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CHECK report for flowBeads on tokay1

This page was generated on 2019-04-13 11:22:55 -0400 (Sat, 13 Apr 2019).

Package 524/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowBeads 1.20.1
Nikolas Pontikos
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/flowBeads
Branch: RELEASE_3_8
Last Commit: f1f1b24
Last Changed Date: 2019-01-04 13:31:32 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowBeads
Version: 1.20.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowBeads_1.20.1.tar.gz
StartedAt: 2019-04-13 02:14:45 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:16:55 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 130.0 seconds
RetCode: 0
Status:  OK  
CheckDir: flowBeads.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowBeads_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowBeads.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowBeads/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowBeads' version '1.20.1'
* 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 whether package 'flowBeads' 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' 'rrcov'
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
Namespaces in Imports field not imported from:
  'knitr' 'rrcov' 'xtable'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Biobase' 'methods' 'rrcov'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BeadFlowFrame: no visible binding for global variable 'filename'
BeadFlowFrame: no visible global function definition for 'read.csv2'
BeadFlowFrame: no visible global function definition for 'new'
mefTransform: no visible global function definition for 'new'
absoluteNormalise,GatedBeadFlowFrame-data.frame: no visible global
  function definition for 'lm'
gateBeads,BeadFlowFrame: no visible global function definition for 'as'
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
  definition for 'quantile'
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
  definition for 'kmeans'
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
  definition for 'median'
gateBeads,BeadFlowFrame: no visible binding for global variable 'sd'
gateBeads,BeadFlowFrame: no visible global function definition for 'lm'
plot,BeadFlowFrame-character: no visible global function definition for
  'par'
plot,BeadFlowFrame-character: no visible global function definition for
  'hist'
plot,BeadFlowFrame-character: no visible global function definition for
  'segments'
plot,BeadFlowFrame-character: no visible global function definition for
  'title'
plot,GatedBeadFlowFrame-character: no visible global function
  definition for 'par'
plot,GatedBeadFlowFrame-character: no visible global function
  definition for 'hist'
plot,GatedBeadFlowFrame-character: no visible global function
  definition for 'abline'
plot,GatedBeadFlowFrame-character: no visible global function
  definition for 'segments'
plot,GatedBeadFlowFrame-character: no visible global function
  definition for 'title'
relativeNormalise,GatedBeadFlowFrame-GatedBeadFlowFrame: no visible
  global function definition for 'lm'
Undefined global functions or variables:
  abline as filename hist kmeans lm median new par quantile read.csv2
  sd segments title
Consider adding
  importFrom("graphics", "abline", "hist", "par", "segments", "title")
  importFrom("methods", "as", "new")
  importFrom("stats", "kmeans", "lm", "median", "quantile", "sd")
  importFrom("utils", "read.csv2")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowBeads.Rcheck/00check.log'
for details.



Installation output

flowBeads.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flowBeads_1.20.1.tar.gz && rm -rf flowBeads.buildbin-libdir && mkdir flowBeads.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowBeads.buildbin-libdir flowBeads_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowBeads_1.20.1.zip && rm flowBeads_1.20.1.tar.gz flowBeads_1.20.1.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  590k  100  590k    0     0  10.9M      0 --:--:-- --:--:-- --:--:-- 11.7M

install for i386

* installing *source* package 'flowBeads' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowBeads'
    finding HTML links ... done
    BeadFlowFrame-class                     html  
    finding level-2 HTML links ... done

    GatedBeadFlowFrame-class                html  
    absoluteNormalise-methods               html  
    beads1                                  html  
    beads2                                  html  
    cytocalmef                              html  
    dakomef                                 html  
    flowBeads-package                       html  
    gateBeads-methods                       html  
    generateReport-methods                  html  
    getClusteringStats-methods              html  
    getDate-methods                         html  
    getMEFparams-methods                    html  
    getMEFtransform-methods                 html  
    getParams-methods                       html  
    getTransformFunction-methods            html  
    hasMEF-methods                          html  
    length-methods                          html  
    mefTransform                            html  
    plot-methods                            html  
    relativeNormalise-methods               html  
    show-methods                            html  
    toMEF-methods                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowBeads' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowBeads' as flowBeads_1.20.1.zip
* DONE (flowBeads)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowBeads' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

flowBeads.Rcheck/examples_i386/flowBeads-Ex.timings

nameusersystemelapsed
gateBeads-methods0.380.050.55

flowBeads.Rcheck/examples_x64/flowBeads-Ex.timings

nameusersystemelapsed
gateBeads-methods0.690.030.72