Package: cqn

Version: 1.29.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cqn.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cqn_1.29.1.tar.gz

StartedAt: 2019-04-09 02:04:03 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:05:22 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 79.1 seconds

RetCode: 0

Status:  OK

CheckDir: cqn.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cqn.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings cqn_1.29.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/cqn.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 'cqn/DESCRIPTION' ... OK
* this is package 'cqn' version '1.29.1'
* 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 'cqn' 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:
  'splines'
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:
  'mclust' 'preprocessCore' 'quantreg'
  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
SQN2: no visible binding for global variable 'median'
SQN2: no visible global function definition for 'Mclust'
cqn : fixPredictor: no visible global function definition for
  'quantile'
cqn: no visible global function definition for 'median'
cqn : <anonymous>: no visible global function definition for 'rq'
cqn : <anonymous>: no visible global function definition for 'predict'
cqn : <anonymous>: no visible global function definition for 'coef'
cqnplot: no visible global function definition for 'matplot'
cqnplot: no visible global function definition for 'rug'
mix.qn: no visible global function definition for 'ecdf'
mix.qn: no visible global function definition for 'quantile'
norm.pickrell: no visible global function definition for 'quantile'
norm.pickrell : <anonymous>: no visible global function definition for
  'smooth.spline'
norm.pickrell : <anonymous>: no visible global function definition for
  'predict'
Undefined global functions or variables:
  Mclust coef ecdf matplot median predict quantile rq rug smooth.spline
Consider adding
  importFrom("graphics", "matplot", "rug")
  importFrom("stats", "coef", "ecdf", "median", "predict", "quantile",
             "smooth.spline")
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 or elapsed time > 5s
    user system elapsed
cqn 4.89    0.4    5.28
* 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-3.9-bioc/meat/cqn.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/cqn_1.29.1.tar.gz && rm -rf cqn.buildbin-libdir && mkdir cqn.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cqn.buildbin-libdir cqn_1.29.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL cqn_1.29.1.zip && rm cqn_1.29.1.tar.gz cqn_1.29.1.zip
###
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install for i386

* installing *source* package 'cqn' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cqn'
    finding HTML links ... done
    cqn                                     html  
    cqnplot                                 html  
    montgomery.subset                       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 'cqn' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cqn' as cqn_1.29.1.zip
* DONE (cqn)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'cqn' successfully unpacked and MD5 sums checked