rcheck/NanoStringNCTools-Ex.timings

nameusersystemelapsed
NanoStringRccSet-autoplot0.8880.0350.957
NanoStringRccSet-class2.4770.4973.017
SignatureSet0.0530.0020.055
geom_beeswarm_interactive0.6590.0110.686
log2t0.0010.0000.001
normalize0.5350.0080.547
readNanoStringRccSet1.6800.0191.717
readRccFile0.1090.0050.114
readRlfFile0.0930.0010.097
sScale0.0060.0020.009
setQCFlags1.2380.0141.261
writeNanoStringRccSet0.8890.0210.920