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BioC 2.14: CHECK report for CAMERA on morelia

This page was generated on 2014-10-08 09:03:52 -0700 (Wed, 08 Oct 2014).

Package 117/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAMERA 1.20.0
Carsten Kuhl
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/CAMERA
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: CAMERA
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CAMERA_1.20.0.tar.gz
StartedAt: 2014-10-07 21:39:46 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:43:34 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 228.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CAMERA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CAMERA_1.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/CAMERA.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAMERA/DESCRIPTION’ ... OK
* this is package ‘CAMERA’ version ‘1.20.0’
* 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 ... [20s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 the chapter ‘System and foreign language interfaces’ of 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’
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 binding for global variable ‘graphMethod’
findAdducts,xsAnnotate: no visible global function definition for
  ‘mpi.comm.size’
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ... [61s/67s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
cleanParallel     3.648  2.995  11.631
groupCorr-methods 6.216  0.205   6.427
getIsotopeCluster 5.417  0.106   5.527
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [45s/49s]
 [45s/49s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/CAMERA.Rcheck/00check.log’
for details.

CAMERA.Rcheck/00install.out:

* installing *source* package ‘CAMERA’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fastMatch.c -o fastMatch.o
clang -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-2.14-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-methods4.3180.0694.423
annotateDiffreport4.3020.1224.724
calcCaS-methods2.1020.0642.168
cleanParallel 3.648 2.99511.631
combinexsAnnos0.0010.0000.001
findAdducts-methods4.6050.0414.650
findIsotopes-methods0.8440.0120.856
findKendrickMasses1.7650.0371.804
findNeutralLoss0.7780.0080.787
findNeutralLossSpecs0.7620.0110.774
getAllPeakEICs-methods2.0780.0522.131
getIsotopeCluster5.4170.1065.527
getPeaklist-methods4.5890.0394.632
getpspectra0.7670.0090.777
groupCorr-methods6.2160.2056.427
groupDen-methods2.6830.0432.728
groupFWHM-methods2.4580.0562.514
pspec2metfrag4.5280.0444.573
ruleSet-class0.0910.0020.094
xsAnnotate1.8200.0391.860