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CHECK report for EBSeq on tokay2

This page was generated on 2020-10-17 11:56:30 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE EBSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 523/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeq 1.28.0
Ning Leng
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/EBSeq
Branch: RELEASE_3_11
Last Commit: 85f5918
Last Changed Date: 2020-04-27 14:34:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EBSeq
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings EBSeq_1.28.0.tar.gz
StartedAt: 2020-10-17 03:37:52 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:40:08 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 136.1 seconds
RetCode: 0
Status:  OK  
CheckDir: EBSeq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings EBSeq_1.28.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/EBSeq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.28.0'
* 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 '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
  qqplot quantile rainbow rbeta rect smoothScatter var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "par", "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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
EBMultiTest 5.44      0    5.43
* 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/EBSeq.Rcheck/00check.log'
for details.



Installation output

EBSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/EBSeq_1.28.0.tar.gz && rm -rf EBSeq.buildbin-libdir && mkdir EBSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EBSeq.buildbin-libdir EBSeq_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL EBSeq_1.28.0.zip && rm EBSeq_1.28.0.tar.gz EBSeq_1.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  240k  100  240k    0     0  2752k      0 --:--:-- --:--:-- --:--:-- 3000k

install for i386

* installing *source* package 'EBSeq' ...
** using staged installation
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'EBSeq'
    finding HTML links ... done
    DenNHist                                html  
    EBMultiTest                             html  
    EBSeq_NingLeng-package                  html  
    EBTest                                  html  
    GeneMat                                 html  
    GetDEResults                            html  
    GetMultiFC                              html  
    GetMultiPP                              html  
    GetNg                                   html  
    GetNormalizedMat                        html  
    GetPP                                   html  
    GetPPMat                                html  
    GetPatterns                             html  
    IsoList                                 html  
    IsoMultiList                            html  
    Likefun                                 html  
    LikefunMulti                            html  
    LogN                                    html  
    LogNMulti                               html  
    MedianNorm                              html  
    MultiGeneMat                            html  
    PlotPattern                             html  
    PlotPostVsRawFC                         html  
    PolyFitPlot                             html  
    PostFC                                  html  
    QQP                                     html  
    QuantileNorm                            html  
    RankNorm                                html  
    beta.mom                                html  
    crit_fun                                html  
    f0                                      html  
    f1                                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'EBSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBSeq' as EBSeq_1.28.0.zip
* DONE (EBSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'EBSeq' successfully unpacked and MD5 sums checked

Tests output


Example timings

EBSeq.Rcheck/examples_i386/EBSeq-Ex.timings

nameusersystemelapsed
DenNHist2.590.022.61
EBMultiTest404
EBSeq_NingLeng-package0.360.000.36
EBTest0.360.000.36
GeneMat0.010.000.01
GetDEResults0.360.000.36
GetMultiFC3.990.003.99
GetMultiPP4.20.04.2
GetNg0.020.000.01
GetNormalizedMat0.010.010.04
GetPP0.70.00.7
GetPPMat0.860.000.86
GetPatterns000
IsoList0.000.020.01
IsoMultiList000
Likefun000
LikefunMulti000
LogN000
LogNMulti000
MedianNorm000
MultiGeneMat000
PlotPattern0.020.000.02
PlotPostVsRawFC0.940.000.94
PolyFitPlot0.010.000.01
PostFC0.560.000.56
QQP2.740.002.74
QuantileNorm0.000.020.01
RankNorm0.010.000.02
beta.mom000
crit_fun0.660.010.67
f0000
f1000

EBSeq.Rcheck/examples_x64/EBSeq-Ex.timings

nameusersystemelapsed
DenNHist2.430.002.44
EBMultiTest5.440.005.43
EBSeq_NingLeng-package0.530.020.54
EBTest0.360.020.38
GeneMat0.000.010.01
GetDEResults0.360.000.36
GetMultiFC4.360.024.38
GetMultiPP4.220.014.23
GetNg0.000.020.02
GetNormalizedMat0.020.000.01
GetPP0.350.000.36
GetPPMat0.490.000.49
GetPatterns000
IsoList000
IsoMultiList000
Likefun000
LikefunMulti000
LogN000
LogNMulti000
MedianNorm000
MultiGeneMat0.000.010.02
PlotPattern000
PlotPostVsRawFC0.710.020.72
PolyFitPlot0.010.000.01
PostFC0.50.00.5
QQP2.140.022.16
QuantileNorm000
RankNorm0.020.000.01
beta.mom000
crit_fun0.580.000.58
f0000
f1000