Greg Finak
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/flowStats |
| Branch: RELEASE_3_9 |
| Last Commit: c6a56bb |
| Last Changed Date: 2019-05-02 11:53:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:22:36 -0400 (Wed, 16 Oct 2019).
| Package 579/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowStats 3.42.0 Greg Finak
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: flowStats |
| Version: 3.42.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flowStats_3.42.0.tar.gz |
| StartedAt: 2019-10-16 03:46:15 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:51:05 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 289.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowStats.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings flowStats_3.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/flowStats.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '3.42.0'
* package encoding: UTF-8
* 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 'flowStats' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/autoGate.Rd:21: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/gate_singlet.Rd:47: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/lymphGate.Rd:83: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/normalize.Rd:58: file link 'ncdfFlowSet' in package 'ncdfFlow' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/quadrantGate.Rd:71: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/quadrantGate.Rd:79: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/rangeGate.Rd:135: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/rangeGate.Rd:145: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/flowStats.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
Missing object imported by a ':::' call: 'flowWorkspace:::.isBooleanGate.graphNEL'
Unexported objects imported by ':::' calls:
'flowCore:::checkClass' 'flowCore:::copyFlowSet'
'flowCore:::findTimeChannel' 'flowCore:::inPolygon'
'flowViz:::evalError' 'flowViz:::plotType'
'flowWorkspace:::.isBoolGate'
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
.plotGPAprocess: no visible binding for global variable 'whichS'
.plotGPAprocess: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'bogus'
.usingSVD: no visible binding for global variable 'params'
density1d_simple: no visible binding for global variable 'y'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
Undefined global functions or variables:
bogus cluster group hasPeak params whichS y
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
warpSet 19.56 0.61 20.17
gaussNorm 8.70 0.22 8.92
rangeGate 5.05 0.22 5.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
warpSet 20.25 0.36 20.61
gaussNorm 6.55 0.28 6.83
* 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-3.9-bioc/meat/flowStats.Rcheck/00check.log'
for details.
flowStats.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/flowStats_3.42.0.tar.gz && rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowStats.buildbin-libdir flowStats_3.42.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL flowStats_3.42.0.zip && rm flowStats_3.42.0.tar.gz flowStats_3.42.0.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 1508k 100 1508k 0 0 3515k 0 --:--:-- --:--:-- --:--:-- 3573k
install for i386
* installing *source* package 'flowStats' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flowStats'
finding HTML links ... done
BackGating html
ITN html
addName-methods html
autoGate html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/autoGate.Rd:21: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
binByRef html
calcPBChiSquare html
calcPearsonChi html
curv1Filter-class html
finding level-2 HTML links ... done
curv2Filter-class html
curvPeaks html
density1d html
fdPar html
flowStats-package html
gate_singlet html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/gate_singlet.Rd:47: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
gaussNorm html
gpaSet html
iProcrustes html
idFeaturesByBackgating html
landmarkMatrix html
lymphGate html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/lymphGate.Rd:83: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
normQA html
normalize html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/normalize.Rd:58: file link 'ncdfFlowSet' in package 'ncdfFlow' does not exist and so has been treated as a topic
overton_like html
plotBins html
proBin html
quadrantGate html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/quadrantGate.Rd:71: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/quadrantGate.Rd:79: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
rangeGate html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/rangeGate.Rd:135: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4gVE0V/R.INSTALL14981af71278/flowStats/man/rangeGate.Rd:145: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
spillover_ng-flowSet html
warpSet 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 'flowStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowStats' as flowStats_3.42.0.zip
* DONE (flowStats)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'flowStats' successfully unpacked and MD5 sums checked
|
flowStats.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(flowStats)
Loading required package: flowCore
Loading required package: cluster
Loading required package: flowWorkspace
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
>
> test_check("flowStats")
== testthat results ===========================================================
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
5.26 0.39 5.65
|
flowStats.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(flowStats)
Loading required package: flowCore
Loading required package: cluster
Loading required package: flowWorkspace
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
>
> test_check("flowStats")
== testthat results ===========================================================
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
6.60 0.39 6.98
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flowStats.Rcheck/examples_i386/flowStats-Ex.timings
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flowStats.Rcheck/examples_x64/flowStats-Ex.timings
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