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BioC 3.2: CHECK report for CAMERA on perceval

This page was generated on 2015-11-10 14:46:19 -0800 (Tue, 10 Nov 2015).

Package 134/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAMERA 1.26.0
Steffen Neumann
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CAMERA
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAMERA
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAMERA_1.26.0.tar.gz
StartedAt: 2015-11-10 02:49:50 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 02:53:43 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 233.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CAMERA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CAMERA_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CAMERA.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAMERA/DESCRIPTION’ ... OK
* this is package ‘CAMERA’ version ‘1.26.0’
* 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 ... [18s/19s] 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.
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 ... [55s/56s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getIsotopeCluster  7.976  0.539   8.516
annotateDiffreport 6.981  0.533   8.083
groupCorr-methods  5.202  0.201   5.404
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [68s/68s]
 [68s/68s] 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
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/CAMERA.Rcheck/00check.log’
for details.


CAMERA.Rcheck/00install.out:

* installing *source* package ‘CAMERA’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c fastMatch.c -o fastMatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -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-3.2-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-methods3.5150.0743.676
annotateDiffreport6.9810.5338.083
calcCaS-methods1.8170.0571.875
cleanParallel0.0010.0010.001
combinexsAnnos0.0010.0000.001
findAdducts-methods4.0460.0584.104
findIsotopes-methods0.7260.0160.742
findKendrickMasses1.6140.0091.622
findNeutralLoss0.6480.0140.662
findNeutralLossSpecs0.6560.0150.671
getAllPeakEICs-methods1.8430.0321.876
getIsotopeCluster7.9760.5398.516
getPeaklist-methods3.8820.0173.900
getpspectra0.6550.0120.667
groupCorr-methods5.2020.2015.404
groupDen-methods2.3770.0262.402
groupFWHM-methods2.4710.0162.487
pspec2metfrag3.9150.0213.936
ruleSet-class0.0780.0010.078
xsAnnotate1.5910.0031.594