Mike Jiang
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/flowViz |
| Branch: RELEASE_3_8 |
| Last Commit: ae31755 |
| Last Changed Date: 2019-01-04 13:33:12 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:20:05 -0400 (Sat, 13 Apr 2019).
| Package 552/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowViz 1.46.1 Mike Jiang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: flowViz |
| Version: 1.46.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowViz_1.46.1.tar.gz |
| StartedAt: 2019-04-13 02:19:40 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:23:35 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 234.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowViz.Rcheck |
| Warnings: 1 |
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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:flowViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowViz_1.46.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowViz.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 'flowViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowViz' version '1.46.1'
* 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 'flowViz' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpsDRcPd/R.INSTALL12a41c22139f/flowViz/man/xyplot.Rd:104: file link 'filtersList-class' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpsDRcPd/R.INSTALL12a41c22139f/flowViz/man/xyplot.Rd:174: file link 'sqrt' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowViz.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'flowCore' 'lattice'
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:
'lattice:::hist.constructor' 'lattice:::updateList'
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
flowPlot,flowFrame: warning in log(xd, b = 10): partial argument match
of 'b' to 'base'
flowPlot,flowFrame: warning in log(yd, b = 10): partial argument match
of 'b' to 'base'
.process_overlay_flowSet : <anonymous>: no visible global function
definition for 'extends'
.xyplot.flowSet: no visible global function definition for 'as.formula'
panel.densityplot.flowset.stack: no visible binding for global variable
'rl'
panel.xyplot.flowframe: no visible global function definition for
'densCols'
panel.xyplot.flowframe.old: no visible global function definition for
'densCols'
prepanel.densityplot.flowset.stack: no visible global function
definition for 'extends'
contour,flowFrame: no visible global function definition for
'contourLines'
flowPlot,flowFrame: no visible global function definition for 'rainbow'
glpoints,filter-flowFrame-missing: no visible binding for global
variable 'parms'
glpoints,filter-flowFrame-missing: no visible binding for global
variable 'strict'
gpoints,quadGate-flowFrame-character: no visible binding for global
variable 'filterResult'
gpolygon,ellipsoidGate-character: no visible binding for global
variable 'fd'
Undefined global functions or variables:
as.formula contourLines densCols extends fd filterResult parms
rainbow rl strict
Consider adding
importFrom("grDevices", "contourLines", "densCols", "rainbow")
importFrom("methods", "extends")
importFrom("stats", "as.formula")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: glines-methods.Rd:149-151: Dropping empty section 'Methods'
prepare_Rd: timeLinePlot.Rd:72-74: Dropping empty section 'Methods'
* 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' ... NOTE
Files named as vignettes but with no recognized vignette engine:
'vignettes/densityplot_vs_histogram.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
densityplot 11.21 0.25 11.45
xyplot 10.34 0.07 10.40
splom 9.75 0.27 10.01
lattice-methods 9.11 0.25 9.36
timeLinePlot 6.05 0.04 6.10
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
xyplot 10.88 0.13 11.00
splom 9.97 0.14 10.11
lattice-methods 9.42 0.34 9.77
densityplot 8.91 0.23 9.14
timeLinePlot 5.95 0.06 6.01
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: 'data.table'
* 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, 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowViz.Rcheck/00check.log'
for details.
flowViz.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/flowViz_1.46.1.tar.gz && rm -rf flowViz.buildbin-libdir && mkdir flowViz.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowViz.buildbin-libdir flowViz_1.46.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowViz_1.46.1.zip && rm flowViz_1.46.1.tar.gz flowViz_1.46.1.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 804k 100 804k 0 0 17.3M 0 --:--:-- --:--:-- --:--:-- 19.1M
install for i386
* installing *source* package 'flowViz' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flowViz'
finding HTML links ... done
addName-methods html
contour-methods html
densityplot html
ecdfplot html
flowPlot html
flowViz-package html
flowViz.par.get html
glines-methods html
glpoints-methods html
glpolygon-methods html
gpoints-methods html
gpolygon-methods html
lattice-methods html
plot html
splom html
timeLinePlot html
xyplot html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpsDRcPd/R.INSTALL12a41c22139f/flowViz/man/xyplot.Rd:104: file link 'filtersList-class' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpsDRcPd/R.INSTALL12a41c22139f/flowViz/man/xyplot.Rd:174: file link 'sqrt' in package 'base' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
'filters.Rmd'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'flowViz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowViz' as flowViz_1.46.1.zip
* DONE (flowViz)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowViz' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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flowViz.Rcheck/examples_i386/flowViz-Ex.timings
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flowViz.Rcheck/examples_x64/flowViz-Ex.timings
|