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BioC 3.4: CHECK report for OrderedList on moscato1

This page was generated on 2016-09-21 03:41:47 -0700 (Wed, 21 Sep 2016).

Package 851/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OrderedList 1.45.0
Claudio Lottaz
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OrderedList
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OrderedList
Version: 1.45.0
Command: rm -rf OrderedList.buildbin-libdir OrderedList.Rcheck && mkdir OrderedList.buildbin-libdir OrderedList.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrderedList.buildbin-libdir OrderedList_1.45.0.tar.gz >OrderedList.Rcheck\00install.out 2>&1 && cp OrderedList.Rcheck\00install.out OrderedList-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OrderedList.buildbin-libdir --install="check:OrderedList-install.out" --force-multiarch --no-vignettes --timings OrderedList_1.45.0.tar.gz
StartedAt: 2016-09-20 13:26:20 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:27:22 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 61.3 seconds
RetCode: 0
Status:  OK  
CheckDir: OrderedList.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OrderedList.buildbin-libdir OrderedList.Rcheck && mkdir OrderedList.buildbin-libdir OrderedList.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrderedList.buildbin-libdir OrderedList_1.45.0.tar.gz >OrderedList.Rcheck\00install.out 2>&1 && cp OrderedList.Rcheck\00install.out OrderedList-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OrderedList.buildbin-libdir --install="check:OrderedList-install.out" --force-multiarch --no-vignettes --timings OrderedList_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/OrderedList.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OrderedList/DESCRIPTION' ... OK
* this is package 'OrderedList' version '1.45.0'
* 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 'OrderedList' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase' 'methods' 'twilight'
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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'OrderedList/R/a.R':
  .First.lib has wrong argument list 'libname, pkgname, where'

Package startup functions should have two arguments with names starting
  with 'lib' and 'pkg', respectively.
See section 'Good practice' in '?.onAttach'.
* 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 ... OK
* checking installed files from 'inst/doc' ... 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/OrderedList.Rcheck/00check.log'
for details.


OrderedList.Rcheck/00install.out:


install for i386

* installing *source* package 'OrderedList' ...
** R
** data
** 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 'OrderedList' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OrderedList' as OrderedList_1.45.0.zip
* DONE (OrderedList)

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

nameusersystemelapsed
OL.result000
OrderedList0.250.000.25
compareLists1.120.021.22
getOverlap1.120.001.12
plot.OrderedList0.070.010.08
prepareData0.120.000.12
print.OrderedList0.000.000.11

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

nameusersystemelapsed
OL.result000
OrderedList0.140.030.17
compareLists0.860.000.86
getOverlap0.760.000.76
plot.OrderedList0.050.000.05
prepareData0.090.000.09
print.OrderedList000