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Package 62/389HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: CAMERA
Version: 1.4.3
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings CAMERA_1.4.3.tar.gz
StartedAt: 2010-10-04 16:30:39 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 16:32:49 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 130.5 seconds
RetCode: 1
Status:  ERROR 
CheckDir: CAMERA.Rcheck
Warnings: NA

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/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 for sufficient/correct file permissions ... 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:

> ### * groupCorr-methods
> 
> flush(stderr()); flush(stdout())
> 
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: groupCorr-methods
> ### Title: EIC correlation grouping of LC/ESI-MS data
> ### Aliases: groupCorr groupCorr,xsAnnotate-method
> ### Keywords: methods
> 
> ### ** Examples
> 
>  library(CAMERA)
>  file        <- system.file('mzdata/MM14.mzdata', package = "CAMERA");
>  xs          <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5, 10));
MM14: 
 Detecting mass traces at 30 ppm ... 
 % finished: 0 10 20 30 40 50 60 70 80 90 100 
 456 m/z ROI's.

 Detecting chromatographic peaks ... 
 % finished: 0 10 20 30 40 50 60 70 80 90 100 
 126  Peaks.
>  an          <- xsAnnotate(xs);
>  an.group    <- groupFWHM(an);
Created 14 groups.
>  an.iso      <- findIsotopes(an.group); #optional step
Run isotope peak annotation
Found isotopes: 36 
>  index       <- c(1,4); #Only group one and four will be calculate
>  an.grp.corr <- groupCorr(an.iso, psg_list=index, polarity="positive");
Generating EIC's .. 
Isotope annotation found, used as grouping information.

Calculating peak correlations in 2 Groups... 
 % finished: 100  

Calculating graph cross linking in 2 Groups... 
 % finished: 100  
xsAnnotate has now 17 groups, instead of 14 
>  
>  #For csv output
>  # write.csv(file="peaklist_with_isotopes.csv",getPeaklist(an))
> 
>  #Multiple sample 
>  library(faahKO)
>  xs.grp       <- group(faahko)
262 325 387 450 512 575 
>  
>  #With selected sample
>  xsa          <- xsAnnotate(xs.grp, sample=1)
>  xsa.group    <- groupFWHM(xsa)
Created 108 groups.
>  xsa.iso      <- findIsotopes(xsa.group) #optional step
Run isotope peak annotation
Found isotopes: 60 
>  index        <- c(1,4) #Only group one and four will be calculate
>  xsa.grp.corr <- groupCorr(xsa.iso, psg_list=index, polarity="positive")
Generating EIC's .. 
Isotope annotation found, used as grouping information.

Calculating peak correlations in 2 Groups... 
 % finished: 100  

Calculating graph cross linking in 2 Groups... 
 % finished: 100  Error: subscript out of bounds
Execution halted

CAMERA.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'CAMERA' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c fastMatch.c -o fastMatch.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o CAMERA.so fastMatch.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/CAMERA.Rcheck/CAMERA/libs
** 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)

CAMERA.Rcheck/CAMERA-Ex.timings:

nameusersystemelapsed
annotate13.404 0.04013.447
annotateDiffreport25.602 0.50426.730
findAdducts-methods20.641 0.05620.854
findIsotopes-methods1.2360.0081.243
getPeaklist20.142 0.13620.756
getpspectra1.1400.0121.152