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BioC experimental data: CHECK report for Fletcher2013a on moscato2

This page was generated on 2016-10-08 19:31:24 -0700 (Sat, 08 Oct 2016).

Package 93/293HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Fletcher2013a 1.8.0
Mauro Castro
Snapshot Date: 2016-10-08 07:15:25 -0700 (Sat, 08 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/Fletcher2013a
Last Changed Rev: 3760 / Revision: 3935
Last Changed Date: 2016-05-03 14:35:06 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 

Summary

Package: Fletcher2013a
Version: 1.8.0
Command: rm -rf Fletcher2013a.buildbin-libdir Fletcher2013a.Rcheck && mkdir Fletcher2013a.buildbin-libdir Fletcher2013a.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Fletcher2013a.buildbin-libdir Fletcher2013a_1.8.0.tar.gz >Fletcher2013a.Rcheck\00install.out 2>&1 && cp Fletcher2013a.Rcheck\00install.out Fletcher2013a-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=Fletcher2013a.buildbin-libdir --install="check:Fletcher2013a-install.out" --force-multiarch --no-vignettes --timings Fletcher2013a_1.8.0.tar.gz
StartedAt: 2016-10-08 11:59:17 -0700 (Sat, 08 Oct 2016)
EndedAt: 2016-10-08 12:01:45 -0700 (Sat, 08 Oct 2016)
EllapsedTime: 147.9 seconds
RetCode: 0
Status:  OK  
CheckDir: Fletcher2013a.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Fletcher2013a.buildbin-libdir Fletcher2013a.Rcheck && mkdir Fletcher2013a.buildbin-libdir Fletcher2013a.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Fletcher2013a.buildbin-libdir Fletcher2013a_1.8.0.tar.gz >Fletcher2013a.Rcheck\00install.out 2>&1 && cp Fletcher2013a.Rcheck\00install.out Fletcher2013a-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=Fletcher2013a.buildbin-libdir --install="check:Fletcher2013a-install.out" --force-multiarch --no-vignettes --timings Fletcher2013a_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-data-experiment/meat/Fletcher2013a.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 'Fletcher2013a/DESCRIPTION' ... OK
* this is package 'Fletcher2013a' version '1.8.0'
* 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 'Fletcher2013a' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 69.9Mb
  sub-directories of 1Mb or more:
    data  69.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
* 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 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
Exp1signatures: no visible global function definition for 'data'
Exp2signatures: no visible global function definition for 'data'
Exp3signatures: no visible global function definition for 'data'
Fletcher2013pipeline.limma: no visible global function definition for
  'model.matrix'
Fletcher2013pipeline.pca: no visible global function definition for
  'data'
Fletcher2013pipeline.pca: no visible global function definition for
  'na.omit'
Fletcher2013pipeline.pca: no visible global function definition for
  'prcomp'
PlotGroups: no visible global function definition for 'dist'
PlotGroups: no visible binding for global variable 'median'
PlotGroups: no visible binding for global variable 'sd'
PlotGroups: no visible global function definition for 'par'
PlotGroups: no visible global function definition for 'plot'
PlotGroups: no visible global function definition for 'axis'
PlotGroups: no visible global function definition for 'mtext'
PlotGroups: no visible global function definition for 'points'
PlotGroups: no visible global function definition for 'lines'
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for 'pdf'
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for 'layout'
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for 'par'
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for 'barplot'
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for 'mtext'
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for 'legend'
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for 'dev.off'
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for 'pdf'
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for 'layout'
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for 'par'
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for 'barplot'
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for 'mtext'
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for 'legend'
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for 'dev.off'
plotExpDeg : plot.deg.exp3 : plotendsum: no visible global function
  definition for 'par'
plotExpDeg : plot.deg.exp3 : plotendsum: no visible global function
  definition for 'barplot'
plotExpDeg : plot.deg.exp3 : plotendsum: no visible global function
  definition for 'mtext'
plotExpDeg : plot.deg.exp3 : plotendsum: no visible global function
  definition for 'legend'
plotExpDeg : plot.deg.exp3: no visible global function definition for
  'pdf'
plotExpDeg : plot.deg.exp3: no visible global function definition for
  'layout'
plotExpDeg : plot.deg.exp3: no visible global function definition for
  'dev.off'
plotExpPca : plot.pca.exp1: no visible global function definition for
  'pdf'
plotExpPca : plot.pca.exp1: no visible global function definition for
  'plot'
plotExpPca : plot.pca.exp1: no visible global function definition for
  'legend'
plotExpPca : plot.pca.exp1: no visible global function definition for
  'mtext'
plotExpPca : plot.pca.exp1: no visible global function definition for
  'dev.off'
plotExpPca : plot.pca.exp2: no visible global function definition for
  'pdf'
plotExpPca : plot.pca.exp2: no visible global function definition for
  'plot'
plotExpPca : plot.pca.exp2: no visible global function definition for
  'text'
plotExpPca : plot.pca.exp2: no visible global function definition for
  'legend'
plotExpPca : plot.pca.exp2: no visible global function definition for
  'mtext'
plotExpPca : plot.pca.exp2: no visible global function definition for
  'dev.off'
plotExpPca : plot.pca.exp3: no visible global function definition for
  'pdf'
plotExpPca : plot.pca.exp3: no visible global function definition for
  'plot'
plotExpPca : plot.pca.exp3: no visible global function definition for
  'legend'
plotExpPca : plot.pca.exp3: no visible global function definition for
  'mtext'
plotExpPca : plot.pca.exp3: no visible global function definition for
  'dev.off'
plotFollowup: no visible global function definition for 'data'
plotFollowup: no visible global function definition for 'pdf'
plotFollowup: no visible global function definition for 'layout'
plotFollowup: no visible global function definition for 'palette'
plotFollowup: no visible global function definition for 'plot'
plotFollowup: no visible global function definition for 'axis'
plotFollowup: no visible global function definition for 'lines'
plotFollowup: no visible global function definition for 'legend'
plotFollowup: no visible global function definition for 'dev.off'
plotOverlap: no visible global function definition for 'pdf'
plotOverlap: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  axis barplot data dev.off dist layout legend lines median
  model.matrix mtext na.omit palette par pdf plot points prcomp sd text
Consider adding
  importFrom("grDevices", "dev.off", "palette", "pdf")
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "plot", "points", "text")
  importFrom("stats", "dist", "median", "model.matrix", "na.omit",
             "prcomp", "sd")
  importFrom("utils", "data")
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 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
** running examples for arch 'x64' ... OK
* 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
  'E:/biocbld/bbs-3.3-data-experiment/meat/Fletcher2013a.Rcheck/00check.log'
for details.

Fletcher2013a.Rcheck/00install.out:


install for i386

* installing *source* package 'Fletcher2013a' ...
** 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 'Fletcher2013a' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Fletcher2013a' as Fletcher2013a_1.8.0.zip
* DONE (Fletcher2013a)

Fletcher2013a.Rcheck/examples_i386/Fletcher2013a-Ex.timings:

nameusersystemelapsed
Exp10.770.010.78
Exp20.930.061.00
Exp31.590.001.59
Fletcher2013a.pipelines000
siESR10.310.020.32
siOTHERS0.750.030.78

Fletcher2013a.Rcheck/examples_x64/Fletcher2013a-Ex.timings:

nameusersystemelapsed
Exp10.710.000.72
Exp20.850.040.89
Exp31.290.081.37
Fletcher2013a.pipelines0.000.000.24
siESR10.270.000.26
siOTHERS0.620.010.64