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CHECK report for zFPKM on tokay1

This page was generated on 2019-04-13 11:28:08 -0400 (Sat, 13 Apr 2019).

Package 1647/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zFPKM 1.4.1
Ron Ammar
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/zFPKM
Branch: RELEASE_3_8
Last Commit: e1c2a03
Last Changed Date: 2019-01-04 13:18:32 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
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: zFPKM
Version: 1.4.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:zFPKM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings zFPKM_1.4.1.tar.gz
StartedAt: 2019-04-13 06:15:34 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:19:26 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 232.9 seconds
RetCode: 0
Status:  OK  
CheckDir: zFPKM.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:zFPKM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings zFPKM_1.4.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/zFPKM.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 'zFPKM/DESCRIPTION' ... OK
* this is package 'zFPKM' version '1.4.1'
* 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 'zFPKM' 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
PlotGaussianFitDF: no visible global function definition for 'dnorm'
PlotGaussianFitDF: no visible binding for global variable 'density'
PlotGaussianFitDF: no visible binding for global variable 'log2fpkm'
PlotGaussianFitDF: no visible binding for global variable 'sample_name'
zFPKMCalc: no visible global function definition for 'density'
zFPKMTransform: no visible global function definition for 'is'
Undefined global functions or variables:
  density dnorm is log2fpkm sample_name
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "density", "dnorm")
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
** 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/zFPKM.Rcheck/00check.log'
for details.



Installation output

zFPKM.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/zFPKM_1.4.1.tar.gz && rm -rf zFPKM.buildbin-libdir && mkdir zFPKM.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=zFPKM.buildbin-libdir zFPKM_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL zFPKM_1.4.1.zip && rm zFPKM_1.4.1.tar.gz zFPKM_1.4.1.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 86147  100 86147    0     0   539k      0 --:--:-- --:--:-- --:--:--  553k

install for i386

* installing *source* package 'zFPKM' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'zFPKM'
    finding HTML links ... done
    zFPKM                                   html  
    zFPKMPlot                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'zFPKM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'zFPKM' as zFPKM_1.4.1.zip
* DONE (zFPKM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'zFPKM' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

zFPKM.Rcheck/examples_i386/zFPKM-Ex.timings

nameusersystemelapsed
zFPKM0.320.020.86
zFPKMPlot0.970.111.69

zFPKM.Rcheck/examples_x64/zFPKM-Ex.timings

nameusersystemelapsed
zFPKM0.360.050.75
zFPKMPlot1.450.011.87