CAMERA 1.4.3
Carsten Kuhl
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/CAMERA | | Last Changed Rev: 46981 / Revision: 49923 | | Last Changed Date: 2010-05-19 05:16:03 -0700 (Wed, 19 May 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ ERROR ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | ERROR | OK |
* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/CAMERA.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAMERA/DESCRIPTION' ... OK
* this is package 'CAMERA' version '1.4.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'CAMERA' 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 whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
calcCL2: no visible binding for global variable 'psg_list'
calcCL2: no visible global function definition for 'mpi.parSapply'
findAdducts,xsAnnotate: no visible global function definition for
'mpi.comm.size'
groupCorr,xsAnnotate: no visible global function definition for
'mpi.comm.size'
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... ERROR
Running examples in 'CAMERA-Ex.R' failed.
The error most likely occurred in:
> ### * annotateDiffreport
>
> flush(stderr()); flush(stdout())
>
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotateDiffreport
> ### Title: Deconvolute/Annotate LC/ESI-MS data
> ### Aliases: annotateDiffreport annotateDiffreport,xsAnnotate-methods
> ### Keywords: methods
>
> ### ** Examples
>
> #Multiple sample
> library(CAMERA)
> library(faahKO)
> xs.grp <- group(faahko)
262 325 387 450 512 575
> xs.fill <- fillPeaks(xs.grp)
ko15 Error in xcmsRaw(files[i], profmethod = prof$method, profstep = 0) :
File E:/biocbld/bbs-2.6-data-experiment/meat/faahKO.buildbin-libdir/faahKO/cdf/KO/ko15.CDF not exists.
Calls: fillPeaks ... fillPeaks.chrom -> fillPeaks.chrom -> .local -> xcmsRaw
Execution halted
* install options are ' --no-html'
* installing *source* package 'CAMERA' ...
** libs
making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -std=gnu99 -c fastMatch.c -o fastMatch.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o CAMERA.dll tmp.def fastMatch.o -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/CAMERA.Rcheck/CAMERA/libs/x64
... done
** R
** data
** inst
** preparing package for lazy loading
in method for 'psDist' with signature 'object1="xsAnnotate",object2="xsAnnotate"': no definition for class "xsAnnotate"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (CAMERA)