AgiMicroRna 2.21.0
Pedro Lopez-Romero
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AgiMicroRna | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 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 AgiMicroRna_2.21.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AgiMicroRna.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AgiMicroRna/DESCRIPTION’ ... OK
* this is package ‘AgiMicroRna’ version ‘2.21.0’
* 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 ‘AgiMicroRna’ can be installed ... [27s/27s] 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.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’
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 ... NOTE
Warning: no function found corresponding to methods exports from ‘AgiMicroRna’ for: ‘show’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
'library' or 'require' calls to packages already attached by Depends:
‘affy’ ‘affycoretools’ ‘preprocessCore’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘codelink’ ‘gdata’ ‘geneplotter’ ‘gplots’ ‘gtools’ ‘marray’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘affy’ ‘affycoretools’ ‘limma’ ‘methods’ ‘preprocessCore’
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 ... NOTE
Foreign function call to a different package:
.Call("rma_c_complete_copy", ..., PACKAGE = "affy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
DEG.print.info: no visible global function definition for ‘exprs’
HeatMapMicroRna: no visible global function definition for ‘maPalette’
HeatMapMicroRna: no visible global function definition for ‘heatmap.2’
PCAplotMicroRna: no visible global function definition for ‘exprs’
PCAplotMicroRna: no visible global function definition for ‘exprs<-’
PCAplotMicroRna: no visible global function definition for ‘plotPCA’
basicLimma: no visible global function definition for ‘exprs’
basicLimma: no visible global function definition for ‘lmFit’
basicLimma: no visible global function definition for ‘contrasts.fit’
basicLimma: no visible global function definition for ‘eBayes’
esetMicroRna: no visible global function definition for ‘exprs’
getDecideTests: no visible global function definition for ‘decideTests’
read.agiMicroRna: no visible global function definition for
‘read.columns’
rmaMicroRna: no visible global function definition for
‘rma.background.correct’
rmaMicroRna: no visible global function definition for
‘normalizeBetweenArrays’
significantMicroRna: no visible global function definition for ‘exprs’
tgsNormalization: no visible global function definition for
‘normalizeBetweenArrays’
writeEset: no visible global function definition for ‘exprs’
writeEset: no visible global function definition for ‘featureNames’
Undefined global functions or variables:
contrasts.fit decideTests eBayes exprs exprs<- featureNames heatmap.2
lmFit maPalette normalizeBetweenArrays plotPCA read.columns
rma.background.correct
* 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 ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mvaMicroRna 12.303 0.040 12.358
rmaMicroRna 5.553 0.028 5.585
* 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/AgiMicroRna.Rcheck/00check.log’
for details.