Agi4x44PreProcess 1.23.1
Pedro Lopez-Romero
| Snapshot Date: 2014-03-17 17:01:44 -0700 (Mon, 17 Mar 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Agi4x44PreProcess | | Last Changed Rev: 82511 / Revision: 87549 | | Last Changed Date: 2013-11-01 13:05:53 -0700 (Fri, 01 Nov 2013) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | ERROR | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ ERROR ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Agi4x44PreProcess.Rcheck’
* using R version 3.1.0 alpha (2014-03-13 r65184)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Agi4x44PreProcess/DESCRIPTION’ ... OK
* this is package ‘Agi4x44PreProcess’ version ‘1.23.1’
* 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 ‘Agi4x44PreProcess’ can be installed ... [20s/23s] 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘annotate’ ‘genefilter’ ‘limma’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
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
filter.probes: warning in .packages(all = TRUE): partial argument match
of 'all' to 'all.available'
genes.rpt.agi: warning in ensembl.htmlpage(PROBE_ID, probe.chr,
filename, annotation.package, title, table.head = head, table.center
= TRUE, other = list(unlist(GENE_ID), unlist(gene.sym),
unlist(probe.chr))): partial argument match of 'other' to
'othernames'
HeatMap: warning in heatmap.2(DD.s, labCol = samples, labRow = names,
scale = "none", col = rbg, margin = c(10, 10), tracecol = "cyan"):
partial argument match of 'margin' to 'margins'
write.eset: warning in .packages(all = TRUE): partial argument match of
'all' to 'all.available'
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Agi4x44PreProcess-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genes.rpt.agi
> ### Title: Genes interrogated for different probes
> ### Aliases: genes.rpt.agi
> ### Keywords: documentation utilities
>
> ### ** Examples
>
> data(dd)
> library(hgug4112a.db)
Loading required package: org.Hs.eg.db
Loading required package: DBI
> genes.rpt.agi(dd,"hgug4112a.db",raw.data=TRUE,
+ WRITE.html=TRUE,REPORT=TRUE)
GENE SETS: same genes interrogated by different probes
FILTERING BY ControlType FLAG
RAW DATA: PROBES AFTER ControlType FILTERING: 11259
INPUT DATA: RAW
CHIP: hgug4112a.db
PROBE SETS (NON-CTRL prob rep. x 10): 207
GEN-SETS (REPLICATED GENES): 537
PROBES in gen-sets: 1115
Error: object 'chr' not found
Execution halted