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 '/Users/biocbuild/bbs-2.6-bioc/meat/CAMERA.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* 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
* install options are ' --no-html'
* installing *source* package ‘CAMERA’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c fastMatch.c -o fastMatch.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o CAMERA.so fastMatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/CAMERA.Rcheck/CAMERA/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c fastMatch.c -o fastMatch.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o CAMERA.so fastMatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/CAMERA.Rcheck/CAMERA/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c fastMatch.c -o fastMatch.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o CAMERA.so fastMatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/CAMERA.Rcheck/CAMERA/libs/x86_64
** 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)