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BioC 3.4: CHECK report for clst on tokay1

This page was generated on 2017-04-15 16:16:33 -0400 (Sat, 15 Apr 2017).

Package 217/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clst 1.22.0
Noah Hoffman
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/clst
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: clst
Version: 1.22.0
Command: rm -rf clst.buildbin-libdir clst.Rcheck && mkdir clst.buildbin-libdir clst.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clst.buildbin-libdir clst_1.22.0.tar.gz >clst.Rcheck\00install.out 2>&1 && cp clst.Rcheck\00install.out clst-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=clst.buildbin-libdir --install="check:clst-install.out" --force-multiarch --no-vignettes --timings clst_1.22.0.tar.gz
StartedAt: 2017-04-14 21:33:07 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:34:12 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 65.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clst.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clst.buildbin-libdir clst.Rcheck && mkdir clst.buildbin-libdir clst.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clst.buildbin-libdir clst_1.22.0.tar.gz >clst.Rcheck\00install.out 2>&1 && cp clst.Rcheck\00install.out clst-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=clst.buildbin-libdir --install="check:clst-install.out" --force-multiarch --no-vignettes --timings clst_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/clst.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clst/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clst' version '1.22.0'
* 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 'clst' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("ROC", ..., PACKAGE = "ROC")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
findPMMI: no visible binding for global variable 'median'
findPMMI: no visible global function definition for 'quantile'
getTally: no visible binding for global variable 'median'
scaleDistPlot: no visible global function definition for 'cmdscale'
simpleROC: no visible global function definition for 'new'
template: no visible global function definition for 'str'
Undefined global functions or variables:
  cmdscale median new quantile str
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "cmdscale", "median", "quantile")
  importFrom("utils", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  tests/unit/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
scaleDistPlot 5.61   0.04    5.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
scaleDistPlot 7.14   0.04    7.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runalltests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runalltests.R'
 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/clst.Rcheck/00check.log'
for details.


clst.Rcheck/00install.out:


install for i386

* installing *source* package 'clst' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'clst' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clst' as clst_1.22.0.zip
* DONE (clst)

clst.Rcheck/examples_i386/clst-Ex.timings:

nameusersystemelapsed
actino0.020.000.01
bvseqs0.000.010.02
classify0.170.020.19
clst-package0.090.000.09
findThreshold0.070.000.06
plotDistances0.140.000.14
printClst000
scaleDistPlot5.610.045.66
strep000

clst.Rcheck/examples_x64/clst-Ex.timings:

nameusersystemelapsed
actino0.020.000.01
bvseqs0.010.000.02
classify0.180.010.19
clst-package0.140.000.14
findThreshold0.030.000.03
plotDistances0.140.020.15
printClst000
scaleDistPlot7.140.047.21
strep0.010.000.01