CytoML 1.0.1
Mike Jiang
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/CytoML | | Last Changed Rev: 125516 / Revision: 128728 | | Last Changed Date: 2016-12-29 19:24:05 -0500 (Thu, 29 Dec 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf CytoML.buildbin-libdir CytoML.Rcheck && mkdir CytoML.buildbin-libdir CytoML.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CytoML.buildbin-libdir CytoML_1.0.1.tar.gz >CytoML.Rcheck\00install.out 2>&1 && cp CytoML.Rcheck\00install.out CytoML-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=CytoML.buildbin-libdir --install="check:CytoML-install.out" --force-multiarch --no-vignettes --timings CytoML_1.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/CytoML.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CytoML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoML' version '1.0.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compare.counts 5.69 0.30 9.22
cytobank2GatingSet 4.92 0.42 5.37
GatingSet2cytobank 1.92 0.05 7.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compare.counts 5.64 0.22 5.86
cytobank2GatingSet 5.11 0.20 5.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.4-bioc/meat/CytoML.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'CytoML' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'CytoML' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CytoML' as CytoML_1.0.1.zip
* DONE (CytoML)