Package: LiquidAssociation

Version: 1.36.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LiquidAssociation.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings LiquidAssociation_1.36.0.tar.gz

StartedAt: 2019-04-13 03:23:43 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:26:23 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 160.3 seconds

RetCode: 0

Status:  OK

CheckDir: LiquidAssociation.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LiquidAssociation.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings LiquidAssociation_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/LiquidAssociation.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 'LiquidAssociation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LiquidAssociation' version '1.36.0'
* 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 'LiquidAssociation' 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:
  'methods'
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 ... NOTE
Packages in Depends field not imported from:
  'geepack' 'org.Sc.sgd.db' 'yeastCC'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CNM.full,matrix: no visible global function definition for 'geese'
CNM.full,matrix: no visible binding for global variable 'groupid'
CNM.full,matrix: no visible binding for global variable 'visit'
CNM.full,matrix: no visible global function definition for
  'geese.control'
CNM.simple,matrix: no visible global function definition for 'geese'
CNM.simple,matrix: no visible binding for global variable 'groupid'
CNM.simple,matrix: no visible binding for global variable 'visit'
CNM.simple,matrix: no visible global function definition for
  'geese.control'
Undefined global functions or variables:
  geese geese.control groupid visit
* 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 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/LiquidAssociation.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/LiquidAssociation_1.36.0.tar.gz && rm -rf LiquidAssociation.buildbin-libdir && mkdir LiquidAssociation.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LiquidAssociation.buildbin-libdir LiquidAssociation_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL LiquidAssociation_1.36.0.zip && rm LiquidAssociation_1.36.0.tar.gz LiquidAssociation_1.36.0.zip
###
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100 43518  100 43518    0     0  1032k      0 --:--:-- --:--:-- --:--:-- 1148k

install for i386

* installing *source* package 'LiquidAssociation' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'LiquidAssociation'
    finding HTML links ... done
    CNM-class                               html  
    CNM.full-methods                        html  
    CNM.simple-methods                      html  
    GLA-methods                             html  
    LA-methods                              html  
    LiquidAssociation-Internal              html  
    LiquidAssociation-package               html  
    getsGLA-methods                         html  
    getsLA-methods                          html  
    plotGLA-methods                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'LiquidAssociation' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LiquidAssociation' as LiquidAssociation_1.36.0.zip
* DONE (LiquidAssociation)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'LiquidAssociation' successfully unpacked and MD5 sums checked
In R CMD INSTALL