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CHECK report for flowTrans on tokay1

This page was generated on 2021-02-22 12:38:13 -0500 (Mon, 22 Feb 2021).

To the developers/maintainers of the flowTrans package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 636/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowTrans 1.42.0
Greg Finak
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/flowTrans
Branch: RELEASE_3_12
Last Commit: b7efe1a
Last Changed Date: 2020-10-27 10:38:16 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: flowTrans
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowTrans.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings flowTrans_1.42.0.tar.gz
StartedAt: 2021-02-22 02:55:47 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 02:57:35 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 107.4 seconds
RetCode: 0
Status:   OK   
CheckDir: flowTrans.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowTrans.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings flowTrans_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/flowTrans.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowTrans/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowTrans' version '1.42.0'
* 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 'flowTrans' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'flowCore' 'flowViz' 'flowClust'
A package should be listed in only one of these fields.
* 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 ... NOTE
Unexported object imported by a ':::' call: 'flowCore:::biexponential_transform'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'linlog'
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  summary.flowTransResult
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("_flowCore_biexponential_transform", ..., PACKAGE = "flowCore")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
flowTrans,flowFrame-character-character-logical-logical: no visible
  global function definition for 'norm2Filter'
Undefined global functions or variables:
  norm2Filter
* 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 ... NOTE
S3 methods shown with full name in documentation object 'summary.flowTransResult':
  'summary.flowTransResult'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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: 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/flowTrans.Rcheck/00check.log'
for details.



Installation output

flowTrans.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/flowTrans_1.42.0.tar.gz && rm -rf flowTrans.buildbin-libdir && mkdir flowTrans.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowTrans.buildbin-libdir flowTrans_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL flowTrans_1.42.0.zip && rm flowTrans_1.42.0.tar.gz flowTrans_1.42.0.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  9660  100  9660    0     0  45771      0 --:--:-- --:--:-- --:--:-- 46666

install for i386

* installing *source* package 'flowTrans' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowTrans'
    finding HTML links ... done
    extractParams                           html  
    flowTrans-methods                       html  
    flowTrans-package                       html  
    flowTrans                               html  
    flowTransResult-class                   html  
    summary-methods                         html  
    summary.flowTransResult                 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 'flowTrans' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowTrans' as flowTrans_1.42.0.zip
* DONE (flowTrans)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'flowTrans' successfully unpacked and MD5 sums checked

Tests output


Example timings

flowTrans.Rcheck/examples_i386/flowTrans-Ex.timings

nameusersystemelapsed
extractParams0.480.000.49
flowTrans-package2.990.083.06
flowTrans1.470.081.63
flowTransResult-class0.420.020.44
summary.flowTransResult0.380.030.40

flowTrans.Rcheck/examples_x64/flowTrans-Ex.timings

nameusersystemelapsed
extractParams0.340.000.34
flowTrans-package2.330.052.38
flowTrans1.140.061.22
flowTransResult-class0.360.020.37
summary.flowTransResult0.280.000.28