Mike Jiang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CytoML |
| Branch: RELEASE_3_7 |
| Last Commit: d484433 |
| Last Changed Date: 2018-07-17 02:08:43 -0400 (Tue, 17 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:42:31 -0400 (Wed, 17 Oct 2018).
| Package 340/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CytoML 1.6.5 Mike Jiang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CytoML |
| Version: 1.6.5 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CytoML_1.6.5.tar.gz |
| StartedAt: 2018-10-17 01:26:17 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:32:52 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 394.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoML.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CytoML_1.6.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CytoML.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.6.5'
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'methods'
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
* 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
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'flowUtils:::.fuEnv' 'flowUtils:::smartTreeParse'
'flowWorkspace:::.cpp_getCompensation'
'flowWorkspace:::.fix_channel_slash' 'flowWorkspace:::.groupByTree'
'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
.preprocessorDiva: no visible binding for global variable 'specimen'
.preprocessorDiva: no visible binding for global variable
'sampleSelected'
GatingSet2flowJo: no visible global function definition for 'pData<-'
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: no visible binding for global variable 'id'
constructTree: no visible binding for global variable 'name'
export_comp_trans: no visible global function definition for 'logtGml2'
extend.polygonGate: no visible binding for global variable '..dim'
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'
read.gatingML.cytobank: no visible binding for global variable 'id'
read.gatingML.cytobank: no visible binding for global variable
'comp_ref'
getTransformations,graphGML : <anonymous>: no visible global function
definition for 'logtGml2_trans'
Undefined global functions or variables:
. ..dim comp_ref count fcs fcs_filename gate_def gate_id id
is.smaller logtGml2 logtGml2_trans name pData<- parent parent_count
population sampleSelected specimen x y
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compare.counts 5.17 0.34 5.55
** running examples for arch 'x64' ... OK
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/CytoML.Rcheck/00check.log'
for details.
CytoML.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CytoML_1.6.5.tar.gz && rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_1.6.5.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CytoML_1.6.5.zip && rm CytoML_1.6.5.tar.gz CytoML_1.6.5.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 830k 100 830k 0 0 13.1M 0 --:--:-- --:--:-- --:--:-- 15.0M
install for i386
* installing *source* package 'CytoML' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CytoML'
finding HTML links ... done
GatingSet2cytobank html
GatingSet2flowJo html
addCustomInfo html
compare.counts html
compensate-GatingSet-graphGML-method html
constructTree html
cytobank2GatingSet html
divaWorkspace-class html
finding level-2 HTML links ... done
extend html
gating-methods html
getChildren-graphGML-character-method html
getCompensationMatrices-graphGML-method
html
getGate-graphGML-character-method html
getNodes-graphGML-method html
getParent-graphGML-character-method html
getTransformations-graphGML-method html
graphGML-class html
matchPath html
openDiva html
parse.gateInfo html
plot-graphGML-missing-method html
range.GatingHierarchy html
read.gatingML.cytobank html
show-graphGML-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'CytoML' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CytoML' as CytoML_1.6.5.zip
* DONE (CytoML)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CytoML' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
CytoML.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
== testthat results ===========================================================
OK: 26 SKIPPED: 0 FAILED: 0
>
> #devtools::test()
>
>
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R")
>
> proc.time()
user system elapsed
87.10 3.79 92.40
|
CytoML.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
windows version of flowJo workspace recognized.
version X
== testthat results ===========================================================
OK: 26 SKIPPED: 0 FAILED: 0
>
> #devtools::test()
>
>
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> #test_file("˜/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R")
>
> proc.time()
user system elapsed
92.31 2.95 95.60
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CytoML.Rcheck/examples_i386/CytoML-Ex.timings
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CytoML.Rcheck/examples_x64/CytoML-Ex.timings
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