BioC experimental data: CHECK report for ggtut on moscato1

Package: ggtut

Version: 0.0.46

Command: rm -rf ggtut.buildbin-libdir && mkdir ggtut.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggtut.buildbin-libdir ggtut_0.0.46.tar.gz >ggtut-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=ggtut.buildbin-libdir --install="check:ggtut-install.out" --force-multiarch --no-vignettes --timings ggtut_0.0.46.tar.gz && mv ggtut.buildbin-libdir/* ggtut.Rcheck/ && rmdir ggtut.buildbin-libdir

StartedAt: 2014-04-04 11:43:20 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 11:54:42 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 681.8 seconds

RetCode: 0

Status:  OK

CheckDir: ggtut.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-data-experiment/meat/ggtut.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '0.0.46'
* 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 '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
* 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
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' ... [27s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
rules.n43 7.07   0.06    7.13
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
rules.n43 7.62   0.06    7.69
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-data-experiment/meat/ggtut.Rcheck/00check.log'
for details.

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_0.0.46.zip
* DONE (ggtut)

name	user	system	elapsed
c17imp	1.53	0.02	1.55
g17rngsnr	0.12	0.00	0.14
ggtut-package	0.21	0.02	0.24
observed17ceu	0.25	0.00	0.24
rules.n43	7.07	0.06	7.13
snpgr17	0.55	0.03	0.60

name	user	system	elapsed
c17imp	1.73	0.02	1.75
g17rngsnr	0.13	0.00	1.84
ggtut-package	0.22	0.00	0.21
observed17ceu	0.22	0.00	0.22
rules.n43	7.62	0.06	7.69
snpgr17	0.47	0.03	0.50