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CHECK report for Polyfit on tokay2

This page was generated on 2020-10-17 11:57:26 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Polyfit PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1333/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Polyfit 1.22.0
Conrad Burden
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Polyfit
Branch: RELEASE_3_11
Last Commit: 9e8420a
Last Changed Date: 2020-04-27 14:41:26 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Polyfit
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Polyfit.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Polyfit_1.22.0.tar.gz
StartedAt: 2020-10-17 06:59:21 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:04:53 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 331.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Polyfit.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Polyfit.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Polyfit_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Polyfit.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 'Polyfit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Polyfit' version '1.22.0'
* 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 'Polyfit' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Polyfit.Rcheck/00install.out' for details.
* 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
levelPValues: no visible global function definition for 'hist'
levelPValues: no visible global function definition for 'lm'
levelPValues: no visible global function definition for 'nlm'
levelPValues: no visible global function definition for 'density'
levelPValues: no visible global function definition for 'p.adjust'
levelPValues: no visible global function definition for 'par'
levelPValues: no visible global function definition for 'mtext'
levelPValues: no visible global function definition for 'abline'
levelPValues: no visible global function definition for 'points'
pfNbinomTest: no visible global function definition for 'is'
pfNbinomTest: no visible global function definition for 'fData'
pfNbinomTest: no visible global function definition for 'p.adjust'
pfNbinomTestForMatrices : <anonymous>: no visible global function
  definition for 'dnbinom'
twoSidedPValueFromDiscrete: no visible global function definition for
  'runif'
Undefined global functions or variables:
  abline density dnbinom fData hist is lm mtext nlm p.adjust par points
  runif
Consider adding
  importFrom("graphics", "abline", "hist", "mtext", "par", "points")
  importFrom("methods", "is")
  importFrom("stats", "density", "dnbinom", "lm", "nlm", "p.adjust",
             "runif")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
pfNbinomTest    39.44   0.00   39.43
Polyfit-package 20.69   0.07   20.75
levelPValues    18.68   0.08   18.77
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
pfNbinomTest    37.33   0.00   37.33
levelPValues    18.70   0.00   18.71
Polyfit-package 18.62   0.04   18.66
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/Polyfit.Rcheck/00check.log'
for details.



Installation output

Polyfit.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Polyfit_1.22.0.tar.gz && rm -rf Polyfit.buildbin-libdir && mkdir Polyfit.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Polyfit.buildbin-libdir Polyfit_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Polyfit_1.22.0.zip && rm Polyfit_1.22.0.tar.gz Polyfit_1.22.0.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  152k  100  152k    0     0  2452k      0 --:--:-- --:--:-- --:--:-- 2769k

install for i386

* installing *source* package 'Polyfit' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2 
** help
*** installing help indices
  converting help for package 'Polyfit'
    finding HTML links ... done
    Polyfit-package                         html  
    finding level-2 HTML links ... done

    levelPValues                            html  
    pfNbinomTest                            html  
    twoSidedPValueFromDiscrete              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
** testing if installed package can be loaded from final location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Polyfit' ...
** testing if installed package can be loaded
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
* MD5 sums
packaged installation of 'Polyfit' as Polyfit_1.22.0.zip
* DONE (Polyfit)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Polyfit' successfully unpacked and MD5 sums checked

Tests output


Example timings

Polyfit.Rcheck/examples_i386/Polyfit-Ex.timings

nameusersystemelapsed
Polyfit-package20.69 0.0720.75
levelPValues18.68 0.0818.77
pfNbinomTest39.44 0.0039.43
twoSidedPValueFromDiscrete0.410.000.41

Polyfit.Rcheck/examples_x64/Polyfit-Ex.timings

nameusersystemelapsed
Polyfit-package18.62 0.0418.66
levelPValues18.70 0.0018.71
pfNbinomTest37.33 0.0037.33
twoSidedPValueFromDiscrete0.450.000.45