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BioC experimental data: CHECK report for ggtut on moscato2

This page was generated on 2014-10-04 17:41:35 -0700 (Sat, 04 Oct 2014).

Package 86/197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtut 0.2.0
VJ Carey
Snapshot Date: 2014-10-04 07:15:22 -0700 (Sat, 04 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs/ggtut
Last Changed Rev: 2799 / Revision: 3055
Last Changed Date: 2014-04-11 14:27:08 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ggtut
Version: 0.2.0
Command: rm -rf ggtut.buildbin-libdir && mkdir ggtut.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggtut.buildbin-libdir ggtut_0.2.0.tar.gz >ggtut-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ggtut.buildbin-libdir --install="check:ggtut-install.out" --force-multiarch --no-vignettes --timings ggtut_0.2.0.tar.gz
StartedAt: 2014-10-04 10:05:25 -0700 (Sat, 04 Oct 2014)
EndedAt: 2014-10-04 10:18:30 -0700 (Sat, 04 Oct 2014)
EllapsedTime: 784.7 seconds
RetCode: 0
Status:  OK  
CheckDir: ggtut.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   rm -rf ggtut.buildbin-libdir && mkdir ggtut.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggtut.buildbin-libdir ggtut_0.2.0.tar.gz >ggtut-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ggtut.buildbin-libdir --install="check:ggtut-install.out" --force-multiarch --no-vignettes --timings ggtut_0.2.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-data-experiment/meat/ggtut.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggtut/DESCRIPTION' ... OK
* this is package 'ggtut' version '0.2.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'GGtools' 'ff' 'GenomicRanges' 'snpStats' 'GGdata' 'GenomicFeatures'
  'ChIPpeakAnno' 'Rsamtools' 'cheung2010'
  'SNPlocs.Hsapiens.dbSNP.20120608' 'hmyriB36'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'ggtut' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 189.3Mb
  sub-directories of 1Mb or more:
    bam          15.1Mb
    data         22.3Mb
    ffarchives  136.9Mb
    ffobjects     1.6Mb
    images       12.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'GenomicFeatures' 'ChIPpeakAnno'
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 ... NOTE
Packages in Depends field not imported from:
  'ChIPpeakAnno' 'GGdata' 'GGtools' 'GenomicFeatures' 'GenomicRanges'
  'Rsamtools' 'SNPlocs.Hsapiens.dbSNP.20120608' 'cheung2010' 'ff'
  'hmyriB36' 'snpStats'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
File 'ggtut/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\n\nggtut: as of 10 Jan 2013, SNPlocs requested are hg19-based, but all serialized")
    packageStartupMessage("objects have hg18 coordinates.  Liftovers will be conducted soon.")
    packageStartupMessage("In the mean time, this package is primarily for demonstration that the software functions.\n")

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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [26s] OK
** running examples for arch 'x64' ... [31s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
rules.n43 5.16   0.03    5.19
* checking PDF version of manual ... OK

NOTE: There were 5 notes.
See
  'E:/biocbld/bbs-2.14-data-experiment/meat/ggtut.Rcheck/00check.log'
for details.

ggtut.Rcheck/00install.out:


install for i386

* installing *source* package 'ggtut' ...
** 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 'ggtut' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggtut' as ggtut_0.2.0.zip
* DONE (ggtut)

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

nameusersystemelapsed
c17imp1.450.031.48
g17rngsnr0.140.000.14
ggtut-package0.240.000.23
observed17ceu0.550.000.55
rules.n433.890.013.90
snpgr171.030.001.03

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

nameusersystemelapsed
c17imp1.320.021.34
g17rngsnr0.190.000.50
ggtut-package0.30.00.3
observed17ceu0.750.030.78
rules.n435.160.035.19
snpgr171.260.001.27