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BioC 3.1: CHECK report for CAMERA on zin2

This page was generated on 2015-10-09 09:23:46 -0700 (Fri, 09 Oct 2015).

Package 129/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAMERA 1.24.1
Carsten Kuhl
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CAMERA
Last Changed Rev: 105917 / Revision: 109384
Last Changed Date: 2015-07-08 14:20:51 -0700 (Wed, 08 Jul 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ TIMEOUT ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAMERA
Version: 1.24.1
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings CAMERA_1.24.1.tar.gz
StartedAt: 2015-10-08 23:01:37 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:41:37 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 2400.3 seconds
RetCode: None
Status:  TIMEOUT 
CheckDir: CAMERA.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings CAMERA_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/CAMERA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAMERA/DESCRIPTION’ ... OK
* this is package ‘CAMERA’ version ‘1.24.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘xcms’ ‘igraph’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Unexported objects imported by ':::' calls:
  ‘xcms:::descendMin’ ‘xcms:::xcmsClusterApply’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘annotateGrp’ ‘combineHypothese’ ‘fastMatch’ ‘naOmit’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("getEIC", ..., PACKAGE = "xcms")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
File ‘CAMERA/R/zzz.R’:
  .onLoad calls:
    require(methods)

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

annotateGrpMPI2: no visible binding for global variable
  ‘papply_commondata’
cleanParallel: no visible global function definition for
  ‘mpi.close.Rslaves’
cleanParallel: no visible global function definition for ‘stopCluster’
fragments2metfusion : <anonymous>: no visible binding for global
  variable ‘object’
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’
plotPeakEICs,xsAnnotate : .local : <anonymous>: no visible binding for
  global variable ‘pc’
plotPeakEICs,xsAnnotate : .local: no visible binding for global
  variable ‘pspec’
* checking Rd files ... NOTE
prepare_Rd: findKendrickMasses.Rd:21-22: Dropping empty section \details
* 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 GNU extensions in Makefiles ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/44s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getIsotopeCluster  5.965  0.220   6.186
annotateDiffreport 4.992  0.672   5.665
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’

CAMERA.Rcheck/00install.out:

* installing *source* package ‘CAMERA’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fastMatch.c -o fastMatch.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o CAMERA.so fastMatch.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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
** testing if installed package can be loaded
* DONE (CAMERA)

CAMERA.Rcheck/CAMERA-Ex.timings:

nameusersystemelapsed
annotate-methods2.7440.0122.760
annotateDiffreport4.9920.6725.665
calcCaS-methods1.5480.0321.579
cleanParallel0.0010.0000.001
combinexsAnnos0.0010.0000.001
findAdducts-methods3.2620.0563.319
findIsotopes-methods0.5740.0040.577
findKendrickMasses1.3920.0001.392
findNeutralLoss0.5750.0040.578
findNeutralLossSpecs0.5810.0000.580
getAllPeakEICs-methods1.4530.0041.457
getIsotopeCluster5.9650.2206.186
getPeaklist-methods3.2170.0083.226
getpspectra0.5610.0120.577
groupCorr-methods4.3880.0204.410
groupDen-methods2.1400.0082.153
groupFWHM-methods2.0390.0042.043
pspec2metfrag3.1580.0043.171
ruleSet-class0.0540.0000.054
xsAnnotate1.4150.0041.418