Mike Jiang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ggcyto |
| Branch: RELEASE_3_7 |
| Last Commit: ad88ca1 |
| Last Changed Date: 2018-07-13 03:07:15 -0400 (Fri, 13 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:41:32 -0400 (Wed, 17 Oct 2018).
| Package 614/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggcyto 1.8.2 Mike Jiang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ggcyto |
| Version: 1.8.2 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ggcyto_1.8.2.tar.gz |
| StartedAt: 2018-10-17 02:20:31 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:31:46 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 675.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ggcyto.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ggcyto_1.8.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ggcyto.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 'ggcyto/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ggcyto' version '1.8.2'
* 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 'ggcyto' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpOOz7u1/R.INSTALL1dc430ce4ea0/ggcyto/man/marginalFilter.Rd:14: file link 'boundaryFilter' in package 'flowCore' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ggcyto.Rcheck/00install.out' for details.
* 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
* 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
Namespace in Imports field not imported from: 'scales'
All declared Imports should be used.
Unexported objects imported by ':::' calls:
'flowWorkspace:::.mergeGates' 'flowWorkspace:::compact'
'flowWorkspace:::fix_y_axis' 'flowWorkspace:::isNegated'
'ggplot2:::+.gg' 'ggplot2:::add_group' 'ggplot2:::as_gg_data_frame'
'ggplot2:::check_aesthetics' 'ggplot2:::is.waive'
'ggplot2:::is_calculated_aes' 'ggplot2:::make_labels'
'ggplot2:::make_scale' 'ggplot2:::plot_clone'
'ggplot2:::print.ggplot' 'ggplot2:::scales_add_defaults'
'ggplot2:::scales_list' 'ggplot2:::update_theme'
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
.fs2dt: no visible binding for global variable 'name'
add_ggcyto: no visible binding for global variable 'name'
add_ggcyto: no visible binding for global variable 'axis'
add_ggcyto: no visible binding for global variable 'desc'
add_par: no visible global function definition for 'modifyList'
as.ggplot: no visible binding for global variable 'axis'
as.ggplot: no visible binding for global variable 'name'
as.ggplot: no visible binding for global variable 'density'
autoplot.GatingHierarchy : <anonymous>: no visible global function
definition for 'gray'
autoplot.GatingSetList: no visible global function definition for
'getS3method'
autoplot.ncdfFlowList: no visible global function definition for
'getS3method'
density_fr_all : <anonymous>: no visible global function definition for
'gray'
fortify.GatingSetList: no visible global function definition for
'getS3method'
fortify.ncdfFlowList: no visible global function definition for
'getS3method'
fortify.polygonGate : <anonymous>: no visible global function
definition for 'dist'
fortify.polygonGate : <anonymous>: no visible global function
definition for 'approx'
fortify_fs.GatingSetList: no visible global function definition for
'getS3method'
getFlowFrame.GatingSetList: no visible global function definition for
'getS3method'
getFlowFrame.ncdfFlowList: no visible global function definition for
'getS3method'
ggcyto.GatingSetList: no visible global function definition for
'getS3method'
ggcyto.flowSet: no visible binding for global variable 'name'
ggcyto.flowSet: no visible binding for global variable 'axis'
ggcyto.ncdfFlowList: no visible global function definition for
'getS3method'
ggcyto_arrange: no visible binding for global variable 'name'
Undefined global functions or variables:
approx axis density desc dist getS3method gray modifyList name
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "axis")
importFrom("stats", "approx", "density", "dist")
importFrom("utils", "getS3method", "modifyList")
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
autoplot 11.37 0.25 11.63
ggcyto.flowSet 5.91 0.08 5.99
plus-.ggcyto_GatingLayout 5.03 0.03 5.06
scale_x_flowJo_fasinh 1.37 0.11 28.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot 11.53 0.27 66.41
ggcyto.flowSet 6.39 0.17 6.56
plus-.ggcyto_GatingLayout 5.63 0.00 5.63
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/ggcyto.Rcheck/00check.log'
for details.
ggcyto.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/ggcyto_1.8.2.tar.gz && rm -rf ggcyto.buildbin-libdir && mkdir ggcyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggcyto.buildbin-libdir ggcyto_1.8.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ggcyto_1.8.2.zip && rm ggcyto_1.8.2.tar.gz ggcyto_1.8.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 10.2M 100 10.2M 0 0 63.6M 0 --:--:-- --:--:-- --:--:-- 66.5M
install for i386
* installing *source* package 'ggcyto' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for '%+%' from package 'ggplot2' in package 'ggcyto'
** help
*** installing help indices
converting help for package 'ggcyto'
finding HTML links ... done
as.ggplot html
autoplot html
finding level-2 HTML links ... done
axis_x_inverse_trans html
compute_stats html
flowCore_asinht_trans html
fortify.ellipsoidGate html
fortify.filterList html
fortify.flowSet html
fortify.polygonGate html
fortify.rectangleGate html
fortify_fs html
geom_gate html
geom_hvline html
geom_overlay html
geom_stats html
getFlowFrame html
ggcyto.GatingSet html
ggcyto html
ggcyto.flowSet html
ggcyto_GatingSet_add html
ggcyto_arrange html
ggcyto_flowSet_add html
ggcyto_par_default html
ggcyto_par_set html
is.ggcyto html
is.ggcyto_flowSet html
is.ggcyto_par html
labs_cyto html
marginalFilter html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpOOz7u1/R.INSTALL1dc430ce4ea0/ggcyto/man/marginalFilter.Rd:14: file link 'boundaryFilter' in package 'flowCore' does not exist and so has been treated as a topic
merge.quad.gates html
plus-.ggcyto_GatingLayout html
print.ggcyto html
print.ggcyto_GatingLayout html
replace_data html
scale_x_flowCore_fasinh html
scale_x_flowJo_biexp html
scale_x_flowJo_fasinh html
scale_x_logicle html
stat_position html
transform-gate html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ggcyto' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggcyto' as ggcyto_1.8.2.zip
* DONE (ggcyto)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ggcyto' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
ggcyto.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(ggcyto)
Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: flowWorkspace
> library(vdiffr)
>
> test_check("ggcyto")
loading R object...
loading tree object...
Done
== testthat results ===========================================================
OK: 41 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
67.28 3.17 123.68
|
ggcyto.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(ggcyto)
Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: flowWorkspace
> library(vdiffr)
>
> test_check("ggcyto")
loading R object...
loading tree object...
Done
== testthat results ===========================================================
OK: 41 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
68.73 2.93 76.37
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ggcyto.Rcheck/examples_i386/ggcyto-Ex.timings
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ggcyto.Rcheck/examples_x64/ggcyto-Ex.timings
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