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BioC 3.4: CHECK report for flowCHIC on moscato1

This page was generated on 2016-09-21 03:46:26 -0700 (Wed, 21 Sep 2016).

Package 412/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCHIC 1.7.0
Author: Joachim Schumann
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowCHIC
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowCHIC
Version: 1.7.0
Command: rm -rf flowCHIC.buildbin-libdir flowCHIC.Rcheck && mkdir flowCHIC.buildbin-libdir flowCHIC.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCHIC.buildbin-libdir flowCHIC_1.7.0.tar.gz >flowCHIC.Rcheck\00install.out 2>&1 && cp flowCHIC.Rcheck\00install.out flowCHIC-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=flowCHIC.buildbin-libdir --install="check:flowCHIC-install.out" --force-multiarch --no-vignettes --timings flowCHIC_1.7.0.tar.gz
StartedAt: 2016-09-20 08:16:09 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:19:32 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 202.9 seconds
RetCode: 0
Status:  OK  
CheckDir: flowCHIC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowCHIC.buildbin-libdir flowCHIC.Rcheck && mkdir flowCHIC.buildbin-libdir flowCHIC.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCHIC.buildbin-libdir flowCHIC_1.7.0.tar.gz >flowCHIC.Rcheck\00install.out 2>&1 && cp flowCHIC.Rcheck\00install.out flowCHIC-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=flowCHIC.buildbin-libdir --install="check:flowCHIC-install.out" --force-multiarch --no-vignettes --timings flowCHIC_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/flowCHIC.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowCHIC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowCHIC' version '1.7.0'
* 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 'flowCHIC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
fcs_to_img,character: warning in hexbin(x, y, xbin = 128): partial
  argument match of 'xbin' to 'xbins'
img_sub,character: warning in hexbin(x, y, xbin = xbin): partial
  argument match of 'xbin' to 'xbins'
fcs_to_img,character: no visible global function definition for 'png'
fcs_to_img,character: no visible binding for global variable 'count'
fcs_to_img,character: no visible global function definition for
  'dev.off'
img_sub,character: no visible global function definition for 'png'
img_sub,character: no visible binding for global variable 'count'
img_sub,character: no visible global function definition for 'dev.off'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'as.dist'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'par'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'plot'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'hclust'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'points'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'text'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'legend'
Undefined global functions or variables:
  as.dist count dev.off hclust legend par plot png points text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "par", "plot", "points", "text")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'flowCyBar'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
calculate_overlaps_xor 9.19   2.51   20.38
plot_nmds              6.33   1.13    8.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
calculate_overlaps_xor 10.12   2.25   12.45
plot_nmds               6.18   1.27    8.05
* 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/flowCHIC.Rcheck/00check.log'
for details.


flowCHIC.Rcheck/00install.out:


install for i386

* installing *source* package 'flowCHIC' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'flowCHIC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCHIC' as flowCHIC_1.7.0.zip
* DONE (flowCHIC)

flowCHIC.Rcheck/examples_i386/flowCHIC-Ex.timings:

nameusersystemelapsed
calculate_overlaps_xor 9.19 2.5120.38
fcs_to_img1.200.484.35
img_sub2.540.594.06
plot_nmds6.331.138.22

flowCHIC.Rcheck/examples_x64/flowCHIC-Ex.timings:

nameusersystemelapsed
calculate_overlaps_xor10.12 2.2512.45
fcs_to_img1.240.431.68
img_sub2.640.533.81
plot_nmds6.181.278.05