BioC experimental data: CHECK report for pd.atdschip.tiling on malbec2

Package: pd.atdschip.tiling

Version: 0.14.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pd.atdschip.tiling_0.14.0.tar.gz

StartedAt: 2017-08-15 10:57:30 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 11:00:06 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 155.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pd.atdschip.tiling.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pd.atdschip.tiling_0.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/pd.atdschip.tiling.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pd.atdschip.tiling/DESCRIPTION’ ... OK
* this is package ‘pd.atdschip.tiling’ version ‘0.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pd.atdschip.tiling’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 256.4Mb
  sub-directories of 1Mb or more:
    data      43.3Mb
    extdata  213.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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' call to ‘RSQLite’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘IRanges’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘methods’ ‘oligo’ ‘oligoClasses’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘pd.atdschip.tiling/R/all.R’:
  .onLoad calls:
    require(RSQLite, quietly = TRUE)

Package startup functions should not change the search path.
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 ... WARNING
Found the following file(s) containing GNU extensions:
  inst/UnitTests/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 examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
probeSequences 5.564  0.176    5.74
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-data-experiment/meat/pd.atdschip.tiling.Rcheck/00check.log’
for details.

* installing *source* package ‘pd.atdschip.tiling’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (pd.atdschip.tiling)

name	user	system	elapsed
probeSequences	5.564	0.176	5.740