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BioC 3.4: CHECK report for ggcyto on zin1

This page was generated on 2016-09-21 03:40:29 -0700 (Wed, 21 Sep 2016).

Package 513/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggcyto 1.1.11
Mike Jiang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggcyto
Last Changed Rev: 121014 / Revision: 121152
Last Changed Date: 2016-09-16 14:20:24 -0700 (Fri, 16 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ggcyto
Version: 1.1.11
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ggcyto_1.1.11.tar.gz
StartedAt: 2016-09-20 07:16:23 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:18:14 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 110.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ggcyto.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ggcyto_1.1.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ggcyto.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.11’
* 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’ ‘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 10.232  0.064  10.294
* 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-3.4-bioc/meat/ggcyto.Rcheck/00check.log’
for details.


ggcyto.Rcheck/00install.out:

* installing *source* package ‘ggcyto’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggcyto)

ggcyto.Rcheck/ggcyto-Ex.timings:

nameusersystemelapsed
as.ggplot1.1400.0201.159
autoplot10.232 0.06410.294
axis_x_inverse_trans0.9520.0040.959
compute_stats0.7800.0080.791
fortify.ellipsoidGate0.0040.0000.008
fortify.filterList0.0520.0000.053
fortify.flowSet0.1320.0120.144
fortify.polygonGate0.0040.0000.008
fortify.rectangleGate0.0080.0000.009
fortify_fs0.5720.0040.573
geom_gate2.4080.0162.435
geom_hvline0.2440.0040.245
geom_overlay1.6280.0321.660
geom_stats0.8800.0040.883
getFlowFrame0.5520.0240.577
ggcyto.GatingSet0.6800.0000.682
ggcyto2.9920.0283.017
ggcyto.flowSet4.5360.0484.585
ggcyto_GatingSet_add1.1240.0121.138
ggcyto_arrange0.0000.0000.001
ggcyto_flowSet_add2.1240.0042.128
ggcyto_par_default0.0040.0000.001
ggcyto_par_set1.3560.0121.369
is.ggcyto0.5520.0240.576
is.ggcyto_flowSet0.6720.0080.682
is.ggcyto_par0.0000.0000.001
labs_cyto1.2920.0001.294
marginalFilter1.8720.0161.890
plus-.ggcyto_GatingLayout4.8800.0044.891
scale_x_flowJo_biexp1.0760.0161.093
scale_x_flowJo_fasinh1.0360.0041.040
scale_x_logicle1.0240.0081.032
stat_position0.6840.0120.695