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CHECK report for ASSET on tokay1

This page was generated on 2018-04-12 13:23:12 -0400 (Thu, 12 Apr 2018).

Package 76/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASSET 1.16.0
William Wheeler
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/ASSET
Branch: RELEASE_3_6
Last Commit: ee17e30
Last Changed Date: 2017-10-30 12:40:07 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ASSET
Version: 1.16.0
Command: rm -rf ASSET.buildbin-libdir ASSET.Rcheck && mkdir ASSET.buildbin-libdir ASSET.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ASSET.buildbin-libdir ASSET_1.16.0.tar.gz >ASSET.Rcheck\00install.out 2>&1 && cp ASSET.Rcheck\00install.out ASSET-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ASSET.buildbin-libdir --install="check:ASSET-install.out" --force-multiarch --no-vignettes --timings ASSET_1.16.0.tar.gz
StartedAt: 2018-04-11 22:17:14 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:22:46 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 332.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ASSET.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ASSET.buildbin-libdir ASSET.Rcheck && mkdir ASSET.buildbin-libdir ASSET.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ASSET.buildbin-libdir ASSET_1.16.0.tar.gz >ASSET.Rcheck\00install.out 2>&1 && cp ASSET.Rcheck\00install.out ASSET-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ASSET.buildbin-libdir --install="check:ASSET-install.out" --force-multiarch --no-vignettes --timings ASSET_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ASSET.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ASSET/DESCRIPTION' ... OK
* this is package 'ASSET' version '1.16.0'
* 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 'ASSET' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcduKd6/R.INSTALL28dc352b421/ASSET/man/p.dlm.Rd:63: missing file link 'set.seed'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ASSET.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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
calcP1: no visible global function definition for 'pbinom'
dlm.pval: no visible global function definition for 'qnorm'
getCI: no visible global function definition for 'qnorm'
h.forest: no visible global function definition for 'title'
h.traits1: no visible global function definition for 'pnorm'
h.traits1: no visible global function definition for 'qnorm'
h.traits1: no visible global function definition for 'pchisq'
h.traits2: no visible global function definition for 'pchisq'
h.types0: no visible global function definition for 'pnorm'
h.types0: no visible global function definition for 'qnorm'
h.types0: no visible global function definition for 'pchisq'
p.bon: no visible global function definition for 'pnorm'
p.boot: no visible global function definition for 'qnorm'
prob.sim: no visible global function definition for 'qnorm'
traits.forest: no visible global function definition for 'pnorm'
traits.forest0: no visible global function definition for 'pnorm'
traits.meta: no visible global function definition for 'pnorm'
tube.pval: no visible global function definition for 'qnorm'
tube.pval: no visible global function definition for 'pnorm'
tubeSim: no visible global function definition for 'pnorm'
tubeSim: no visible global function definition for 'rbinom'
tubeSim: no visible global function definition for 'rnorm'
types.score: no visible global function definition for 'model.matrix'
types.score: no visible global function definition for 'as.formula'
types.score: no visible global function definition for 'glm'
types.score: no visible global function definition for 'binomial'
types.wald: no visible global function definition for 'model.frame'
types.wald: no visible global function definition for 'as.formula'
types.wald : <anonymous>: no visible global function definition for
  'glm'
types.wald : <anonymous>: no visible global function definition for
  'binomial'
types.wald : <anonymous>: no visible global function definition for
  'as.formula'
types.wald: no visible global function definition for 'pnorm'
z.max: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula binomial glm model.frame model.matrix pbinom pchisq pnorm
  qnorm rbinom rnorm title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "as.formula", "binomial", "glm", "model.frame",
             "model.matrix", "pbinom", "pchisq", "pnorm", "qnorm",
             "rbinom", "rnorm")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
h.traits     42.03   0.00   42.03
h.forestPlot 40.39   0.03   40.43
h.summary    39.97   0.08   40.04
h.types      24.79   0.00   24.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
h.types      23.25   0.01   23.27
h.forestPlot 11.61   0.05   11.65
h.traits     11.28   0.04   11.31
h.summary    11.22   0.01   11.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/ASSET.Rcheck/00check.log'
for details.



Installation output

ASSET.Rcheck/00install.out


install for i386

* installing *source* package 'ASSET' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ASSET'
    finding HTML links ... done
    ASSET                                   html  
    ex_trait                                html  
    ex_types                                html  
    h.forestPlot                            html  
    h.summary                               html  
    h.traits                                html  
    h.types                                 html  
    p.dlm                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpcduKd6/R.INSTALL28dc352b421/ASSET/man/p.dlm.Rd:63: missing file link 'set.seed'
    z.max                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ASSET' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ASSET' as ASSET_1.16.0.zip
* DONE (ASSET)
In R CMD INSTALL
In R CMD INSTALL

Tests output

ASSET.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("ASSET")


RUNIT TEST PROTOCOL -- Wed Apr 11 22:22:26 2018 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ASSET RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  20.06    0.04   20.09 

ASSET.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("ASSET")


RUNIT TEST PROTOCOL -- Wed Apr 11 22:22:41 2018 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ASSET RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  14.01    0.17   14.18 

Example timings

ASSET.Rcheck/examples_i386/ASSET-Ex.timings

nameusersystemelapsed
ex_trait0.000.010.01
ex_types0.020.000.02
h.forestPlot40.39 0.0340.43
h.summary39.97 0.0840.04
h.traits42.03 0.0042.03
h.types24.79 0.0024.79
p.dlm2.620.002.62
z.max0.020.000.02

ASSET.Rcheck/examples_x64/ASSET-Ex.timings

nameusersystemelapsed
ex_trait0.030.000.03
ex_types000
h.forestPlot11.61 0.0511.65
h.summary11.22 0.0111.24
h.traits11.28 0.0411.31
h.types23.25 0.0123.27
p.dlm0.580.000.57
z.max0.010.000.02