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BioC 3.4: CHECK report for EBSeq on moscato1

This page was generated on 2016-09-21 03:44:50 -0700 (Wed, 21 Sep 2016).

Package 352/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeq 1.13.0
Ning Leng
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EBSeq
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  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists 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: EBSeq
Version: 1.13.0
Command: rm -rf EBSeq.buildbin-libdir EBSeq.Rcheck && mkdir EBSeq.buildbin-libdir EBSeq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBSeq.buildbin-libdir EBSeq_1.13.0.tar.gz >EBSeq.Rcheck\00install.out 2>&1 && cp EBSeq.Rcheck\00install.out EBSeq-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=EBSeq.buildbin-libdir --install="check:EBSeq-install.out" --force-multiarch --no-vignettes --timings EBSeq_1.13.0.tar.gz
StartedAt: 2016-09-20 07:35:24 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:37:07 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 103.0 seconds
RetCode: 0
Status:  OK  
CheckDir: EBSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EBSeq.buildbin-libdir EBSeq.Rcheck && mkdir EBSeq.buildbin-libdir EBSeq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBSeq.buildbin-libdir EBSeq_1.13.0.tar.gz >EBSeq.Rcheck\00install.out 2>&1 && cp EBSeq.Rcheck\00install.out EBSeq-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=EBSeq.buildbin-libdir --install="check:EBSeq-install.out" --force-multiarch --no-vignettes --timings EBSeq_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/EBSeq.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 'EBSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EBSeq' version '1.13.0'
* 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 'EBSeq' can be installed ... OK
* checking installed package size ... OK
* 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
* 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
DenNHist: no visible global function definition for 'hist'
DenNHist: no visible global function definition for 'lines'
DenNHist: no visible global function definition for 'dbeta'
DenNHist: no visible global function definition for 'legend'
EBMultiTest : <anonymous>: no visible global function definition for
  'quantile'
EBMultiTest: no visible global function definition for 'quantile'
EBMultiTest : <anonymous>: no visible binding for global variable 'var'
EBMultiTest: no visible binding for global variable 'var'
EBTest : <anonymous>: no visible global function definition for
  'quantile'
EBTest: no visible global function definition for 'quantile'
EBTest: no visible binding for global variable 'var'
GetDEResults: no visible binding for global variable 'median'
LogN: no visible global function definition for 'optim'
LogNMulti: no visible global function definition for 'optim'
MedianNorm : <anonymous>: no visible global function definition for
  'median'
MedianNorm : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
PlotPattern: no visible global function definition for 'par'
PlotPattern: no visible global function definition for 'rainbow'
PlotPattern: no visible global function definition for 'heatmap'
PlotPostVsRawFC: no visible global function definition for 'par'
PlotPostVsRawFC: no visible global function definition for 'plot'
PlotPostVsRawFC: no visible global function definition for 'abline'
PlotPostVsRawFC: no visible global function definition for 'rect'
PolyFitPlot: no visible global function definition for 'lm'
PolyFitPlot: no visible global function definition for 'smoothScatter'
PolyFitPlot: no visible global function definition for 'axis'
PolyFitPlot: no visible global function definition for 'lines'
QQP: no visible global function definition for 'rbeta'
QQP: no visible global function definition for 'qqplot'
QQP: no visible global function definition for 'lm'
QQP: no visible global function definition for 'abline'
QuantileNorm : <anonymous>: no visible global function definition for
  'quantile'
beta.mom: no visible global function definition for 'var'
Undefined global functions or variables:
  abline axis dbeta heatmap hist legend lines lm median optim par plot
  qqplot quantile rainbow rbeta rect smoothScatter var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "par", "plot", "rect", "smoothScatter")
  importFrom("stats", "dbeta", "heatmap", "lm", "median", "optim",
             "qqplot", "quantile", "rbeta", "var")
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
Examples with CPU or elapsed time > 5s
            user system elapsed
EBMultiTest 5.15   0.03    5.18
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
GetMultiPP  6.60      0    6.60
GetMultiFC  6.51      0    6.50
EBMultiTest 6.38      0    6.38
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/EBSeq.Rcheck/00check.log'
for details.


EBSeq.Rcheck/00install.out:


install for i386

* installing *source* package 'EBSeq' ...
** R
** data
** demo
** 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 'EBSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBSeq' as EBSeq_1.13.0.zip
* DONE (EBSeq)

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

nameusersystemelapsed
DenNHist3.320.033.36
EBMultiTest5.150.035.18
EBSeq_NingLeng-package0.480.000.48
EBTest0.470.000.47
GeneMat0.020.000.01
GetDEResults0.460.000.47
GetMultiFC4.980.025.00
GetMultiPP4.960.004.96
GetNg0.020.000.01
GetNormalizedMat0.010.000.02
GetPP0.520.000.51
GetPPMat0.650.010.67
GetPatterns0.020.000.02
IsoList000
IsoMultiList000
Likefun0.010.000.01
LikefunMulti000
LogN000
LogNMulti000
MedianNorm000
MultiGeneMat000
PlotPattern000
PlotPostVsRawFC1.020.001.02
PolyFitPlot0.020.000.02
PostFC0.70.00.7
QQP3.530.003.53
QuantileNorm000
RankNorm0.010.000.01
beta.mom000
crit_fun0.860.000.86
f0000
f1000

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

nameusersystemelapsed
DenNHist3.440.023.45
EBMultiTest6.380.006.38
EBSeq_NingLeng-package0.50.00.5
EBTest0.560.000.56
GeneMat000
GetDEResults0.530.000.53
GetMultiFC6.510.006.50
GetMultiPP6.60.06.6
GetNg0.020.000.01
GetNormalizedMat0.010.000.02
GetPP0.520.000.51
GetPPMat0.720.000.72
GetPatterns0.010.000.02
IsoList000
IsoMultiList000
Likefun000
LikefunMulti0.020.000.01
LogN000
LogNMulti000
MedianNorm000
MultiGeneMat0.010.000.02
PlotPattern000
PlotPostVsRawFC1.020.011.03
PolyFitPlot0.010.020.03
PostFC0.750.000.75
QQP3.530.033.55
QuantileNorm000
RankNorm0.020.000.01
beta.mom000
crit_fun0.830.000.83
f0000
f1000