Package: ctc

Version: 1.56.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ctc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ctc_1.56.0.tar.gz

StartedAt: 2019-04-15 23:18:08 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:18:30 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 21.4 seconds

RetCode: 0

Status:  OK

CheckDir: ctc.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ctc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ctc_1.56.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ctc.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ctc/DESCRIPTION’ ... OK
* this is package ‘ctc’ version ‘1.56.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/ctc.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ctc
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ctc’ ...
** R
** demo
** exec
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ctc)

name	user	system	elapsed
hc2Newick	0.019	0.003	0.022
hclust2treeview	0.048	0.025	0.074
r2cluster	0.004	0.001	0.004
r2gtr	0.017	0.001	0.018
r2xcluster	0.003	0.001	0.004
xcluster	0	0	0
xcluster2r	0.005	0.001	0.006