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RForgeTools log file (check_x86_64_linux)

Mon Apr 16 12:41:52 2012: Checking package RForgeTools (SVN revision 232) ...
* using log directory ‘/mnt/building/build_2012-04-13-10-57/RF_PKG_CHECK/PKGS/RForgeTools.Rcheck’
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘RForgeTools/DESCRIPTION’ ... OK
* this is package ‘RForgeTools’ version ‘0.4-13’
* checking CRAN incoming feasibility ... NOTE
New submission
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘RdbiPgSQL’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking whether package ‘RForgeTools’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
build_SQL: no visible binding for global variable ‘pkg_name’
build_SQL: no visible binding for global variable ‘vars’
build_SQL: no visible binding for global variable ‘cran’
build_SQL: no visible global function definition for ‘dbSendQuery’
build_SQL: no visible binding for global variable ‘con’
build_packages: warning in create_package_db_src(svn =
  sprintf("file:%s", file.path(path_to_pkg_tarballs, "src",
  "contrib")), src = sprintf("file:%s", path_to_contrib_dir)): partial
  argument match of 'svn' to 'svn_url'
build_packages: warning in create_package_db_src(svn =
  sprintf("file:%s", file.path(path_to_pkg_tarballs, "src",
  "contrib")), src = sprintf("file:%s", path_to_contrib_dir)): partial
  argument match of 'src' to 'src_url'
build_packages: warning in create_package_db_src(svn =
  sprintf("file://%s", path_to_pkg_src), src =
  contrib.url(sprintf("file://%s", path_to_pkg_root), type =
  "source")): partial argument match of 'svn' to 'svn_url'
build_packages: warning in create_package_db_src(svn =
  sprintf("file://%s", path_to_pkg_src), src =
  contrib.url(sprintf("file://%s", path_to_pkg_root), type =
  "source")): partial argument match of 'src' to 'src_url'
check_packages: warning in create_package_db_src(svn =
  sprintf("file:///%s", path_to_pkg_src), src = URL_pkg_sources):
  partial argument match of 'svn' to 'svn_url'
check_packages: warning in create_package_db_src(svn =
  sprintf("file:///%s", path_to_pkg_src), src = URL_pkg_sources):
  partial argument match of 'src' to 'src_url'
check_packages: no visible binding for global variable ‘donotcompile’
check_svn_package_list_sanity: no visible binding for global variable
  ‘pkgs’
check_svn_package_list_sanity: no visible binding for global variable
  ‘pkg_name’
check_svn_package_list_sanity: no visible binding for global variable
  ‘vars’
check_svn_package_list_sanity: no visible binding for global variable
  ‘descname’
check_svn_package_list_sanity: no visible binding for global variable
  ‘desc’
get_available_packages_from_db: no visible global function definition
  for ‘dbGetQuery’
prepare_packages: no visible global function definition for
  ‘get_available_packages_from_svn’
svn_export: no visible binding for global variable ‘desc’
svn_export: no visible binding for global variable ‘svn_dir’
svn_export: no visible binding for global variable ‘pkg_name’
svn_export: no visible binding for global variable ‘vars’
update_package_library: warning in update.packages(lib = lib, repos =
  repository_url, ask = FALSE, checkBuilt = TRUE, ...): partial
  argument match of 'lib' to 'lib.loc'
update_package_library: warning in installed.packages(lib = lib):
  partial argument match of 'lib' to 'lib.loc'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘rforge_server_info’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'RForgeTools':
build_packages
  Code: function(email, platform = c("Linux", "Windows", "MacOSX"),
                 architecture = c("x86_32", "x86_64"), rforge_url =
                 "http://R-Forge.R-project.org", cran_url =
                 "http://CRAN.R-project.org", bioc_url =
                 "http://bioconductor.org/packages/release/bioc",
                 bioc_data =
                 "http://bioconductor.org/packages/release/data/annotation",
                 bioc_experiment =
                 "http://bioconductor.org/packages/release/data/experiment",
                 omega_hat_url = "http://www.omegahat.org/R", control =
                 list(), Ncpus = 1L)
  Docs: function(email, platform = c("Linux", "Windows", "MacOSX"),
                 architecture = c("x86_32", "x86_64"), rforge_url =
                 "http://R-Forge.R-project.org", cran_url =
                 "http://CRAN.R-project.org", bioc_url =
                 "http://bioconductor.org/packages/release/bioc",
                 control = list())
  Argument names in code not in docs:
    bioc_data bioc_experiment omega_hat_url Ncpus
  Mismatches in argument names:
    Position: 7 Code: bioc_data Docs: control
check_packages
  Code: function(email, platform = c("Linux", "Windows", "MacOSX"),
                 architecture = c("x86_32", "x86_64"), rforge_url =
                 "http://R-Forge.R-project.org", cran_url =
                 "http://CRAN.R-project.org", bioc_url =
                 "http://bioconductor.org/packages/release/bioc",
                 bioc_data =
                 "http://bioconductor.org/packages/release/data/annotation",
                 omega_hat_url = "http://www.omegahat.org/R",
                 global_check_arg = NULL, check_time_limit = 600,
                 control = list())
  Docs: function(email, platform = c("Linux", "Windows", "MacOSX"),
                 architecture = c("x86_32", "x86_64"), rforge_url =
                 "http://R-Forge.R-project.org", cran_url =
                 "http://CRAN.R-project.org", bioc_url =
                 "http://bioconductor.org/packages/release/bioc",
                 control = list())
  Argument names in code not in docs:
    bioc_data omega_hat_url global_check_arg check_time_limit
  Mismatches in argument names:
    Position: 7 Code: bioc_data Docs: control

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [0s/0s] OK
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  ‘/mnt/building/build_2012-04-13-10-57/RF_PKG_CHECK/PKGS/RForgeTools.Rcheck/00check.log’
for details.

Run time: 21.26 seconds.
Additional Logs:
00install.out