faahKO 1.2.1
Colin A. Smith
| Snapshot Date: 2008-10-16 12:02:11 -0700 (Thu, 16 Oct 2008) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/faahKO | | Last Changed Rev: 695 / Revision: 729 | | Last Changed Date: 2008-07-16 14:26:39 -0700 (Wed, 16 Jul 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ ERROR ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | ERROR | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-data-experiment/meat/faahKO.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'faahKO/DESCRIPTION' ... OK
* this is package 'faahKO' version '1.2.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'faahKO' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating faahKO-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'faahKO-Ex.R' failed.
The error most likely occurred in:
> ### * faahko
>
> flush(stderr()); flush(stdout())
>
> ### Name: faahko
> ### Title: FAAH knockout LC/MS data xcmsSet
> ### Aliases: faahko faahKO
> ### Keywords: datasets
>
> ### ** Examples
>
> ## The directory with the NetCDF LC/MS files
> cdfpath <- file.path(.find.package("faahKO"), "cdf")
> cdfpath
[1] "E:/biocbld/bbs-2.2-data-experiment/meat/faahKO.Rcheck/faahKO/cdf"
> list.files(cdfpath, recursive = TRUE)
[1] "KO/ko15.CDF" "KO/ko16.CDF" "KO/ko18.CDF" "KO/ko19.CDF" "KO/ko21.CDF"
[6] "KO/ko22.CDF" "WT/wt15.CDF" "WT/wt16.CDF" "WT/wt18.CDF" "WT/wt19.CDF"
[11] "WT/wt21.CDF" "WT/wt22.CDF"
>
> if (require(xcms)) {
+
+ ## xcmsSet Summary
+ show(faahko)
+
+ ## Access raw data file
+ ko15 <- xcmsRaw(filepaths(faahko)[1], profmethod = "bin", profstep = 0.1)
+ ko15
+
+ }
Loading required package: xcms
An "xcmsSet" object with 12 samples
Time range: 2506.1-4147.7 seconds (41.8-69.1 minutes)
Mass range: 200.1-599.3338 m/z
Peaks: 4776 (about 398 per sample)
Peak Groups: 0
Sample classes: KO, WT
Profile settings: method = bin
step = 0.1
Memory usage: 0.641 MB
Error in file.exists(filename) : could not find function "filepaths"
Calls: xcmsRaw -> file.exists
Execution halted
installing R.css in E:/biocbld/bbs-2.2-data-experiment/meat/faahKO.Rcheck
---------- Making package faahKO ------------
adding build stamp to DESCRIPTION
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'faahKO'
Formats: text html latex example chm
faahko text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.2-data-experiment\meat\faahKO.Rcheck\00_pkg_src\faahKO\chm\faahKO.chm
Compile time: 0 minutes, 0 seconds
2 Topics
3 Local links
1 Internet link
1 Graphic
Created e:\biocbld\bbs-2.2-data-experiment\meat\faahKO.Rcheck\00_pkg_src\faahKO\chm\faahKO.chm, 17,605 bytes
Compression increased file by 8,999 bytes.
adding MD5 sums
* DONE (faahKO)