beadarraySNP 1.30.0
Jan Oosting
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/beadarraySNP | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings beadarraySNP_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/beadarraySNP.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarraySNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘beadarraySNP’ version ‘1.30.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘beadarraySNP’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* 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
* 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 ... NOTE
Package in Depends field not imported from: ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘getMidMaxIdx’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotQC,QCIllumina: warning in rgb(0, 0:255, 0, max = 255): partial
argument match of 'max' to 'maxColorValue'
plotQC,QCIllumina: warning in rgb(0:255, 0, 0, max = 255): partial
argument match of 'max' to 'maxColorValue'
reportSamplePanelQC,QCIllumina: warning in rgb(r = 0, b = 0, g =
colstart:colend, maxColorValue = colend): partial argument match of
'r' to 'red'
reportSamplePanelQC,QCIllumina: warning in rgb(r = 0, b = 0, g =
colstart:colend, maxColorValue = colend): partial argument match of
'g' to 'green'
reportSamplePanelQC,QCIllumina: warning in rgb(r = 0, b = 0, g =
colstart:colend, maxColorValue = colend): partial argument match of
'b' to 'blue'
reportSamplePanelQC,QCIllumina: warning in rgb(r = colstart:colend, b =
0, g = 0, maxColorValue = colend): partial argument match of 'r' to
'red'
reportSamplePanelQC,QCIllumina: warning in rgb(r = colstart:colend, b =
0, g = 0, maxColorValue = colend): partial argument match of 'g' to
'green'
reportSamplePanelQC,QCIllumina: warning in rgb(r = colstart:colend, b =
0, g = 0, maxColorValue = colend): partial argument match of 'b' to
'blue'
read.SnpSetIllumina: no visible global function definition for
‘createBeadSummaryData’
* 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 ... [5s/5s] 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/beadarraySNP.Rcheck/00check.log’
for details.