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BioC 3.5: CHECK report for parglms on tokay2

This page was generated on 2017-08-16 13:24:08 -0400 (Wed, 16 Aug 2017).

Package 946/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
parglms 1.8.0
VJ Carey
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/parglms
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: parglms
Version: 1.8.0
Command: rm -rf parglms.buildbin-libdir parglms.Rcheck && mkdir parglms.buildbin-libdir parglms.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=parglms.buildbin-libdir parglms_1.8.0.tar.gz >parglms.Rcheck\00install.out 2>&1 && cp parglms.Rcheck\00install.out parglms-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=parglms.buildbin-libdir --install="check:parglms-install.out" --force-multiarch --no-vignettes --timings parglms_1.8.0.tar.gz
StartedAt: 2017-08-16 01:47:27 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:48:41 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 73.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: parglms.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf parglms.buildbin-libdir parglms.Rcheck && mkdir parglms.buildbin-libdir parglms.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=parglms.buildbin-libdir parglms_1.8.0.tar.gz >parglms.Rcheck\00install.out 2>&1 && cp parglms.Rcheck\00install.out parglms-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=parglms.buildbin-libdir --install="check:parglms-install.out" --force-multiarch --no-vignettes --timings parglms_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/parglms.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'parglms/DESCRIPTION' ... OK
* this is package 'parglms' version '1.8.0'
* 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 'parglms' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
.parglm: no visible binding for global variable 'ind'
getX: no visible global function definition for 'model.matrix'
getY: no visible global function definition for 'model.response'
getY: no visible global function definition for 'model.frame'
predict.parglm: no visible binding for global variable 'z'
predict.parglm: no visible global function definition for 'model.frame'
predict.parglm: no visible global function definition for
  'model.extract'
predict.parglm: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  ind model.extract model.frame model.matrix model.response z
Consider adding
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
* 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' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'parglms.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
parGLM-methods 5.51   0.34    5.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
parGLM-methods 8.88   0.47    9.45
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'parglms_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'parglms_unit_tests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/parglms.Rcheck/00check.log'
for details.


parglms.Rcheck/00install.out:


install for i386

* installing *source* package 'parglms' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'parglms' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'parglms' as parglms_1.8.0.zip
* DONE (parglms)

parglms.Rcheck/examples_i386/parglms-Ex.timings:

nameusersystemelapsed
parGLM-methods5.510.345.87
parglms-package000

parglms.Rcheck/examples_x64/parglms-Ex.timings:

nameusersystemelapsed
parGLM-methods8.880.479.45
parglms-package000