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CHECK report for parglms on tokay2

This page was generated on 2019-04-09 12:22:31 -0400 (Tue, 09 Apr 2019).

Package 1146/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
parglms 1.15.1
VJ Carey
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/parglms
Branch: master
Last Commit: a6306f3
Last Changed Date: 2019-04-02 16:14:18 -0400 (Tue, 02 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: parglms
Version: 1.15.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:parglms.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings parglms_1.15.1.tar.gz
StartedAt: 2019-04-09 04:46:30 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:47:47 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 76.6 seconds
RetCode: 0
Status:  OK  
CheckDir: parglms.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:parglms.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings parglms_1.15.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/parglms.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.15.1'
* 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 'build' 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
* 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
.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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
parGLM-methods 5.82   0.41    6.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
parGLM-methods 6.56   0.31    6.89
* 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 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/parglms.Rcheck/00check.log'
for details.



Installation output

parglms.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/parglms_1.15.1.tar.gz && rm -rf parglms.buildbin-libdir && mkdir parglms.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=parglms.buildbin-libdir parglms_1.15.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL parglms_1.15.1.zip && rm parglms_1.15.1.tar.gz parglms_1.15.1.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  7877  100  7877    0     0   121k      0 --:--:-- --:--:-- --:--:--  137k

install for i386

* installing *source* package 'parglms' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'parglms'
    finding HTML links ... done
    parGLM-methods                          html  
    finding level-2 HTML links ... done

    parglms-package                         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 'parglms' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'parglms' as parglms_1.15.1.zip
* DONE (parglms)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'parglms' successfully unpacked and MD5 sums checked

Tests output

parglms.Rcheck/tests_i386/parglms_unit_tests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("parglms")


RUNIT TEST PROTOCOL -- Tue Apr 09 04:47:37 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
parglms RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.15    0.07    1.21 

parglms.Rcheck/tests_x64/parglms_unit_tests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("parglms")


RUNIT TEST PROTOCOL -- Tue Apr 09 04:47:38 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
parglms RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.14    0.18    1.31 

Example timings

parglms.Rcheck/examples_i386/parglms-Ex.timings

nameusersystemelapsed
parGLM-methods5.820.416.36
parglms-package000

parglms.Rcheck/examples_x64/parglms-Ex.timings

nameusersystemelapsed
parGLM-methods6.560.316.89
parglms-package000