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BioC 3.1: CHECK report for Rariant on moscato2

This page was generated on 2015-10-09 09:31:07 -0700 (Fri, 09 Oct 2015).

Package 781/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rariant 1.4.0
Julian Gehring
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/Rariant
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rariant
Version: 1.4.0
Command: rm -rf Rariant.buildbin-libdir Rariant.Rcheck && mkdir Rariant.buildbin-libdir Rariant.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rariant.buildbin-libdir Rariant_1.4.0.tar.gz >Rariant.Rcheck\00install.out 2>&1 && cp Rariant.Rcheck\00install.out Rariant-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=Rariant.buildbin-libdir --install="check:Rariant-install.out" --force-multiarch --no-vignettes --timings Rariant_1.4.0.tar.gz
StartedAt: 2015-10-09 05:18:21 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 05:26:35 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 494.0 seconds
RetCode: 0
Status:  OK  
CheckDir: Rariant.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rariant.buildbin-libdir Rariant.Rcheck && mkdir Rariant.buildbin-libdir Rariant.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rariant.buildbin-libdir Rariant_1.4.0.tar.gz >Rariant.Rcheck\00install.out 2>&1 && cp Rariant.Rcheck\00install.out Rariant-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=Rariant.buildbin-libdir --install="check:Rariant-install.out" --force-multiarch --no-vignettes --timings Rariant_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/Rariant.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rariant/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rariant' version '1.4.0'
* package encoding: UTF-8
* 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 'Rariant' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.2Mb
* 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
** 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
tallyBamRegion: no visible global function definition for 'PileupParam'
tallyBamRegion: no visible global function definition for
  'ScanBamParam'
tallyBamRegion: no visible global function definition for 'pileup'
* 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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'rariant-inspect-ci.png', 'rariant-inspect-shift.png'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [19s] OK
** running examples for arch 'x64' ... [23s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test_all.R' [17s]
 [17s] OK
** running tests for arch 'x64' ...
  Running 'test_all.R' [21s]
 [21s] 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 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/Rariant.Rcheck/00check.log'
for details.


Rariant.Rcheck/00install.out:


install for i386

* installing *source* package 'Rariant' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Note: the specification for S3 class "cluster" in package 'NMF' seems equivalent to one from package 'BiocParallel': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Note: the specification for S3 class "cluster" in package 'NMF' seems equivalent to one from package 'BiocParallel': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'Rariant' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Note: the specification for S3 class "cluster" in package 'NMF' seems equivalent to one from package 'BiocParallel': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'Rariant' as Rariant_1.4.0.zip
* DONE (Rariant)

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

nameusersystemelapsed
Rariant-package0.240.032.22
ci-adjust000
ci-assessment0.010.000.01
ci-utils0.020.000.02
convert-utils0.090.000.09
mismatch-plot2.830.012.90
plot-cis1.060.001.09
prop-cis0.020.000.02
prop-tests000
rariant0.280.021.07
shiny000
split-sample000

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

nameusersystemelapsed
Rariant-package0.200.060.26
ci-adjust0.020.000.02
ci-assessment0.010.000.01
ci-utils0.020.000.02
convert-utils0.110.010.12
mismatch-plot3.550.043.74
plot-cis1.480.001.50
prop-cis0.020.000.02
prop-tests000
rariant0.290.002.86
shiny0.020.000.00
split-sample000