Package: ctc

Version: 1.57.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ctc.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ctc_1.57.0.tar.gz

StartedAt: 2019-04-09 02:05:25 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:05:54 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 28.3 seconds

RetCode: 0

Status:  OK

CheckDir: ctc.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:ctc.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ctc_1.57.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ctc.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 'ctc/DESCRIPTION' ... OK
* this is package 'ctc' version '1.57.0'
* 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 'ctc' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to 'amap' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'amap'
  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
.First.lib: warning in .packages(all = TRUE): partial argument match of
  'all' to 'all.available'
.onLoad: warning in .packages(all = TRUE): partial argument match of
  'all' to 'all.available'
hclust2treeview: warning in .packages(all = TRUE): partial argument
  match of 'all' to 'all.available'
hclust2treeview: no visible global function definition for 'hclust'
hclust2treeview: no visible global function definition for 'dist'
r2atr: no visible global function definition for 'write.table'
r2cdt: no visible global function definition for 'write.table'
r2cluster: no visible global function definition for 'write.table'
r2gtr: no visible global function definition for 'write.table'
r2xcluster: no visible global function definition for 'write.table'
read.eisen: no visible global function definition for 'read.table'
xcluster2r: no visible global function definition for 'read.table'
Undefined global functions or variables:
  dist hclust read.table write.table
Consider adding
  importFrom("stats", "dist", "hclust")
  importFrom("utils", "read.table", "write.table")
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 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-3.9-bioc/meat/ctc.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/ctc_1.57.0.tar.gz && rm -rf ctc.buildbin-libdir && mkdir ctc.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ctc.buildbin-libdir ctc_1.57.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ctc_1.57.0.zip && rm ctc_1.57.0.tar.gz ctc_1.57.0.zip
###
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install for i386

* installing *source* package 'ctc' ...
** R
** demo
** exec
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ctc'
    finding HTML links ... done
    hc2Newick                               html  
    hclust2treeview                         html  
    r2cluster                               html  
    r2gtr                                   html  
    r2xcluster                              html  
    read.eisen                              html  
    xcluster                                html  
    xcluster2r                              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 'ctc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ctc' as ctc_1.57.0.zip
* DONE (ctc)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ctc' successfully unpacked and MD5 sums checked