Nikolas Pontikos
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/flowBeads |
| Branch: RELEASE_3_8 |
| Last Commit: f1f1b24 |
| Last Changed Date: 2019-01-04 13:31:32 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:55 -0400 (Sat, 13 Apr 2019).
| Package 524/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowBeads 1.20.1 Nikolas Pontikos
| 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: flowBeads |
| Version: 1.20.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowBeads_1.20.1.tar.gz |
| StartedAt: 2019-04-13 02:14:45 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:16:55 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 130.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowBeads.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:flowBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowBeads_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowBeads.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 'flowBeads/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowBeads' version '1.20.1'
* 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 'flowBeads' 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' 'rrcov'
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
Namespaces in Imports field not imported from:
'knitr' 'rrcov' 'xtable'
All declared Imports should be used.
Packages in Depends field not imported from:
'Biobase' 'methods' 'rrcov'
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
BeadFlowFrame: no visible binding for global variable 'filename'
BeadFlowFrame: no visible global function definition for 'read.csv2'
BeadFlowFrame: no visible global function definition for 'new'
mefTransform: no visible global function definition for 'new'
absoluteNormalise,GatedBeadFlowFrame-data.frame: no visible global
function definition for 'lm'
gateBeads,BeadFlowFrame: no visible global function definition for 'as'
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
definition for 'quantile'
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
definition for 'kmeans'
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
definition for 'median'
gateBeads,BeadFlowFrame: no visible binding for global variable 'sd'
gateBeads,BeadFlowFrame: no visible global function definition for 'lm'
plot,BeadFlowFrame-character: no visible global function definition for
'par'
plot,BeadFlowFrame-character: no visible global function definition for
'hist'
plot,BeadFlowFrame-character: no visible global function definition for
'segments'
plot,BeadFlowFrame-character: no visible global function definition for
'title'
plot,GatedBeadFlowFrame-character: no visible global function
definition for 'par'
plot,GatedBeadFlowFrame-character: no visible global function
definition for 'hist'
plot,GatedBeadFlowFrame-character: no visible global function
definition for 'abline'
plot,GatedBeadFlowFrame-character: no visible global function
definition for 'segments'
plot,GatedBeadFlowFrame-character: no visible global function
definition for 'title'
relativeNormalise,GatedBeadFlowFrame-GatedBeadFlowFrame: no visible
global function definition for 'lm'
Undefined global functions or variables:
abline as filename hist kmeans lm median new par quantile read.csv2
sd segments title
Consider adding
importFrom("graphics", "abline", "hist", "par", "segments", "title")
importFrom("methods", "as", "new")
importFrom("stats", "kmeans", "lm", "median", "quantile", "sd")
importFrom("utils", "read.csv2")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowBeads.Rcheck/00check.log'
for details.
flowBeads.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/flowBeads_1.20.1.tar.gz && rm -rf flowBeads.buildbin-libdir && mkdir flowBeads.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowBeads.buildbin-libdir flowBeads_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowBeads_1.20.1.zip && rm flowBeads_1.20.1.tar.gz flowBeads_1.20.1.zip
###
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install for i386
* installing *source* package 'flowBeads' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flowBeads'
finding HTML links ... done
BeadFlowFrame-class html
finding level-2 HTML links ... done
GatedBeadFlowFrame-class html
absoluteNormalise-methods html
beads1 html
beads2 html
cytocalmef html
dakomef html
flowBeads-package html
gateBeads-methods html
generateReport-methods html
getClusteringStats-methods html
getDate-methods html
getMEFparams-methods html
getMEFtransform-methods html
getParams-methods html
getTransformFunction-methods html
hasMEF-methods html
length-methods html
mefTransform html
plot-methods html
relativeNormalise-methods html
show-methods html
toMEF-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'flowBeads' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowBeads' as flowBeads_1.20.1.zip
* DONE (flowBeads)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowBeads' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
flowBeads.Rcheck/examples_i386/flowBeads-Ex.timings
|
flowBeads.Rcheck/examples_x64/flowBeads-Ex.timings
|