Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:31:20 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the flowStats package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 634/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowStats 4.2.0 (landing page) Greg Finak
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: flowStats |
Version: 4.2.0 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings flowStats_4.2.0.tar.gz |
StartedAt: 2021-05-06 02:53:21 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 02:59:15 -0400 (Thu, 06 May 2021) |
EllapsedTime: 353.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flowStats.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings flowStats_4.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/flowStats.Rcheck' * using R version 4.0.5 (2021-03-31) * 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 '4.2.0' * 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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/autoGate.Rd:25: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/autoGate.Rd:54: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/gate_singlet.Rd:65: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/lymphGate.Rd:79: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/lymphGate.Rd:141: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/spillover-flowSet.Rd:41: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.12-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 ... 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 (user + system) or elapsed time > 5s user system elapsed warpSet 19.34 0.82 20.15 gaussNorm 4.87 0.20 5.08 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed warpSet 19.50 0.72 20.22 gaussNorm 5.09 0.44 5.53 * 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-3.12-bioc/meat/flowStats.Rcheck/00check.log' for details.
flowStats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/flowStats_4.2.0.tar.gz && rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowStats.buildbin-libdir flowStats_4.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL flowStats_4.2.0.zip && rm flowStats_4.2.0.tar.gz flowStats_4.2.0.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 1519k 100 1519k 0 0 44.7M 0 --:--:-- --:--:-- --:--:-- 46.3M 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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/autoGate.Rd:25: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/autoGate.Rd:54: file link 'norm2Filter' in package 'flowStats' 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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/gate_singlet.Rd:65: 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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/lymphGate.Rd:79: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/lymphGate.Rd:141: file link 'norm2Filter' in package 'flowStats' does not exist and so has been treated as a topic norm2Filter-class html normQA html normalize html Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/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-3.12-bioc/tmpdir/RtmpeCKKjZ/R.INSTALL2eec25b62f4b/flowStats/man/spillover-flowSet.Rd:41: 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_4.2.0.zip * DONE (flowStats) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'flowStats' successfully unpacked and MD5 sums checked
flowStats.Rcheck/tests_i386/testthat.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 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 ... [ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ] > > proc.time() user system elapsed 15.50 1.03 16.53 |
flowStats.Rcheck/tests_x64/testthat.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 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 ... [ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ] > > proc.time() user system elapsed 14.43 0.51 15.01 |
flowStats.Rcheck/examples_i386/flowStats-Ex.timings
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flowStats.Rcheck/examples_x64/flowStats-Ex.timings
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