BioC 2.12: CHECK report for CAMERA on lamb2

Package: CAMERA

Version: 1.15.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings CAMERA_1.15.1.tar.gz

StartedAt: 2013-01-16 01:12:08 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:15:45 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 216.8 seconds

RetCode: 0

Status: OK

CheckDir: CAMERA.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAMERA/DESCRIPTION’ ... OK
* this is package ‘CAMERA’ version ‘1.15.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CAMERA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
Foreign function call with ‘PACKAGE’ argument in a different package:
  .Call("getEIC", ..., PACKAGE = "xcms")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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’
xsAnnotate: no visible global function definition for ‘mpi.comm.size’
xsAnnotate: no visible global function definition for
  ‘mpi.spawn.Rslaves’
xsAnnotate: no visible binding for global variable ‘graphMethod’
findAdducts,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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
groupCorr-methods   10.093  0.116  10.219
annotateDiffreport   7.649  0.128   7.911
getIsotopeCluster    7.533  0.060   7.592
getPeaklist-methods  5.144  0.008   5.157
annotate-methods     4.968  0.048   5.015
cleanParallel        1.096  0.056  11.368
* checking for unstated dependencies in tests ... OK
* 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

NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck/00check.log’
for details.

* installing *source* package ‘CAMERA’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -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-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/CAMERA.Rcheck/CAMERA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘CAMERA.Rnw’ 
** testing if installed package can be loaded

* DONE (CAMERA)

name	user	system	elapsed
annotate-methods	4.968	0.048	5.015
annotateDiffreport	7.649	0.128	7.911
calcCaS-methods	2.760	0.036	2.803
cleanParallel	1.096	0.056	11.368
combinexsAnnos	0.004	0.000	0.004
findAdducts-methods	4.980	0.016	4.997
findIsotopes-methods	1.236	0.016	1.254
findNeutralLoss	0.912	0.004	0.915
findNeutralLossSpecs	0.888	0.016	0.907
getAllPeakEICs-methods	3.388	0.024	3.417
getIsotopeCluster	7.533	0.060	7.592
getPeaklist-methods	5.144	0.008	5.157
getpspectra	0.952	0.004	0.954
groupCorr-methods	10.093	0.116	10.219
groupFWHM-methods	3.320	0.004	3.324
ruleSet-class	0.092	0.008	0.105
xsAnnotate	2.220	0.004	2.225

Summary

Command output