Multiple platform build/check report for BioC 3.13 - CHECK results for NanoStringNCTools on tokay2

Package: NanoStringNCTools

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NanoStringNCTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NanoStringNCTools_1.0.0.tar.gz

StartedAt: 2021-10-15 02:37:25 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 02:40:19 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 174.0 seconds

RetCode: 0

Status: OK

CheckDir: NanoStringNCTools.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NanoStringNCTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NanoStringNCTools_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/NanoStringNCTools.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NanoStringNCTools/DESCRIPTION' ... OK
* this is package 'NanoStringNCTools' version '1.0.0'
* 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 ... OK
* checking top-level files ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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: 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  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 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/NanoStringNCTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/NanoStringNCTools_1.0.0.tar.gz && rm -rf NanoStringNCTools.buildbin-libdir && mkdir NanoStringNCTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NanoStringNCTools.buildbin-libdir NanoStringNCTools_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL NanoStringNCTools_1.0.0.zip && rm NanoStringNCTools_1.0.0.tar.gz NanoStringNCTools_1.0.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  144k  100  144k    0     0   756k      0 --:--:-- --:--:-- --:--:--  758k

install for i386

* installing *source* package 'NanoStringNCTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NanoStringNCTools'
    finding HTML links ... done
    NanoStringRccSet-autoplot               html  
    NanoStringRccSet-class                  html  
    finding level-2 HTML links ... done

    SignatureSet                            html  
    geom_beeswarm_interactive               html  
    log2t                                   html  
    normalize                               html  
    readNanoStringRccSet                    html  
    readRccFile                             html  
    readRlfFile                             html  
    sScale                                  html  
    setQCFlags                              html  
    writeNanoStringRccSet                   html  
** 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

install for x64

* installing *source* package 'NanoStringNCTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NanoStringNCTools' as NanoStringNCTools_1.0.0.zip
* DONE (NanoStringNCTools)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'NanoStringNCTools' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ggplot2
[1] TRUE
> BiocGenerics:::testPackage("NanoStringNCTools")


RUNIT TEST PROTOCOL -- Fri Oct 15 02:39:55 2021 
*********************************************** 
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 
  13.56    0.32   13.87


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ggplot2
[1] TRUE
> BiocGenerics:::testPackage("NanoStringNCTools")


RUNIT TEST PROTOCOL -- Fri Oct 15 02:40:10 2021 
*********************************************** 
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 
  14.54    0.20   14.73

name	user	system	elapsed
NanoStringRccSet-autoplot	0.42	0.00	0.42
NanoStringRccSet-class	1.07	0.02	1.08
SignatureSet	0.02	0.00	0.02
geom_beeswarm_interactive	0.25	0.00	0.25
log2t	0	0	0
normalize	0.25	0.01	0.26
readNanoStringRccSet	0.86	0.02	0.88
readRccFile	0.06	0.00	0.06
readRlfFile	0.06	0.00	0.06
sScale	0	0	0
setQCFlags	0.55	0.00	0.55
writeNanoStringRccSet	0.44	0.00	0.44

name	user	system	elapsed
NanoStringRccSet-autoplot	0.44	0.00	0.44
NanoStringRccSet-class	1.11	0.02	1.12
SignatureSet	0.02	0.00	0.01
geom_beeswarm_interactive	0.27	0.00	0.27
log2t	0	0	0
normalize	0.26	0.00	0.26
readNanoStringRccSet	0.89	0.00	0.89
readRccFile	0.08	0.00	0.08
readRlfFile	0.06	0.00	0.07
sScale	0.02	0.00	0.01
setQCFlags	0.59	0.00	0.59
writeNanoStringRccSet	0.44	0.00	0.44

CHECK results for NanoStringNCTools on tokay2

Summary

Command output

Installation output

Tests output

Example timings