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CHECK report for Cormotif on tokay1

This page was generated on 2019-04-13 11:21:42 -0400 (Sat, 13 Apr 2019).

Package 330/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cormotif 1.28.0
Yingying Wei
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/Cormotif
Branch: RELEASE_3_8
Last Commit: 24775d3
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Cormotif
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Cormotif.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Cormotif_1.28.0.tar.gz
StartedAt: 2019-04-13 01:30:24 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:32:24 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 119.3 seconds
RetCode: 0
Status:  OK  
CheckDir: Cormotif.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Cormotif.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Cormotif_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Cormotif.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Cormotif/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Cormotif' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'Cormotif' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'affy'
A package should be listed in only one of these fields.
* 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
cmfit: no visible global function definition for 'runif'
limmafit: no visible global function definition for 'new'
modt.f0.loglike: no visible global function definition for 'dt'
modt.f1.loglike: no visible global function definition for 'dt'
Undefined global functions or variables:
  dt new runif
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dt", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/Cormotif.Rcheck/00check.log'
for details.



Installation output

Cormotif.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Cormotif_1.28.0.tar.gz && rm -rf Cormotif.buildbin-libdir && mkdir Cormotif.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Cormotif.buildbin-libdir Cormotif_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Cormotif_1.28.0.zip && rm Cormotif_1.28.0.tar.gz Cormotif_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  168k  100  168k    0     0  3778k      0 --:--:-- --:--:-- --:--:-- 4203k

install for i386

* installing *source* package 'Cormotif' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Cormotif'
    finding HTML links ... done
    cormotif-internal                       html  
    cormotiffit                             html  
    cormotiffitall                          html  
    cormotiffitfull                         html  
    cormotiffitsep                          html  
    generank                                html  
    plotIC                                  html  
    plotMotif                               html  
    simudata2                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Cormotif' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Cormotif' as Cormotif_1.28.0.zip
* DONE (Cormotif)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Cormotif' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

Cormotif.Rcheck/examples_i386/Cormotif-Ex.timings

nameusersystemelapsed
cormotiffit0.890.030.92
cormotiffitall0.310.010.33
cormotiffitfull0.780.020.79
cormotiffitsep0.830.000.83
generank0.950.030.98
plotIC1.140.021.15
plotMotif0.770.010.78

Cormotif.Rcheck/examples_x64/Cormotif-Ex.timings

nameusersystemelapsed
cormotiffit0.750.000.75
cormotiffitall0.250.020.26
cormotiffitfull0.670.010.68
cormotiffitsep0.560.020.58
generank0.830.020.85
plotIC0.670.010.68
plotMotif0.690.000.69