Mike Jiang
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CytoML |
| Branch: RELEASE_3_8 |
| Last Commit: b12fab2 |
| Last Changed Date: 2019-01-04 13:27:54 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:52 -0400 (Sat, 13 Apr 2019).
| Package 364/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CytoML 1.8.1 Mike Jiang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CytoML |
| Version: 1.8.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CytoML_1.8.1.tar.gz |
| StartedAt: 2019-04-13 01:37:13 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:44:25 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 431.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoML.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CytoML_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/CytoML.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.8.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 ... OK
* 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'
DerivedParameterNode: no visible global function definition for
'write.csv'
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'
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'
Undefined global functions or variables:
. ..dim comp_ref count fcs fcs_filename gate_def gate_id id
is.smaller name parent parent_count population sampleSelected
specimen write.csv x y
Consider adding
importFrom("utils", "write.csv")
to your NAMESPACE file.
* 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 5.89 1.28 6.33
cytobank2GatingSet 5.61 1.05 5.76
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
compare.counts 6.05 0.79 5.91
cytobank2GatingSet 4.92 1.14 5.37
* 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-3.8-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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/CytoML_1.8.1.tar.gz && rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CytoML_1.8.1.zip && rm CytoML_1.8.1.tar.gz CytoML_1.8.1.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1194k 100 1194k 0 0 23.7M 0 --:--:-- --:--:-- --:--:-- 25.3M
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_1.8.1.zip
* DONE (CytoML)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'CytoML' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
CytoML.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-cytobank.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-diva2gs.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-extend.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-flowJo.R")
>
> proc.time()
user system elapsed
96.15 12.98 99.17
|
CytoML.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-cytobank.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-diva2gs.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-extend.R")
> # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-flowJo.R")
>
> proc.time()
user system elapsed
83.87 9.14 85.98
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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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