BioC 2.12: CHECK report for clstutils on moscato2

Package: clstutils

Version: 1.8.0

Command: rm -rf clstutils.buildbin-libdir && mkdir clstutils.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clstutils.buildbin-libdir clstutils_1.8.0.tar.gz >clstutils-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=clstutils.buildbin-libdir --install="check:clstutils-install.out" --force-multiarch --no-vignettes --timings clstutils_1.8.0.tar.gz && mv clstutils.buildbin-libdir/* clstutils.Rcheck/ && rmdir clstutils.buildbin-libdir

StartedAt: 2013-10-09 01:35:34 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:38:41 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 186.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: clstutils.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/clstutils.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clstutils/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clstutils' version '1.8.0'
* 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 'clstutils' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'ape' was built under R version 3.0.2
  Warning: package 'ape' was built under R version 3.0.2
  Warning: package 'ape' was built under R version 3.0.2
See 'E:/biocbld/bbs-2.12-bioc/meat/clstutils.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call with 'PACKAGE' argument in a different package:
  .Call("seq_root2tip", ..., PACKAGE = "ape")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... OK
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [22s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
classifyPlacements 10.14   0.86   11.34
treeDists           7.34   0.72    8.06
** running examples for arch 'x64' ... [26s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
classifyPlacements 12.49   0.78   13.59
treeDists           8.63   0.84    9.47
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runalltests.R' [43s]
 [44s] OK
** running tests for arch 'x64'
  Running 'runalltests.R' [43s]
 [43s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/clstutils.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'clstutils' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: package 'ape' was built under R version 3.0.2
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'ape' was built under R version 3.0.2

install for x64

* installing *source* package 'clstutils' ...
** testing if installed package can be loaded
Warning: package 'ape' was built under R version 3.0.2
* MD5 sums
packaged installation of 'clstutils' as clstutils_1.8.0.zip
* DONE (clstutils)

BioC 2.12: CHECK report for clstutils on moscato2

Summary

Command output