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CHECK report for ASSET on tokay2

This page was generated on 2018-10-17 08:37:36 -0400 (Wed, 17 Oct 2018).

Package 78/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASSET 1.98.0
Samsiddhi Bhattacharjee
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ASSET
Branch: RELEASE_3_7
Last Commit: 24e9cb5
Last Changed Date: 2018-06-12 03:17:04 -0400 (Tue, 12 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ASSET
Version: 1.98.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASSET.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ASSET_1.98.0.tar.gz
StartedAt: 2018-10-17 00:33:58 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:35:39 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 101.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ASSET.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASSET.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ASSET_1.98.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ASSET.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.98.0'
* 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-3.7-bioc/tmpdir/Rtmpy28bXu/R.INSTALL11644951116a/ASSET/man/h.traits.Rd:41: missing link 'p.tube'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy28bXu/R.INSTALL11644951116a/ASSET/man/h.types.Rd:38: missing link 'p.tube'
See 'C:/Users/biocbuild/bbs-3.7-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
Malformed Description field: should contain one or more complete sentences.
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
* 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 ... NOTE
Package in Depends field not imported from: 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dlm.pval: no visible global function definition for 'pnorm'
getCI: no visible global function definition for 'qnorm'
h.forest: no visible global function definition for 'meta.colors'
h.forest: no visible global function definition for 'title'
h.traits1: no visible global function definition for 'qnorm'
h.traits2: no visible global function definition for 'pchisq'
h.types0: no visible global function definition for 'qnorm'
p.bon: no visible global function definition for 'pnorm'
qxd.prod.coef: no visible global function definition for 'pnorm'
qxd.prod.cor: no visible global function definition for 'pnorm'
qxd.prod.int: no visible global function definition for 'integrate'
qxd.prod.int : <anonymous>: no visible global function definition for
  'dnorm'
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 'pnorm'
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 dnorm glm integrate meta.colors model.frame
  model.matrix pchisq pnorm qnorm rnorm title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "as.formula", "binomial", "dnorm", "glm",
             "integrate", "model.frame", "model.matrix", "pchisq",
             "pnorm", "qnorm", "rnorm")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'h.traits.Rd':
  'p.tube'

Missing link or links in documentation object 'h.types.Rd':
  'p.tube'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'p.tube'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
h.types 7.27   0.16    7.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
h.types 7.52   0.06    7.58
* 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: 3 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/ASSET.Rcheck/00check.log'
for details.



Installation output

ASSET.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ASSET_1.98.0.tar.gz && rm -rf ASSET.buildbin-libdir && mkdir ASSET.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASSET.buildbin-libdir ASSET_1.98.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ASSET_1.98.0.zip && rm ASSET_1.98.0.tar.gz ASSET_1.98.0.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  128k  100  128k    0     0  2057k      0 --:--:-- --:--:-- --:--:-- 2330k

install for i386

* installing *source* package 'ASSET' ...
** R
** data
** inst
** byte-compile and prepare 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  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy28bXu/R.INSTALL11644951116a/ASSET/man/h.traits.Rd:41: missing link 'p.tube'
    h.types                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpy28bXu/R.INSTALL11644951116a/ASSET/man/h.types.Rd:38: missing link 'p.tube'
    p.dlm                                   html  
    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_1.98.0.zip
* DONE (ASSET)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ASSET' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

ASSET.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 Oct 17 00:35:23 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 
> 
> proc.time()
   user  system elapsed 
   7.85    0.12    7.95 

ASSET.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 Oct 17 00:35:33 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 
> 
> proc.time()
   user  system elapsed 
   9.81    0.17    9.96 

Example timings

ASSET.Rcheck/examples_i386/ASSET-Ex.timings

nameusersystemelapsed
ex_trait0.010.010.03
ex_types0.020.000.02
h.forestPlot0.640.000.64
h.summary0.530.000.53
h.traits0.550.000.55
h.types7.270.167.42
p.dlm0.030.000.03
z.max0.010.000.02

ASSET.Rcheck/examples_x64/ASSET-Ex.timings

nameusersystemelapsed
ex_trait0.030.000.03
ex_types0.030.000.03
h.forestPlot0.630.000.63
h.summary0.370.000.37
h.traits0.410.000.41
h.types7.520.067.58
p.dlm0.010.000.02
z.max0.010.000.01