##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:NanoStringNCTools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings NanoStringNCTools_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/NanoStringNCTools.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘NanoStringNCTools/DESCRIPTION’ ... OK
* this is package ‘NanoStringNCTools’ version ‘1.15.0’
* 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 ‘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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NanoStringRccSet-class.Rd: ExpressionSet-class, AnnotatedDataFrame,
    MIAME, ExpressionSet, experimentData, preproc
  SignatureSet.Rd: NumericList
  readRlfFile.Rd: DataFrame-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/NanoStringNCTools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL NanoStringNCTools
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 Nov 21 03:19:50 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 
  9.213   0.332   9.537