BioC 2.14: CHECK report for pgUtils on petty

Package: pgUtils

Version: 1.35.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pgUtils_1.35.1.tar.gz

StartedAt: 2014-03-18 01:41:22 -0700 (Tue, 18 Mar 2014)

EndedAt: 2014-03-18 01:42:03 -0700 (Tue, 18 Mar 2014)

EllapsedTime: 40.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pgUtils.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/pgUtils.Rcheck’
* using R version 3.1.0 alpha (2014-03-13 r65184)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pgUtils/DESCRIPTION’ ... OK
* this is package ‘pgUtils’ version ‘1.35.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pgUtils’ can be installed ... [3s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘RPostgreSQL’
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 ... WARNING
Subdirectory ‘inst’ contains no files.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createDBTable: no visible global function definition for
  ‘dbBeginTransaction’
deleteDBEntry: no visible global function definition for
  ‘dbBeginTransaction’
insertIntoTable: no visible global function definition for
  ‘dbBeginTransaction’
updateDBTable: no visible global function definition for
  ‘dbBeginTransaction’
* checking Rd files ... NOTE
prepare_Rd: AutoReference.Rd:33-35: Dropping empty section \note
prepare_Rd: AutoReference.Rd:31: Dropping empty section \references
prepare_Rd: AutoReference.Rd:43-45: Dropping empty section \examples
prepare_Rd: auto.fk.name.Rd:14-15: Dropping empty section \details
prepare_Rd: auto.fk.name.Rd:16: Dropping empty section \references
prepare_Rd: auto.fk.name.Rd:19-20: Dropping empty section \seealso
prepare_Rd: auto.fk.name.Rd:22-23: Dropping empty section \examples
prepare_Rd: auto.pk.name.Rd:13-14: Dropping empty section \details
prepare_Rd: auto.pk.name.Rd:15: Dropping empty section \references
prepare_Rd: auto.pk.name.Rd:18-19: Dropping empty section \seealso
prepare_Rd: auto.pk.name.Rd:21-22: Dropping empty section \examples
prepare_Rd: auto.pk.seq.Rd:13-14: Dropping empty section \details
prepare_Rd: auto.pk.seq.Rd:15: Dropping empty section \references
prepare_Rd: auto.pk.seq.Rd:18-19: Dropping empty section \seealso
prepare_Rd: auto.pk.seq.Rd:21-22: Dropping empty section \examples
prepare_Rd: createDBTable.Rd:26: Dropping empty section \references
prepare_Rd: createSequence.Rd:19: Dropping empty section \references
prepare_Rd: dbListSequences.Rd:18: Dropping empty section \references
prepare_Rd: deleteDBEntry.Rd:21: Dropping empty section \references
prepare_Rd: deleteDBEntry.Rd:28-29: Dropping empty section \examples
prepare_Rd: do.log.Rd:13: Dropping empty section \references
prepare_Rd: insertIntoTable.Rd:22: Dropping empty section \references
prepare_Rd: log.file.Rd:13: Dropping empty section \references
prepare_Rd: log.level.Rd:10-11: Dropping empty section \details
prepare_Rd: log.level.Rd:12: Dropping empty section \references
prepare_Rd: loggit.Rd:14-15: Dropping empty section \details
prepare_Rd: loggit.Rd:16: Dropping empty section \references
prepare_Rd: loggit.Rd:19-20: Dropping empty section \seealso
prepare_Rd: loggit.Rd:22-23: Dropping empty section \examples
prepare_Rd: searchIn.Rd:19: Dropping empty section \references
prepare_Rd: searchIn.Rd:23-24: Dropping empty section \examples
prepare_Rd: updateDBTable.Rd:24: Dropping empty section \references
prepare_Rd: updateDBTable.Rd:32-33: Dropping empty section \examples
* 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 files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/pgUtils.Rcheck/00check.log’
for details.

* installing *source* package ‘pgUtils’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pgUtils)

name	user	system	elapsed
createDBTable	0.001	0.000	0.000
insertIntoTable	0.000	0.001	0.001