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CHECK report for ggcyto on malbec1

This page was generated on 2018-04-12 13:14:26 -0400 (Thu, 12 Apr 2018).

Package 583/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggcyto 1.6.2
Mike Jiang
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/ggcyto
Branch: RELEASE_3_6
Last Commit: 773ee9d
Last Changed Date: 2018-04-04 18:26:31 -0400 (Wed, 04 Apr 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ggcyto
Version: 1.6.2
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ggcyto_1.6.2.tar.gz
StartedAt: 2018-04-11 23:54:51 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:57:03 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 131.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ggcyto.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ggcyto_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ggcyto.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
* 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                  14.980  0.100  15.626
ggcyto.flowSet             6.292  0.044   6.388
plus-.ggcyto_GatingLayout  5.528  0.004   5.535
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/ggcyto.Rcheck/00check.log’
for details.



Installation output

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)

Tests output


Example timings

ggcyto.Rcheck/ggcyto-Ex.timings

nameusersystemelapsed
as.ggplot2.0680.0322.114
autoplot14.980 0.10015.626
axis_x_inverse_trans1.1560.0161.175
compute_stats0.6960.0160.710
flowCore_asinht_trans0.0040.0000.002
fortify.ellipsoidGate0.0040.0000.007
fortify.filterList0.0200.0000.021
fortify.flowSet0.1280.0080.159
fortify.polygonGate0.0080.0000.010
fortify.rectangleGate0.0120.0000.012
fortify_fs0.7040.0280.733
geom_gate2.2800.0202.303
geom_hvline0.3520.0000.354
geom_overlay1.4760.0081.488
geom_stats1.5280.0081.533
getFlowFrame0.5440.0120.557
ggcyto.GatingSet0.6600.0040.661
ggcyto3.9520.0243.977
ggcyto.flowSet6.2920.0446.388
ggcyto_GatingSet_add1.2280.0041.233
ggcyto_arrange000
ggcyto_flowSet_add2.1720.0002.173
ggcyto_par_default0.0040.0000.003
ggcyto_par_set1.4240.0081.433
is.ggcyto0.5040.0240.529
is.ggcyto_flowSet0.5560.0240.581
is.ggcyto_par0.0000.0000.001
labs_cyto1.1120.0081.124
marginalFilter1.700.021.72
merge.quad.gates0.2120.0040.217
plus-.ggcyto_GatingLayout5.5280.0045.535
replace_data1.1240.0121.417
scale_x_flowCore_fasinh1.1720.0241.194
scale_x_flowJo_biexp0.8960.0160.913
scale_x_flowJo_fasinh0.9320.0280.958
scale_x_logicle1.1120.0241.139
stat_position0.5320.0080.541