Package: CAMERA

Version: 1.10.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch CAMERA_1.10.0.tar.gz

StartedAt: 2012-01-09 02:16:16 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 02:18:38 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 142.1 seconds

RetCode: 0

Status:  OK

CheckDir: CAMERA.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/CAMERA.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAMERA/DESCRIPTION' ... OK
* this is package 'CAMERA' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'CAMERA' can be installed ... OK
* checking installed package size ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
File 'CAMERA/R/unix/zzz.R':
  .onLoad calls:
    require(methods)

File 'CAMERA/R/windows/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

cleanParallel: no visible global function definition for
  'mpi.close.Rslaves'
cleanParallel: no visible global function definition for 'stopCluster'
xsAnnotate: no visible global function definition for 'mpi.comm.size'
xsAnnotate: no visible global function definition for
  'mpi.spawn.Rslaves'
xsAnnotate: no visible global function definition for 'makeCluster'
xsAnnotate: no visible binding for global variable 'graphMethod'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'RUnit'
* checking tests ...
  Running 'doRUnit.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'CAMERA' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c fastMatch.c -o fastMatch.o
gcc -shared -s -static-libgcc -o CAMERA.dll tmp.def fastMatch.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/CAMERA.Rcheck/CAMERA/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'CAMERA.Rnw' 
** testing if installed package can be loaded

* DONE (CAMERA)

name	user	system	elapsed
annotate-methods	5.30	0.09	5.47
annotateDiffreport	5.73	0.24	8.57
calcCaS-methods	2.50	0.12	2.72
cleanParallel	1.20	0.04	12.02
findAdducts-methods	6.38	0.03	6.47
findIsotopes-methods	0.78	0.02	0.80
findNeutralLoss	0.88	0.00	0.88
findNeutralLossSpecs	0.84	0.01	0.85
getAllPeakEICs-methods	2.32	0.03	2.38
getIsotopeCluster	7.32	0.32	7.68
getPeaklist-methods	6.71	0.06	6.83
getpspectra	0.79	0.02	0.81
groupCorr-methods	6.40	0.32	6.89
groupFWHM-methods	2.22	0.02	2.25
xsAnnotate	1.4	0.0	1.8