Mike Jiang
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/ggcyto |
| Branch: RELEASE_3_10 |
| Last Commit: 295ca54 |
| Last Changed Date: 2020-03-06 18:02:43 -0400 (Fri, 06 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:25:57 -0400 (Wed, 15 Apr 2020).
| Package 702/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggcyto 1.14.1 Mike Jiang
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ggcyto |
| Version: 1.14.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ggcyto_1.14.1.tar.gz |
| StartedAt: 2020-04-15 03:31:53 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:38:07 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 374.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ggcyto.Rcheck |
| Warnings: 3 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggcyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ggcyto_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ggcyto.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.14.1'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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-3.10-bioc/tmpdir/Rtmp0YWKo3/R.INSTALL1c705bff47d7/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-3.10-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.
':::' call which should be '::': 'flowWorkspace:::gh_pop_is_negated'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'flowWorkspace:::.mergeGates' 'flowWorkspace:::compact'
'flowWorkspace:::fix_y_axis' 'ggplot2:::+.gg' 'ggplot2:::add_group'
'ggplot2:::as_gg_data_frame' 'ggplot2:::check_aesthetics'
'ggplot2:::hex_binwidth' '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'
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 global function definition for 'modifyList'
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 : <anonymous>: no visible binding for global variable 'axis'
as.ggplot : <anonymous>: 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_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:
axis density desc getS3method gray modifyList name
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "axis")
importFrom("stats", "density")
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 ... WARNING
Undocumented S4 methods:
generic '%+%' and siglist 'ggcyto'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'fortify.filterList'
'data' 'nPoints'
Undocumented arguments in documentation object 'fortify.polygonGate'
'nPoints'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 12.08 0.66 12.31
ggcyto.flowSet 6.64 0.08 6.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot 10.97 0.49 11.20
ggcyto.flowSet 6.92 0.14 7.03
ggcyto 6.13 0.10 6.18
plus-.ggcyto_GatingLayout 5.10 0.04 5.10
* 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 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-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://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ggcyto_1.14.1.tar.gz && rm -rf ggcyto.buildbin-libdir && mkdir ggcyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggcyto.buildbin-libdir ggcyto_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ggcyto_1.14.1.zip && rm ggcyto_1.14.1.tar.gz ggcyto_1.14.1.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
100 9813k 100 9813k 0 0 73.3M 0 --:--:-- --:--:-- --:--:-- 75.4M
install for i386
* installing *source* package 'ggcyto' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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-3.10-bioc/tmpdir/Rtmp0YWKo3/R.INSTALL1c705bff47d7/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'ggcyto' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggcyto' as ggcyto_1.14.1.zip
* DONE (ggcyto)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ggcyto' successfully unpacked and MD5 sums checked
|
ggcyto.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 7 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
73.39 5.15 78.81
|
ggcyto.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 7 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
68.06 3.40 71.32
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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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