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BioC 3.4: CHECK report for SNPchip on moscato1

This page was generated on 2016-09-21 03:41:45 -0700 (Wed, 21 Sep 2016).

Package 1135/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPchip 2.19.0
Robert Scharpf
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SNPchip
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SNPchip
Version: 2.19.0
Command: rm -rf SNPchip.buildbin-libdir SNPchip.Rcheck && mkdir SNPchip.buildbin-libdir SNPchip.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SNPchip.buildbin-libdir SNPchip_2.19.0.tar.gz >SNPchip.Rcheck\00install.out 2>&1 && cp SNPchip.Rcheck\00install.out SNPchip-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SNPchip.buildbin-libdir --install="check:SNPchip-install.out" --force-multiarch --no-vignettes --timings SNPchip_2.19.0.tar.gz
StartedAt: 2016-09-20 16:48:26 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 16:52:36 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 250.1 seconds
RetCode: 0
Status:  OK  
CheckDir: SNPchip.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SNPchip.buildbin-libdir SNPchip.Rcheck && mkdir SNPchip.buildbin-libdir SNPchip.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SNPchip.buildbin-libdir SNPchip_2.19.0.tar.gz >SNPchip.Rcheck\00install.out 2>&1 && cp SNPchip.Rcheck\00install.out SNPchip-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SNPchip.buildbin-libdir --install="check:SNPchip-install.out" --force-multiarch --no-vignettes --timings SNPchip_2.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/SNPchip.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SNPchip/DESCRIPTION' ... OK
* this is package 'SNPchip' version '2.19.0'
* 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 'SNPchip' 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
centromereData: no visible global function definition for 'read.delim'
dataFrameFromRange: no visible binding for global variable 'data'
getCytoband: no visible global function definition for 'read.table'
Undefined global functions or variables:
  data read.delim read.table
Consider adding
  importFrom("utils", "data", "read.delim", "read.table")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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
xyplotLrrBaf 8.30   0.07    8.77
xyplot       6.21   0.06    6.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
xyplotLrrBaf 8.70   0.03    8.74
xyplot       6.85   0.08    6.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  Running 'doRUnit.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
  'D:/biocbld/bbs-3.4-bioc/meat/SNPchip.Rcheck/00check.log'
for details.


SNPchip.Rcheck/00install.out:


install for i386

* installing *source* package 'SNPchip' ...
** R
** inst
** preparing 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 'SNPchip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNPchip' as SNPchip_2.19.0.zip
* DONE (SNPchip)

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

nameusersystemelapsed
centromere0.060.020.08
getCytoband0.050.000.04
plotIdiogram0.590.030.63
xypanel000
xyplot6.210.066.33
xyplotLrrBaf8.300.078.77

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

nameusersystemelapsed
centromere0.060.000.06
getCytoband0.040.000.03
plotIdiogram0.540.030.58
xypanel000
xyplot6.850.086.92
xyplotLrrBaf8.700.038.74