CHECK report for FlowSOM on celaya2
This page was generated on 2020-01-16 13:41:04 -0500 (Thu, 16 Jan 2020).
FlowSOM 1.19.1
Sofie Van Gassen
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/FlowSOM |
| Branch: master |
| Last Commit: 40e8291 |
| Last Changed Date: 2020-01-02 04:07:59 -0500 (Thu, 02 Jan 2020) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FlowSOM_1.19.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘1.19.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘FlowSOM’ can be installed ... WARNING
Found the following significant warnings:
som.c:37:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
som.c:47:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
som.c:134:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/FlowSOM.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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AddFlowFrame: no visible global function definition for ‘is’
ReadInput: no visible global function definition for ‘is’
Undefined global functions or variables:
is
Consider adding
importFrom("methods", "is")
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 ... WARNING
Codoc mismatches from documentation object 'PlotStars':
PlotStars
Code: function(fsom, markers = fsom$map$colsUsed, view = "MST",
colorPalette =
grDevices::colorRampPalette(c("#00007F", "blue",
"#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00",
"red", "#7F0000")), starBg = "white", backgroundValues
= NULL, backgroundColor = function(n) {
grDevices::rainbow(n, alpha = 0.3)}, backgroundLim =
NULL, backgroundBreaks = NULL, backgroundSize = NULL,
thresholds = NULL, legend = TRUE, query = NULL, range
= "all", main = "")
Docs: function(fsom, markers = fsom$map$colsUsed, view = "MST",
colorPalette =
grDevices::colorRampPalette(c("#00007F", "blue",
"#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00",
"red", "#7F0000")), starBg = "white", backgroundValues
= NULL, backgroundColor = function(n) {
grDevices::rainbow(n, alpha = 0.3)}, backgroundLim =
NULL, backgroundBreaks = NULL, backgroundSize = NULL,
thresholds = NULL, legend = TRUE, query = NULL, main =
"")
Argument names in code not in docs:
range
Mismatches in argument names:
Position: 14 Code: range Docs: main
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CountGroups 15.920 2.458 18.415
PlotOverview2D 16.352 1.461 18.088
FlowSOM 11.544 1.602 13.250
TestOutliers 7.224 1.157 8.401
MetaclusterMFIs 6.834 1.045 7.944
GetFlowJoLabels 6.580 0.879 7.484
FlowSOMSubset 6.495 0.887 7.403
ReadInput 6.233 1.019 7.382
MetaClustering 6.173 1.025 7.220
PlotPies 6.208 0.887 7.104
PlotLabels 6.028 0.828 6.866
GetMetaclusters 6.031 0.785 6.963
GetMFIs 5.772 0.849 6.639
MetaclusterCVs 5.651 0.813 6.489
GetClusters 5.581 0.809 6.427
PlotNode 5.115 0.832 5.952
metaClustering_consensus 4.948 0.812 5.773
NewData 5.079 0.637 5.723
* 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: 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.
Installation output
FlowSOM.Rcheck/00install.out
Tests output
Example timings
FlowSOM.Rcheck/FlowSOM-Ex.timings