Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:42:08 -0400 (Thu, 12 Apr 2018).
Package 583/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ggcyto 1.6.2 Mike Jiang
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![]() |
Package: ggcyto |
Version: 1.6.2 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggcyto_1.6.2.tar.gz |
StartedAt: 2018-04-12 04:27:56 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 04:30:32 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 156.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ggcyto.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggcyto_1.6.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ggcyto.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ggcyto/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ggcyto’ version ‘1.6.2’ * 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 ‘ggcyto’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: doc 8.7Mb * 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 ... NOTE Namespace in Imports field not imported from: ‘scales’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’ ‘flowWorkspace:::fix_y_axis’ ‘flowWorkspace:::isNegated’ ‘ggplot2:::+.gg’ ‘ggplot2:::add_group’ ‘ggplot2:::check_aesthetics’ ‘ggplot2:::ggplot.data.frame’ ‘ggplot2:::is.waive’ ‘ggplot2:::is_calculated_aes’ ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’ ‘ggplot2:::print.ggplot’ ‘ggplot2:::scales_add_defaults’ ‘ggplot2:::update_theme’ 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 .fs2dt: no visible binding for global variable ‘name’ add_ggcyto: no visible binding for global variable ‘name’ add_ggcyto: no visible binding for global variable ‘density’ add_ggcyto: no visible binding for global variable ‘axis’ add_ggcyto: no visible binding for global variable ‘desc’ add_par: no visible global function definition for ‘modifyList’ as.ggplot: no visible binding for global variable ‘axis’ as.ggplot: no visible binding for global variable ‘name’ autoplot.GatingHierarchy : <anonymous>: no visible global function definition for ‘gray’ autoplot.GatingSetList: no visible global function definition for ‘getS3method’ autoplot.ncdfFlowList: no visible global function definition for ‘getS3method’ density_fr_all : <anonymous>: no visible global function definition for ‘gray’ fortify.GatingSetList: no visible global function definition for ‘getS3method’ fortify.ncdfFlowList: no visible global function definition for ‘getS3method’ fortify.polygonGate : <anonymous>: no visible global function definition for ‘dist’ fortify.polygonGate : <anonymous>: no visible global function definition for ‘approx’ fortify_fs.GatingSetList: no visible global function definition for ‘getS3method’ getFlowFrame.GatingSetList: no visible global function definition for ‘getS3method’ getFlowFrame.ncdfFlowList: no visible global function definition for ‘getS3method’ ggcyto.GatingSetList: no visible global function definition for ‘getS3method’ ggcyto.flowSet: no visible binding for global variable ‘name’ ggcyto.flowSet: no visible binding for global variable ‘axis’ ggcyto.ncdfFlowList: no visible global function definition for ‘getS3method’ ggcyto_arrange: no visible binding for global variable ‘name’ Undefined global functions or variables: approx axis density desc dist getS3method gray modifyList name Consider adding importFrom("grDevices", "gray") importFrom("graphics", "axis") importFrom("stats", "approx", "density", "dist") importFrom("utils", "getS3method", "modifyList") to your NAMESPACE file. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed autoplot 15.236 0.836 16.303 ggcyto.flowSet 8.029 0.473 8.611 plus-.ggcyto_GatingLayout 7.138 0.544 7.827 * 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 ‘/Users/biocbuild/bbs-3.6-bioc/meat/ggcyto.Rcheck/00check.log’ for details.
ggcyto.Rcheck/00install.out
* installing *source* package ‘ggcyto’ ... ** R ** inst ** preparing package for lazy loading Creating a generic function for ‘%+%’ from package ‘ggplot2’ in package ‘ggcyto’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ggcyto)
ggcyto.Rcheck/ggcyto-Ex.timings
name | user | system | elapsed | |
as.ggplot | 2.197 | 0.078 | 2.304 | |
autoplot | 15.236 | 0.836 | 16.303 | |
axis_x_inverse_trans | 1.179 | 0.100 | 1.304 | |
compute_stats | 0.747 | 0.045 | 0.800 | |
flowCore_asinht_trans | 0.002 | 0.000 | 0.002 | |
fortify.ellipsoidGate | 0.008 | 0.000 | 0.009 | |
fortify.filterList | 0.025 | 0.001 | 0.027 | |
fortify.flowSet | 0.275 | 0.059 | 0.342 | |
fortify.polygonGate | 0.007 | 0.000 | 0.008 | |
fortify.rectangleGate | 0.008 | 0.001 | 0.007 | |
fortify_fs | 0.566 | 0.053 | 0.626 | |
geom_gate | 2.476 | 0.196 | 2.725 | |
geom_hvline | 0.399 | 0.002 | 0.414 | |
geom_overlay | 1.853 | 0.229 | 2.104 | |
geom_stats | 1.820 | 0.218 | 2.078 | |
getFlowFrame | 0.591 | 0.061 | 0.655 | |
ggcyto.GatingSet | 0.775 | 0.089 | 0.877 | |
ggcyto | 4.545 | 0.099 | 4.709 | |
ggcyto.flowSet | 8.029 | 0.473 | 8.611 | |
ggcyto_GatingSet_add | 1.150 | 0.094 | 1.265 | |
ggcyto_arrange | 0.001 | 0.000 | 0.002 | |
ggcyto_flowSet_add | 2.439 | 0.156 | 2.629 | |
ggcyto_par_default | 0.006 | 0.001 | 0.006 | |
ggcyto_par_set | 1.703 | 0.175 | 1.906 | |
is.ggcyto | 0.523 | 0.048 | 0.581 | |
is.ggcyto_flowSet | 0.543 | 0.040 | 0.594 | |
is.ggcyto_par | 0.001 | 0.000 | 0.001 | |
labs_cyto | 1.326 | 0.160 | 1.505 | |
marginalFilter | 2.098 | 0.166 | 2.294 | |
merge.quad.gates | 0.310 | 0.002 | 0.318 | |
plus-.ggcyto_GatingLayout | 7.138 | 0.544 | 7.827 | |
replace_data | 1.166 | 0.068 | 1.263 | |
scale_x_flowCore_fasinh | 1.135 | 0.065 | 1.219 | |
scale_x_flowJo_biexp | 1.171 | 0.050 | 1.246 | |
scale_x_flowJo_fasinh | 1.054 | 0.042 | 1.109 | |
scale_x_logicle | 1.002 | 0.043 | 1.051 | |
stat_position | 0.557 | 0.035 | 0.597 | |