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Package 89/609HostnameOS / ArchBUILDCHECKBUILD BIN
CAMERA 1.14.0
Carsten Kuhl
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/CAMERA
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: CAMERA
Version: 1.14.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings CAMERA_1.14.0.tar.gz
StartedAt: 2013-03-24 23:51:42 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:55:31 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 229.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CAMERA.Rcheck
Warnings: 2

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/CAMERA.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.14.0’
* 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 for sufficient/correct file permissions ... 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 ... WARNING
Error in eval(expr, envir, enclos) : could not find function "selfStart"
In addition: Warning message:
Class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘.GlobalEnv’ 
Error: unable to load R code in package ‘xcms’
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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’
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’
findAdducts,xsAnnotate: no visible global function definition for
  ‘mpi.comm.size’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/CAMERA.Rcheck/00_pkg_src/CAMERA/man/annotateDiffreport.Rd’:
  ‘diffreport’

Missing link(s) in documentation object ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/CAMERA.Rcheck/00_pkg_src/CAMERA/man/xsAnnotate-class.Rd’:
  ‘xcmsSet’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.

* 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   8.293  0.136   8.470
getIsotopeCluster   7.293  0.172   7.570
annotateDiffreport  5.400  0.212   8.881
annotate-methods    4.836  0.620   5.758
getPeaklist-methods 5.328  0.052   5.640
findAdducts-methods 5.164  0.036   5.319
cleanParallel       1.260  0.052  13.689
* 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

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/CAMERA.Rcheck/00check.log’
for details.

CAMERA.Rcheck/00install.out:

* installing *source* package ‘CAMERA’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fastMatch.c -o fastMatch.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o CAMERA.so fastMatch.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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)

CAMERA.Rcheck/CAMERA-Ex.timings:

nameusersystemelapsed
annotate-methods4.8360.6205.758
annotateDiffreport5.4000.2128.881
calcCaS-methods2.2490.0322.309
cleanParallel 1.260 0.05213.689
combinexsAnnos000
findAdducts-methods5.1640.0365.319
findIsotopes-methods1.1680.0041.171
findNeutralLoss1.1280.0041.156
findNeutralLossSpecs1.0600.0041.063
getAllPeakEICs-methods2.4440.0202.464
getIsotopeCluster7.2930.1727.570
getPeaklist-methods5.3280.0525.640
getpspectra1.0920.0121.175
groupCorr-methods8.2930.1368.470
groupFWHM-methods3.1960.0083.333
ruleSet-class0.1000.0040.105
xsAnnotate1.6880.0001.700