Rolexa 1.27.0
Jacques Rougemont
| Snapshot Date: 2015-12-14 17:20:10 -0800 (Mon, 14 Dec 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rolexa | | Last Changed Rev: 109592 / Revision: 111478 | | Last Changed Date: 2015-10-13 12:59:53 -0700 (Tue, 13 Oct 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Rolexa_1.27.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Rolexa.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rolexa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rolexa’ version ‘1.27.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘fork’
* 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 ‘Rolexa’ can be installed ... [11s/11s] 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.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘graphics’ ‘grDevices’ ‘methods’ ‘ShortRead’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ChannelHistogram,SolexaIntensity: warning in Mclust(data, G = G, model
= "V"): partial argument match of 'model' to 'modelNames'
ChannelHistogram,SolexaIntensity: warning in mclust1Dplot(data,
parameters = hist$parameters, z = hist$z, what = "density", xlab =
"Intensity", col = "red", new = TRUE): partial argument match of
'col' to 'colors'
ForkBatch: no visible binding for global variable ‘Rolexa.env’
ForkBatch: no visible global function definition for ‘fork’
ForkBatch: no visible global function definition for ‘wait’
QualityBoxPlots: no visible binding for global variable ‘Rolexa.env’
BatchAnalysis,RolexaRun: no visible binding for global variable
‘Rolexa.env’
CombineFastQ,RolexaRun-SolexaPath: no visible binding for global
variable ‘Rolexa.env’
CombineReads,RolexaRun-SolexaPath: no visible binding for global
variable ‘Rolexa.env’
CombinedPlot,RolexaRun: no visible binding for global variable
‘Rolexa.env’
FilterResults,RolexaRun: no visible binding for global variable
‘Rolexa.env’
FilterResults,RolexaRun: possible error in DNAStringSet(read2 =
apply(str[nrow + I, ], 1, paste, collapse = "")): unused argument
(read2 = apply(str[nrow + I, ], 1, paste, collapse = ""))
OneBatch,RolexaRun: no visible binding for global variable ‘Rolexa.env’
PlotCycles,RolexaRun: no visible binding for global variable
‘Rolexa.env’
SaveResults,RolexaRun: no visible binding for global variable
‘Rolexa.env’
SeqScore,RolexaRun: no visible binding for global variable ‘Rolexa.env’
TileNormalize,RolexaRun: no visible binding for global variable
‘Rolexa.env’
Undefined global functions or variables:
Rolexa.env fork wait
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] 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
‘/home/biocbuild/bbs-3.3-bioc/meat/Rolexa.Rcheck/00check.log’
for details.