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BioC 3.4: CHECK report for CAMERA on zin1

This page was generated on 2016-09-21 03:36:43 -0700 (Wed, 21 Sep 2016).

Package 150/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAMERA 1.29.0
Steffen Neumann
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CAMERA
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: 1.29.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CAMERA_1.29.0.tar.gz
StartedAt: 2016-09-20 04:02:55 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:05:42 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 167.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CAMERA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CAMERA_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CAMERA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.29.0’
* 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 ... 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’
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'.

annotateGrp: no visible global function definition for ‘na.omit’
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’
createHypothese: no visible global function definition for ‘cutree’
createHypothese: no visible global function definition for ‘hclust’
createHypothese: no visible global function definition for ‘dist’
extractfragments: no visible global function definition for ‘median’
fast_corr: no visible global function definition for ‘pt’
findKendrickMasses: no visible global function definition for ‘rainbow’
findKendrickMasses : <anonymous>: no visible global function definition
  for ‘lines’
findNeutralLoss: no visible global function definition for ‘dist’
findNeutralLossSpecs : <anonymous>: no visible global function
  definition for ‘dist’
fragments2metfrag : <anonymous>: no visible global function definition
  for ‘write.table’
fragments2metfusion : <anonymous>: no visible binding for global
  variable ‘object’
fragments2metfusion : <anonymous>: no visible global function
  definition for ‘write.table’
getIsotopeCluster : <anonymous>: no visible global function definition
  for ‘na.omit’
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’
groupComplete,xsAnnotate: no visible global function definition for
  ‘dist’
groupComplete,xsAnnotate: no visible global function definition for
  ‘cutree’
groupComplete,xsAnnotate: no visible global function definition for
  ‘hclust’
groupDen,xsAnnotate: no visible global function definition for
  ‘density’
groupFWHM,xsAnnotate : <anonymous>: no visible global function
  definition for ‘na.omit’
plotEICs,xsAnnotate: no visible global function definition for
  ‘rainbow’
plotEICs,xsAnnotate: no visible global function definition for
  ‘na.omit’
plotPeakEICs,xsAnnotate : <anonymous>: no visible binding for global
  variable ‘pc’
plotPeakEICs,xsAnnotate: no visible binding for global variable ‘pspec’
plotPeakEICs,xsAnnotate: no visible global function definition for
  ‘rainbow’
plotPeakEICs,xsAnnotate: no visible global function definition for
  ‘na.omit’
plotPsSpectrum,xsAnnotate: no visible global function definition for
  ‘median’
plotPsSpectrum,xsAnnotate: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  cutree density dist graphMethod hclust lines makeCluster median
  mpi.close.Rslaves mpi.comm.size mpi.spawn.Rslaves na.omit object
  papply_commondata pc pspec pt rainbow stopCluster write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines")
  importFrom("stats", "cutree", "density", "dist", "hclust", "median",
             "na.omit", "pt")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getIsotopeCluster  2.124  0.048   5.085
annotateDiffreport 1.300  0.024   5.009
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/CAMERA.Rcheck/00check.log’
for details.


CAMERA.Rcheck/00install.out:

* installing *source* package ‘CAMERA’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fastMatch.c -o fastMatch.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o CAMERA.so fastMatch.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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-methods2.5000.0362.537
annotateDiffreport1.3000.0245.009
calcCaS-methods1.7640.0281.793
cleanParallel000
combinexsAnnos0.0000.0000.001
findAdducts-methods2.7520.0082.758
findIsotopes-methods0.5400.0040.544
findKendrickMasses1.2760.0001.276
findNeutralLoss0.4760.0160.493
findNeutralLossSpecs0.4840.0040.487
getAllPeakEICs-methods1.7000.0121.713
getIsotopeCluster2.1240.0485.085
getPeaklist-methods2.7760.0242.797
getpspectra0.4920.0040.495
groupCorr-methods3.7440.0443.790
groupDen-methods1.7320.0081.743
groupFWHM-methods1.8120.0081.822
pspec2metfrag2.6280.0042.634
ruleSet-class0.0520.0000.050
xsAnnotate1.2080.0001.205