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This page was generated on 2016-09-21 03:48:36 -0700 (Wed, 21 Sep 2016).
| Package 284/1257 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| CytoML 0.99.10 Mike Jiang
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK |  | |||||
| 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 | |
| Package: CytoML |
| Version: 0.99.10 |
| Command: rm -rf CytoML.buildbin-libdir CytoML.Rcheck && mkdir CytoML.buildbin-libdir CytoML.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CytoML.buildbin-libdir CytoML_0.99.10.tar.gz >CytoML.Rcheck\00install.out 2>&1 && cp CytoML.Rcheck\00install.out CytoML-install.out && D:\biocbld\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_0.99.10.tar.gz |
| StartedAt: 2016-09-20 06:46:38 -0700 (Tue, 20 Sep 2016) |
| EndedAt: 2016-09-20 06:51:45 -0700 (Tue, 20 Sep 2016) |
| EllapsedTime: 307.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CytoML.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf CytoML.buildbin-libdir CytoML.Rcheck && mkdir CytoML.buildbin-libdir CytoML.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CytoML.buildbin-libdir CytoML_0.99.10.tar.gz >CytoML.Rcheck\00install.out 2>&1 && cp CytoML.Rcheck\00install.out CytoML-install.out && D:\biocbld\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_0.99.10.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/CytoML.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '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 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 5.96 0.23 7.33
cytobank2GatingSet 5.19 0.22 5.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compare.counts 6.65 0.23 9.52
cytobank2GatingSet 5.24 0.33 5.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
Warning message:
running command '"D:/biocbld/BBS-3˜1.4-B/R/bin/i386/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 5
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
> library(CytoML)
>
>
> test_check("CytoML")
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: ggplot2
1. Error: gatingML-cytobank exporting: cytotrol tcell (@test-cytobank.R#24) ----
cannot open the connection
1: file("/dev/null", "r") at testthat/test-cytobank.R:24
** running tests for arch 'x64' ...
Running 'testthat.R'
Warning message:
running command '"D:/biocbld/BBS-3˜1.4-B/R/bin/x64/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
OK: 9 SKIPPED: 0 FAILED: 3
1. Error: gatingML-cytobank exporting: cytotrol tcell (@test-cytobank.R#24)
2. Error: autogating--tcell (@test-flowJo.R#36)
3. Error: GatingSet2flowJo: manual gates with calibration table parsed and stored as biexp (@test-flowJo.R#52)
D:/biocbld/bbs-3.4-bioc/tmpdir/RtmpScB3eX/file17bc1e5818fb.wsp:1: parser error : Unsupported encoding ISO8859-1
<?xml version="1.0" encoding="ISO8859-1"?><Workspace version="20.0" xmlns:xsi="h
^
D:/biocbld/bbs-3.4-bioc/tmpdir/RtmpScB3eX/file17bc7b4d4d9f.wsp:1: parser error : Unsupported encoding ISO8859-1
<?xml version="1.0" encoding="ISO8859-1"?><Workspace version="20.0" xmlns:xsi="h
^
Error: testthat unit tests failed
Execution halted
* 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 ERRORs, 2 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/CytoML.Rcheck/00check.log'
for details.
testthat.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(CytoML)
>
>
> test_check("CytoML")
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: ggplot2
1. Error: gatingML-cytobank exporting: cytotrol tcell (@test-cytobank.R#24) ----
cannot open the connection
1: file("/dev/null", "r") at testthat/test-cytobank.R:24
testthat.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(CytoML)
>
>
> test_check("CytoML")
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: ggplot2
1. Error: gatingML-cytobank exporting: cytotrol tcell (@test-cytobank.R#24) ----
cannot open the connection
1: file("/dev/null", "r") at testthat/test-cytobank.R:24
2. Error: autogating--tcell (@test-flowJo.R#36) --------------------------------
Document not parsed successfully.Check if the path is valid.
1: parseWorkspace(ws, name = 1, path = dataDir) at testthat/test-flowJo.R:36
2: parseWorkspace(ws, name = 1, path = dataDir)
3: .preprocessor(obj, ...)
4: .parseWorkspace(xmlFileName = file.path(obj@path, obj@file), pd = pd, xmlParserOption = obj@options,
wsType = wsType, ws = obj, sampNloc = sampNloc, execute = execute, ...)
5: GatingSet(x = xmlFileName, y = as.character(pd[["sampleID"]]), guids = pd[["guid"]],
includeGates = includeGates, sampNloc = sampNloc, xmlParserOption = xmlParserOption,
wsType = wsType)
6: GatingSet(x = xmlFileName, y = as.character(pd[["sampleID"]]), guids = pd[["guid"]],
includeGates = includeGates, sampNloc = sampNloc, xmlParserOption = xmlParserOption,
wsType = wsType)
7: .local(x, y, ...)
8: .cpp_parseWorkspace(xmlFileName, sampleIDs, guids, includeGates, as.integer(sampNloc),
as.integer(xmlParserOption), as.integer(wsType))
3. Error: GatingSet2flowJo: manual gates with calibration table parsed and stored as biexp (@test-flowJo.R#52)
Document not parsed successfully.Check if the path is valid.
1: parseWorkspace(ws, name = 1, path = dataDir) at testthat/test-flowJo.R:52
2: parseWorkspace(ws, name = 1, path = dataDir)
3: .preprocessor(obj, ...)
4: .parseWorkspace(xmlFileName = file.path(obj@path, obj@file), pd = pd, xmlParserOption = obj@options,
wsType = wsType, ws = obj, sampNloc = sampNloc, execute = execute, ...)
5: GatingSet(x = xmlFileName, y = as.character(pd[["sampleID"]]), guids = pd[["guid"]],
includeGates = includeGates, sampNloc = sampNloc, xmlParserOption = xmlParserOption,
wsType = wsType)
6: GatingSet(x = xmlFileName, y = as.character(pd[["sampleID"]]), guids = pd[["guid"]],
includeGates = includeGates, sampNloc = sampNloc, xmlParserOption = xmlParserOption,
wsType = wsType)
7: .local(x, y, ...)
8: .cpp_parseWorkspace(xmlFileName, sampleIDs, guids, includeGates, as.integer(sampNloc),
as.integer(xmlParserOption), as.integer(wsType))
testthat results ================================================================
OK: 9 SKIPPED: 0 FAILED: 3
1. Error: gatingML-cytobank exporting: cytotrol tcell (@test-cytobank.R#24)
2. Error: autogating--tcell (@test-flowJo.R#36)
3. Error: GatingSet2flowJo: manual gates with calibration table parsed and stored as biexp (@test-flowJo.R#52)
D:/biocbld/bbs-3.4-bioc/tmpdir/RtmpScB3eX/file17bc1e5818fb.wsp:1: parser error : Unsupported encoding ISO8859-1
<?xml version="1.0" encoding="ISO8859-1"?><Workspace version="20.0" xmlns:xsi="h
^
D:/biocbld/bbs-3.4-bioc/tmpdir/RtmpScB3eX/file17bc7b4d4d9f.wsp:1: parser error : Unsupported encoding ISO8859-1
<?xml version="1.0" encoding="ISO8859-1"?><Workspace version="20.0" xmlns:xsi="h
^
Error: testthat unit tests failed
Execution halted
CytoML.Rcheck/00install.out:
install for i386 * 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 install for x64 * installing *source* package 'CytoML' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'CytoML' as CytoML_0.99.10.zip * DONE (CytoML)
CytoML.Rcheck/examples_i386/CytoML-Ex.timings:
| name | user | system | elapsed | |
| GatingSet2cytobank | 2.26 | 0.08 | 2.34 | |
| GatingSet2flowJo | 1.89 | 0.03 | 2.08 | |
| compare.counts | 5.96 | 0.23 | 7.33 | |
| cytobank2GatingSet | 5.19 | 0.22 | 5.47 | |
| extend | 0.08 | 0.02 | 0.10 | |
| getChildren-graphGML-character-method | 0.69 | 0.00 | 0.68 | |
| getNodes-graphGML-method | 0.65 | 0.00 | 0.66 | |
| plot-graphGML-missing-method | 0.71 | 0.00 | 0.70 | |
| read.gatingML.cytobank | 0.65 | 0.00 | 0.66 | |
CytoML.Rcheck/examples_x64/CytoML-Ex.timings:
| name | user | system | elapsed | |
| GatingSet2cytobank | 2.59 | 0.08 | 3.22 | |
| GatingSet2flowJo | 2.35 | 0.02 | 2.91 | |
| compare.counts | 6.65 | 0.23 | 9.52 | |
| cytobank2GatingSet | 5.24 | 0.33 | 5.72 | |
| extend | 0.09 | 0.00 | 0.10 | |
| getChildren-graphGML-character-method | 0.80 | 0.00 | 0.79 | |
| getNodes-graphGML-method | 0.82 | 0.00 | 0.83 | |
| plot-graphGML-missing-method | 0.88 | 0.00 | 0.87 | |
| read.gatingML.cytobank | 0.87 | 0.00 | 0.88 | |