Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2024-02-22 11:37:02 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1386/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoStringNCTools 1.10.0  (landing page)
Nicole Ortogero
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/NanoStringNCTools
git_branch: RELEASE_3_18
git_last_commit: f70ebcf
git_last_commit_date: 2023-10-24 11:29:19 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for NanoStringNCTools on palomino4


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: 1.10.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoStringNCTools.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings NanoStringNCTools_1.10.0.tar.gz
StartedAt: 2024-02-22 04:21:23 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 04:23:16 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 113.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: NanoStringNCTools.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoStringNCTools.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings NanoStringNCTools_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/NanoStringNCTools.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'NanoStringNCTools/DESCRIPTION' ... OK
* this is package 'NanoStringNCTools' version '1.10.0'
* 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 '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 R 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 ... WARNING
checkRd: (5) NanoStringRccSet-class.Rd:147-150: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:151-154: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:155-158: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:163-166: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:167-170: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:171-174: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:175-179: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:180-184: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:185-187: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:188-190: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:191-193: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:194-196: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:202-221: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:229-236: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:237-241: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:242-246: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:247-251: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:252-256: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:257-261: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:262-266: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:267-271: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:277-281: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:282-286: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:287-292: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:298-303: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:304-312: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:318-324: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:330-332: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:338-341: \item in \describe must have non-empty label
checkRd: (5) NanoStringRccSet-class.Rd:342-344: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:65-67: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:68-71: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:72-75: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:76-79: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:80-83: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:84-86: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:87-89: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:90-93: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:94-96: \item in \describe must have non-empty label
checkRd: (5) SignatureSet.Rd:97-99: \item in \describe must have non-empty label
* 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 in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/NanoStringNCTools.Rcheck/00check.log'
for details.



Installation output

NanoStringNCTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL NanoStringNCTools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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, sort, 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 -- Thu Feb 22 04:23:06 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 
   9.92    0.48   10.37 

Example timings

NanoStringNCTools.Rcheck/NanoStringNCTools-Ex.timings

nameusersystemelapsed
NanoStringRccSet-autoplot0.340.010.38
NanoStringRccSet-class0.970.131.09
SignatureSet0.020.000.01
geom_beeswarm_interactive0.280.000.29
log2t000
normalize0.280.000.28
readNanoStringRccSet0.710.010.73
readRccFile0.040.000.05
readRlfFile0.050.000.05
sScale000
setQCFlags0.470.000.46
writeNanoStringRccSet0.390.000.39