Greg Finak
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/flowStats |
| Branch: RELEASE_3_10 |
| Last Commit: 1260965 |
| Last Changed Date: 2019-10-29 13:08:05 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:18:49 -0400 (Wed, 15 Apr 2020).
| Package 602/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowStats 3.44.0 Greg Finak
| 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: flowStats |
| Version: 3.44.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings flowStats_3.44.0.tar.gz |
| StartedAt: 2020-04-15 03:15:18 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:19:59 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 281.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowStats.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings flowStats_3.44.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowStats.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 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '3.44.0'
* 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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/autoGate.Rd:25: missing file link 'norm2Filter-class'
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/autoGate.Rd:54: missing file link 'norm2Filter-class'
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/lymphGate.Rd:79: missing file link 'norm2Filter-class'
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/lymphGate.Rd:133: file link 'ellipsoidGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/lymphGate.Rd:141: missing file link 'norm2Filter-class'
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/rangeGate.Rd:145: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/spillover-flowSet.Rd:34: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-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'
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 ... WARNING
Missing link or links in documentation object 'autoGate.Rd':
'[flowCore:norm2Filter-class]{norm2Filter}'
Missing link or links in documentation object 'lymphGate.Rd':
'[flowCore:norm2Filter-class]{norm2Filter}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '%in%' and siglist 'flowFrame,norm2Filter'
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 ... WARNING
Codoc mismatches from documentation object 'spillover-flowSet':
\S4method{spillover}{flowSet}
Code: function(x, unstained = NULL, fsc = "FSC-A", ssc = "SSC-A",
patt = NULL, method = "median", stain_match =
c("intensity", "ordered", "regexpr"), useNormFilt =
FALSE, prematched = FALSE, exact_match = FALSE)
Docs: function(x, unstained = NULL, fsc = "FSC-A", ssc = "SSC-A",
patt = NULL, method = "median", stain_match =
c("intensity", "ordered", "regexpr"), useNormFilt =
FALSE, prematched = FALSE)
Argument names in code not in docs:
exact_match
* 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 ... WARNING
Warning: package needs dependence on R (>= 2.10)
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
warpSet 22.60 0.98 23.60
gaussNorm 8.86 0.53 9.41
density1d 5.06 0.25 5.32
rangeGate 4.87 0.16 5.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
warpSet 13.17 0.53 13.7
* 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: 5 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowStats.Rcheck/00check.log'
for details.
flowStats.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/flowStats_3.44.0.tar.gz && rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowStats.buildbin-libdir flowStats_3.44.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL flowStats_3.44.0.zip && rm flowStats_3.44.0.tar.gz flowStats_3.44.0.zip
###
##############################################################################
##############################################################################
% 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 1518k 100 1518k 0 0 27.9M 0 --:--:-- --:--:-- --:--:-- 30.8M
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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/autoGate.Rd:25: missing file link 'norm2Filter-class'
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/autoGate.Rd:54: missing file link 'norm2Filter-class'
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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/lymphGate.Rd:79: missing file link 'norm2Filter-class'
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/lymphGate.Rd:133: file link 'ellipsoidGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/lymphGate.Rd:141: missing file link 'norm2Filter-class'
norm2Filter-class html
normQA html
normalize html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/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-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/rangeGate.Rd:145: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
spillover-flowSet html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc5Qtrq/R.INSTALLd703ab03360/flowStats/man/spillover-flowSet.Rd:34: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic
spillover_match-flowSet html
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_3.44.0.zip
* DONE (flowStats)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'flowStats' successfully unpacked and MD5 sums checked
|
flowStats.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(flowStats)
>
> test_check("flowStats")
Estimating landmarks for channel CD4 ...
Registering curves for parameter CD4 ...
== testthat results ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
13.73 0.82 14.54
|
flowStats.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(flowStats)
>
> test_check("flowStats")
Estimating landmarks for channel CD4 ...
Registering curves for parameter CD4 ...
== testthat results ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
12.60 0.53 13.36
|
|
flowStats.Rcheck/examples_i386/flowStats-Ex.timings
|
flowStats.Rcheck/examples_x64/flowStats-Ex.timings
|