Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for CytoML on zin1

This page was generated on 2016-09-21 03:40:57 -0700 (Wed, 21 Sep 2016).

Package 284/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 0.99.10
Mike Jiang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CytoML
Last Changed Rev: 120697 / Revision: 121152
Last Changed Date: 2016-09-02 11:25:15 -0700 (Fri, 02 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CytoML
Version: 0.99.10
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CytoML_0.99.10.tar.gz
StartedAt: 2016-09-20 05:16:50 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:19:25 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 155.1 seconds
RetCode: 0
Status:  OK 
CheckDir: CytoML.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings CytoML_0.99.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/CytoML.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 ‘CytoML/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CytoML’ version ‘0.99.10’
* 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 ‘CytoML’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘flowUtils:::.fuEnv’ ‘flowUtils:::smartTreeParse’
  ‘flowWorkspace:::.cpp_getCompensation’
  ‘flowWorkspace:::.fix_channel_slash’
  ‘flowWorkspace:::compute.timestep’ ‘flowWorkspace:::isHidden’
  ‘flowWorkspace:::isNegated’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GatingSet2flowJo: no visible global function definition for ‘pData<-’
addCustomInfo : <anonymous>: no visible global function definition for
  ‘is’
addGate: no visible binding for global variable ‘id’
addGate: no visible binding for global variable ‘gate_id’
addGate: no visible binding for global variable ‘fcs’
addGate: no visible binding for global variable ‘gate_def’
addGate: no visible binding for global variable ‘name’
compare.counts: no visible binding for global variable ‘population’
compare.counts: no visible binding for global variable ‘parent’
compare.counts: no visible binding for global variable ‘count’
compare.counts: no visible binding for global variable ‘parent_count’
compare.counts: no visible global function definition for ‘.’
compare.counts: no visible binding for global variable ‘fcs_filename’
constructTree : <anonymous>: no visible binding for global variable
  ‘slot’
constructTree: no visible binding for global variable ‘id’
constructTree: no visible binding for global variable ‘name’
extend.ellipsoidGate: no visible global function definition for ‘as’
extend.polygonGate : <anonymous>: no visible binding for global
  variable ‘y’
extend.polygonGate : <anonymous>: no visible binding for global
  variable ‘x’
extend.polygonGate: no visible binding for global variable ‘id’
extend.polygonGate: no visible binding for global variable ‘x’
extend.polygonGate: no visible binding for global variable ‘y’
extend.polygonGate: no visible binding for global variable ‘is.smaller’
extend.polygonGate: no visible global function definition for ‘rgb’
extend.rectangleGate: no visible global function definition for ‘as’
gateNode.ellipsoidGate: no visible global function definition for ‘as’
inverse.ellipsoidGate: no visible global function definition for ‘as’
inverse.rectangleGate: no visible global function definition for ‘as’
read.gatingML.cytobank: no visible global function definition for ‘is’
read.gatingML.cytobank: no visible binding for global variable ‘id’
read.gatingML.cytobank: no visible binding for global variable
  ‘comp_ref’
read.gatingML.cytobank : <anonymous>: no visible global function
  definition for ‘is’
read.gatingML.cytobank: no visible global function definition for ‘as’
subPopulationNode : <anonymous>: no visible global function definition
  for ‘is’
subPopulationNode : <anonymous> : <anonymous>: no visible global
  function definition for ‘is’
xmlTag: no visible global function definition for ‘is’
compensate,GatingSet-graphGML: no visible global function definition
  for ‘is’
getTransformations,graphGML : <anonymous>: no visible global function
  definition for ‘extends’
transform,ellipsoidGate: no visible global function definition for ‘as’
Undefined global functions or variables:
  . as comp_ref count extends fcs fcs_filename gate_def gate_id id is
  is.smaller name pData<- parent parent_count population rgb slot x y
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "as", "extends", "is", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
compare.counts 5.048  0.192   5.261
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/CytoML.Rcheck/00check.log’
for details.


CytoML.Rcheck/00install.out:

* installing *source* package ‘CytoML’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘CytoML’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CytoML)

CytoML.Rcheck/CytoML-Ex.timings:

nameusersystemelapsed
GatingSet2cytobank2.2240.0722.300
GatingSet2flowJo1.8480.0281.880
compare.counts5.0480.1925.261
cytobank2GatingSet4.0720.1604.233
extend0.0760.0000.075
getChildren-graphGML-character-method0.5800.0080.589
getNodes-graphGML-method0.5960.0000.596
plot-graphGML-missing-method0.6320.0000.634
read.gatingML.cytobank0.5880.0000.587