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BioC 3.2: CHECK report for DBChIP on moscato1

This page was generated on 2016-04-23 10:18:38 -0700 (Sat, 23 Apr 2016).

Package 252/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DBChIP 1.14.0
Kun Liang
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DBChIP
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DBChIP
Version: 1.14.0
Command: rm -rf DBChIP.buildbin-libdir DBChIP.Rcheck && mkdir DBChIP.buildbin-libdir DBChIP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DBChIP.buildbin-libdir DBChIP_1.14.0.tar.gz >DBChIP.Rcheck\00install.out 2>&1 && cp DBChIP.Rcheck\00install.out DBChIP-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=DBChIP.buildbin-libdir --install="check:DBChIP-install.out" --force-multiarch --no-vignettes --timings DBChIP_1.14.0.tar.gz
StartedAt: 2016-04-23 01:24:29 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:28:30 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 241.0 seconds
RetCode: 0
Status:  OK  
CheckDir: DBChIP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DBChIP.buildbin-libdir DBChIP.Rcheck && mkdir DBChIP.buildbin-libdir DBChIP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DBChIP.buildbin-libdir DBChIP_1.14.0.tar.gz >DBChIP.Rcheck\00install.out 2>&1 && cp DBChIP.Rcheck\00install.out DBChIP-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=DBChIP.buildbin-libdir --install="check:DBChIP-install.out" --force-multiarch --no-vignettes --timings DBChIP_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/DBChIP.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DBChIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DBChIP' version '1.14.0'
* 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 'DBChIP' 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'DESeq' 'edgeR'
  Please remove these calls from your code.
'library' or 'require' call to 'ShortRead' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
read.AlignedRead: no visible global function definition for 'position'
read.AlignedRead: no visible global function definition for 'strand'
read.AlignedRead: no visible global function definition for 'width'
read.AlignedRead: no visible global function definition for
  'chromosome'
test.diff.binding.DESeq: no visible global function definition for
  'pData'
test.diff.binding.DESeq: no visible global function definition for
  'pData<-'
test.diff.binding.edgeR: possible error in estimateTagwiseDisp(d,
  prior.n = prior.n, verbose = FALSE): unused argument (prior.n =
  prior.n)
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [16s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
DBChIP 5.33   0.13    5.49
** running examples for arch 'x64' ... [17s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
DBChIP 4.96   0.06    5.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [9s]
 [9s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [10s]
 [10s] 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-3.2-bioc/meat/DBChIP.Rcheck/00check.log'
for details.


DBChIP.Rcheck/00install.out:


install for i386

* installing *source* package 'DBChIP' ...
** 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 'DBChIP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DBChIP' as DBChIP_1.14.0.zip
* DONE (DBChIP)

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

nameusersystemelapsed
DBChIP-package1.550.001.55
DBChIP5.330.135.49
binding.site.list0.300.010.31
chip.data.list0.30.00.3
conds0.310.000.31
input.data.list0.420.020.44
load.data0.660.000.70
read.binding.site.list0.440.000.44

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

nameusersystemelapsed
DBChIP-package1.510.041.55
DBChIP4.960.065.03
binding.site.list0.390.030.42
chip.data.list0.320.000.32
conds0.290.010.42
input.data.list0.330.020.34
load.data0.880.000.88
read.binding.site.list0.250.030.29