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CHECK report for EBSeqHMM on tokay2

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

TO THE DEVELOPERS/MAINTAINERS OF THE EBSeqHMM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 524/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeqHMM 1.22.0
Ning Leng
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/EBSeqHMM
Branch: RELEASE_3_11
Last Commit: 42114f3
Last Changed Date: 2020-04-27 14:45:18 -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: EBSeqHMM
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeqHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings EBSeqHMM_1.22.0.tar.gz
StartedAt: 2020-10-17 03:37:57 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:39:23 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 86.8 seconds
RetCode: 0
Status:  OK  
CheckDir: EBSeqHMM.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:EBSeqHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings EBSeqHMM_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/EBSeqHMM.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 'EBSeqHMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EBSeqHMM' version '1.22.0'
* 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 '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 '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 quantile var
Consider adding
  importFrom("graphics", "axis", "lines")
  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-3.11-bioc/meat/EBSeqHMM.Rcheck/00check.log'
for details.



Installation output

EBSeqHMM.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/EBSeqHMM_1.22.0.tar.gz && rm -rf EBSeqHMM.buildbin-libdir && mkdir EBSeqHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EBSeqHMM.buildbin-libdir EBSeqHMM_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL EBSeqHMM_1.22.0.zip && rm EBSeqHMM_1.22.0.tar.gz EBSeqHMM_1.22.0.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  550k  100  550k    0     0  4851k      0 --:--:-- --:--:-- --:--:-- 5142k

install for i386

* installing *source* package 'EBSeqHMM' ...
** using staged installation
** 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_1.22.0.zip
* DONE (EBSeqHMM)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'EBSeqHMM' successfully unpacked and MD5 sums checked

Tests output


Example timings

EBSeqHMM.Rcheck/examples_i386/EBSeqHMM-Ex.timings

nameusersystemelapsed
EBHMMNBMultiEM_2chain0.50.00.5
EBHMMNBfun0.030.000.03
EBHMMNBfunForMulti0.250.000.25
EBSeqHMM-package0.520.000.51
EBSeqHMMTest0.510.000.52
EBTest_ext0.150.000.14
GeneExampleData000
GetAllPaths0.510.000.52
GetConfidentCalls0.520.000.51
GetDECalls0.530.000.54
IsoExampleList0.010.000.01
LikefunNBHMM0.020.000.02
PlotExp0.010.000.01
beta.mom000
f0000

EBSeqHMM.Rcheck/examples_x64/EBSeqHMM-Ex.timings

nameusersystemelapsed
EBHMMNBMultiEM_2chain0.560.000.56
EBHMMNBfun0.040.000.05
EBHMMNBfunForMulti0.230.010.25
EBSeqHMM-package0.630.000.62
EBSeqHMMTest0.590.020.61
EBTest_ext0.160.000.16
GeneExampleData0.020.000.01
GetAllPaths0.570.000.58
GetConfidentCalls0.580.000.58
GetDECalls0.550.000.55
IsoExampleList0.010.000.01
LikefunNBHMM0.020.000.02
PlotExp000
beta.mom000
f0000