Errol Strain
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/plateCore |
| Branch: RELEASE_3_8 |
| Last Commit: 625f4a9 |
| Last Changed Date: 2019-01-04 13:44:25 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:02 -0400 (Sat, 13 Apr 2019).
| Package 1164/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| plateCore 1.40.1 Errol Strain
| malbec1 | Linux (Ubuntu 16.04.6 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: plateCore |
| Version: 1.40.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plateCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings plateCore_1.40.1.tar.gz |
| StartedAt: 2019-04-13 04:34:29 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:38:46 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 257.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: plateCore.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:plateCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings plateCore_1.40.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/plateCore.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 'plateCore/DESCRIPTION' ... OK
* this is package 'plateCore' version '1.40.1'
* 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 'plateCore' can be installed ... OK
* 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
Packages in Depends field not imported from:
'flowViz' 'latticeExtra'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
panel.xyplot.flowPlate: warning in filterBoundary(filter =
filter[[nm]], parameters = c(channel.x.name, channel.y.name), frame =
frames[[nm]]): partial argument match of 'filter' to 'filter.object'
fixAutoFl,flowPlate: no visible binding for global variable
'Sample.Type'
fpbind,flowPlate-flowPlate : <anonymous>: no visible binding for global
variable 'name'
gutterPlot,flowPlate: no visible global function definition for 'plot'
mfiPlot,flowPlate: no visible global function definition for 'plot'
plotPlate,flowPlate: no visible global function definition for 'plot'
setControlGates,flowPlate: no visible binding for global variable
'Sample.Type'
setControlGates,flowPlate: no visible binding for global variable
'Channel'
setControlGates,flowPlate : <anonymous>: no visible binding for global
variable 'Well.Id'
setControlGates,flowPlate : <anonymous>: no visible binding for global
variable 'plateName'
setControlGates,flowPlate : <anonymous>: no visible binding for global
variable 'name'
Undefined global functions or variables:
Channel Sample.Type Well.Id name plateName plot
Consider adding
importFrom("graphics", "plot")
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 'flowPlate,ANY,ANY,ANY'
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mfiPlot-methods 5.32 0.00 5.31
applyControlGates-methods 5.00 0.04 5.04
* 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/plateCore.Rcheck/00check.log'
for details.
plateCore.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/plateCore_1.40.1.tar.gz && rm -rf plateCore.buildbin-libdir && mkdir plateCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plateCore.buildbin-libdir plateCore_1.40.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL plateCore_1.40.1.zip && rm plateCore_1.40.1.tar.gz plateCore_1.40.1.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 2304k 100 2304k 0 0 24.8M 0 --:--:-- --:--:-- --:--:-- 25.8M
install for i386
* installing *source* package 'plateCore' ...
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
** help
*** installing help indices
converting help for package 'plateCore'
finding HTML links ... done
Subset-methods html
applyControlGates-methods html
compensate-methods html
compensationSet html
densityplot-methods html
fixAutoFl-methods html
flowPlate-class html
finding level-2 HTML links ... done
flowPlate-method html
fpbind-methods html
getGroups-methods html
gutterPlot-methods html
mfiPlot-methods html
on-methods html
panel.densityplot.flowPlate html
panel.xyplot.flowPlate html
pbmcPlate html
plateCore-package html
plateSet-methods html
plotPlate-methods html
prepanel.densityplot.flowPlate html
prepanel.xyplot.flowPlate html
setControlGates-methods html
summaryStats-methods html
wellAnnotation-methods html
xyplot-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
In R CMD INSTALL
install for x64
* installing *source* package 'plateCore' ...
** testing if installed package can be loaded
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
* MD5 sums
packaged installation of 'plateCore' as plateCore_1.40.1.zip
* DONE (plateCore)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'plateCore' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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plateCore.Rcheck/examples_i386/plateCore-Ex.timings
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plateCore.Rcheck/examples_x64/plateCore-Ex.timings
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