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CHECK report for EBSeqHMM on tokay2

This page was generated on 2019-04-09 12:22:00 -0400 (Tue, 09 Apr 2019).

Package 474/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeqHMM 1.17.1
Ning Leng
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/EBSeqHMM
Branch: master
Last Commit: 8600f85
Last Changed Date: 2019-01-04 13:30:28 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: EBSeqHMM
Version: 1.17.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeqHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EBSeqHMM_1.17.1.tar.gz
StartedAt: 2019-04-09 02:29:17 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:30:37 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 79.8 seconds
RetCode: 0
Status:  OK  
CheckDir: EBSeqHMM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeqHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EBSeqHMM_1.17.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/EBSeqHMM.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EBSeqHMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EBSeqHMM' version '1.17.1'
* 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 'EBSeqHMM' can be installed ... OK
* checking installed package size ... OK
* 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
* 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
EBHMMNBfun: no visible binding for global variable 'median'
EBHMMNBfun : <anonymous>: no visible global function definition for
  'quantile'
EBHMMNBfun: no visible global function definition for 'optim'
EBHMMNBfunForMulti: no visible binding for global variable 'median'
EBHMMNBfunForMulti : <anonymous>: no visible global function definition
  for 'quantile'
EBHMMNBfunForMulti: no visible global function definition for 'optim'
EBSeqHMMTest : <anonymous>: no visible global function definition for
  'quantile'
EBTest_ext: no visible global function definition for 'quantile'
EBTest_ext: no visible binding for global variable 'var'
PlotExp: no visible global function definition for 'plot'
PlotExp: no visible global function definition for 'axis'
PlotExp : <anonymous>: no visible global function definition for
  'median'
PlotExp: no visible global function definition for 'lines'
beta.mom: no visible global function definition for 'var'
Undefined global functions or variables:
  axis lines median optim plot quantile var
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "median", "optim", "quantile", "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
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/EBSeqHMM.Rcheck/00check.log'
for details.



Installation output

EBSeqHMM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/EBSeqHMM_1.17.1.tar.gz && rm -rf EBSeqHMM.buildbin-libdir && mkdir EBSeqHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EBSeqHMM.buildbin-libdir EBSeqHMM_1.17.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL EBSeqHMM_1.17.1.zip && rm EBSeqHMM_1.17.1.tar.gz EBSeqHMM_1.17.1.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  550k  100  550k    0     0  3723k      0 --:--:-- --:--:-- --:--:-- 3930k

install for i386

* installing *source* package 'EBSeqHMM' ...
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'EBSeqHMM'
    finding HTML links ... done
    EBHMMNBMultiEM_2chain                   html  
    EBHMMNBfun                              html  
    EBHMMNBfunForMulti                      html  
    EBSeqHMM-package                        html  
    EBSeqHMMTest                            html  
    EBTest_ext                              html  
    finding level-2 HTML links ... done

    GeneExampleData                         html  
    GetAllPaths                             html  
    GetConfidentCalls                       html  
    GetDECalls                              html  
    IsoExampleList                          html  
    LikefunNBHMM                            html  
    PlotExp                                 html  
    beta.mom                                html  
    f0                                      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 'EBSeqHMM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBSeqHMM' as EBSeqHMM_1.17.1.zip
* DONE (EBSeqHMM)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'EBSeqHMM' successfully unpacked and MD5 sums checked

Tests output


Example timings

EBSeqHMM.Rcheck/examples_i386/EBSeqHMM-Ex.timings

nameusersystemelapsed
EBHMMNBMultiEM_2chain0.500.010.51
EBHMMNBfun0.050.000.05
EBHMMNBfunForMulti0.220.030.25
EBSeqHMM-package0.50.00.5
EBSeqHMMTest0.530.000.53
EBTest_ext0.090.000.09
GeneExampleData0.000.020.02
GetAllPaths0.840.020.86
GetConfidentCalls0.860.010.87
GetDECalls0.830.020.85
IsoExampleList0.020.010.03
LikefunNBHMM0.010.000.01
PlotExp0.020.000.02
beta.mom000
f0000

EBSeqHMM.Rcheck/examples_x64/EBSeqHMM-Ex.timings

nameusersystemelapsed
EBHMMNBMultiEM_2chain0.620.000.63
EBHMMNBfun0.060.000.06
EBHMMNBfunForMulti0.220.000.21
EBSeqHMM-package0.780.000.79
EBSeqHMMTest1.000.011.01
EBTest_ext0.160.000.16
GeneExampleData0.010.000.01
GetAllPaths0.810.000.82
GetConfidentCalls0.830.000.82
GetDECalls0.750.000.75
IsoExampleList0.000.020.02
LikefunNBHMM0.000.010.01
PlotExp0.020.000.02
beta.mom000
f00.010.000.02