climates - Functions for summarizing climate, weather and extreme event information - check results
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climates

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Package R docs

Version: 0.1-1.6
Result: ERROR
Check time: 2015-11-24 08:47
* using log directory ''
* using R Under development (unstable) (2015-11-18 r69655)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* checking for file 'climates/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'climates' version '0.1-1.6'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'ncdf4'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'climates' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
GPL version 2 or newer
Standardizable: TRUE
Standardized license specification:
GPL (>= 2)
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
'ncdf' 'ncdf4'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'raster'
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
CF_date_range: warning in chron(floor(head(time_dim, 1)), out.format =
c(dates = "year-m-day"), origin = chron_origin): partial argument
match of 'origin' to 'origin.'
CF_date_range: warning in chron(floor(tail(time_dim, 1)), out.format =
c(dates = "year-m-day"), origin = chron_origin): partial argument
match of 'origin' to 'origin.'
CF_date_range: warning in chron(time, origin = chron_origin, out.format
= "month/day/year"): partial argument match of 'origin' to 'origin.'
daily2monthly: warning in chron(time, out.format = c(dates =
"year-m-day"), origin = origin_in): partial argument match of
'origin' to 'origin.'
dap_daily_stats: no visible global function definition for 'nc_open'
dap_daily_stats: no visible global function definition for 'ncvar_put'
dap_daily_stats: no visible global function definition for 'nc_close'
get_dap_data: no visible global function definition for 'ncvar_get'
init_dap: no visible global function definition for 'nc_open'
init_dap: no visible global function definition for 'ncatt_get'
initialize_NetCDF: no visible global function definition for
'ncdim_def'
initialize_NetCDF: no visible global function definition for
'ncvar_def'
initialize_NetCDF: no visible global function definition for
'ncatt_get'
initialize_NetCDF: no visible global function definition for
'nc_create'
initialize_NetCDF: no visible global function definition for
'ncatt_put'
initialize_NetCDF: no visible global function definition for
'ncvar_put'
initialize_NetCDF: no visible global function definition for 'nc_close'
read.nc : instring: no visible global function definition for
'lower.case'
read.nc: no visible global function definition for 'open.ncdf'
read.nc: no visible global function definition for 'att.get.ncdf'
read.nc: no visible global function definition for 'cdfcont'
read.nc: no visible global function definition for 'get.var.ncdf'
read.nc: no visible global function definition for 'close.ncdf'
request_bbox: no visible global function definition for 'ncatt_get'
Undefined global functions or variables:
att.get.ncdf cdfcont close.ncdf get.var.ncdf lower.case nc_close
nc_create nc_open ncatt_get ncatt_put ncdim_def ncvar_def ncvar_get
ncvar_put open.ncdf
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'anom.prec.Rd':
'retrieve.nc' 'extract.monthly.average'

Missing link or links in documentation object 'anom.temp.Rd':
'retrieve.nc' 'extract.monthly.average'

Missing link or links in documentation object 'extremes.Rd':
'bioclim.Rd'

Missing link or links in documentation object 'read.nc.Rd':
'datestr2num' 'mixFields'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented data sets:
'bbox_in' 'grid_mapping_atts' 'grid_mapping_name' 'x_vals' 'y_vals'
'end' 'start' 'time_dim' 'time_units' 'bioclims' 'coords_master'
'prcp_data' 'prj' 'tave_data' 'tmax_data' 'tmin_data' 'year' 'cells'
'origin' 'time_indices' 'thresholds' 'time_PCICt'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'bioclim2geotiff'
'tmax_data' 'tmin_data' 'prcp_data' 'tave_data' 'bioclims'
'coords_master' 'prj'
Documented arguments not in \usage in documentation object 'bioclim2geotiff':
'tmin' 'tmax' 'prec' 'tmean' 'vois' 'coordinates' 'projection'

Undocumented arguments in documentation object 'daily2monthly'
'origin_in'
Documented arguments not in \usage in documentation object 'daily2monthly':
'origin'

Undocumented arguments in documentation object 'daily_indices2geotiff'
'tmax_data' 'tmin_data' 'prcp_data' 'tave_data' 'coords_master' 'prj'
'time_PCICt'
Documented arguments not in \usage in documentation object 'daily_indices2geotiff':
'tmin' 'tmax' 'prec' 'tmean' 'coordinates' 'projection'

Undocumented arguments in documentation object 'dap_daily_stats'
'NetCDF_output' 'fill_nas'
Documented arguments not in \usage in documentation object 'dap_daily_stats':
'NetCDF_output:' 'Cells'

Undocumented arguments in documentation object 'get_dap_data'
'fill_nas'
Documented arguments not in \usage in documentation object 'get_dap_data':
'Cells'

Undocumented arguments in documentation object 'init_dap'
'tave_var'

Undocumented arguments in documentation object 'initialize_NetCDF'
'x_vals' 'y_vals' 't_units' 'p_units'

Undocumented arguments in documentation object 'read.nc'
'silent' 'miss2na'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... WARNING
Argument items with no description in Rd object 'DS.GCM.to.grid':
'nc' 'lon' 'lat' 'cellsize' 'type'

Auto-generated content requiring editing in Rd object 'append.nc':
\author
\note
\arguments, description of item 'nc1'
\arguments, description of item 'nc2'

Auto-generated content requiring editing in Rd object 'extend.global.data':
\author
\note
\arguments, description of item 'nc'

Auto-generated content requiring editing in Rd object 'extract.monthly.averages':
\author
\note
\arguments, description of item 'nc'
\arguments, description of item 'min.year'
\arguments, description of item 'max.year'

Auto-generated content requiring editing in Rd object 'nc2dataframe':
\author
\note
\arguments, description of item 'nc'

* 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 ... WARNING

Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
CF_bbox_grid_example.RData 29Kb 15Kb xz
bioclim2geotiff_example.RData 191Kb 125Kb bzip2
daily2monthly_example.RData 21Kb 5Kb xz
daily_indices2geotiff_example.RData 73Kb 48Kb xz
daily_indices_example.RData 81Kb 59Kb bzip2
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
4: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ncdf4'
5: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ncdf4'
6: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ncdf4'
7: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ncdf4'
8: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ncdf4'
9: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ncdf4'
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 5 WARNINGs, 4 NOTEs
See
'/00check.log'
for details.


Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log


Build log for Windows (R 2.11.x)

* checking for file 'climates/DESCRIPTION' ... OK
* preparing 'climates':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
WARNING: some HTML links may not be found
* installing *source* package 'climates' ...
** libs
making DLL ...
gcc -I"c:/PROGRA~1/r/R-211~1.0/include" -O3 -Wall -std=gnu99 -c interpolate.c -o interpolate.o
gcc -shared -s -static-libgcc -o climates.dll tmp.def interpolate.o -Lc:/PROGRA~1/r/R-211~1.0/bin -lR
installing to c:/tmp/Rinst152409869/climates/libs
... done
** R
** preparing package for lazy loading
** help
Warning: ./man/read.nc.Rd:9: unexpected section header '\usage'
Warning: ./man/read.nc.Rd:19: unexpected section header '\arguments'
Warning: ./man/read.nc.Rd:20: unknown macro '\item'
Warning: ./man/read.nc.Rd:21: unknown macro '\item'
Warning: ./man/read.nc.Rd:22: unknown macro '\item'
Warning: ./man/read.nc.Rd:23: unknown macro '\item'
Warning: ./man/read.nc.Rd:24: unknown macro '\item'
Warning: ./man/read.nc.Rd:25: unknown macro '\item'
Warning: ./man/read.nc.Rd:26: unknown macro '\item'
Warning: ./man/read.nc.Rd:27: unknown macro '\item'
Warning: ./man/read.nc.Rd:28: unknown macro '\item'
Warning: ./man/read.nc.Rd:29: unknown macro '\item'
Warning: ./man/read.nc.Rd:30: unknown macro '\item'
Warning: ./man/read.nc.Rd:31: unknown macro '\item'
Warning: ./man/read.nc.Rd:32: unknown macro '\item'
Warning: ./man/read.nc.Rd:34: unknown macro '\item'
Warning: ./man/read.nc.Rd:35: unknown macro '\item'
Warning: ./man/read.nc.Rd:36: unknown macro '\item'
Warning: ./man/read.nc.Rd:37: unknown macro '\item'
Warning: ./man/read.nc.Rd:38: unknown macro '\item'
Warning: ./man/read.nc.Rd:39: unknown macro '\item'
Warning: ./man/read.nc.Rd:42: unknown macro '\item'
Warning: ./man/read.nc.Rd:46: unexpected section header '\value'
Warning: ./man/read.nc.Rd:67: unexpected section header '\author'
Warning: ./man/read.nc.Rd:68: unexpected section header '\references'
Warning: ./man/read.nc.Rd:69: unexpected section header '\examples'
Warning: ./man/read.nc.Rd:70: unexpected END_OF_INPUT '
'
*** installing help indices
** building package indices ...
** MD5 sums
** testing if installed package can be loaded
packaged installation of 'climates' as climates_0.1-1.zip

* DONE (climates)


Build log for Windows 64-bit (R 2.11.x)

* checking for file 'climates/DESCRIPTION' ... OK
* preparing 'climates':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
WARNING: some HTML links may not be found
* installing *source* package 'climates' ...
** libs
making DLL ...
x86_64-w64-mingw32-gcc -I"c:/PROGRA~1/r/R-211~1.0-X/include" -O2 -Wall -gdwarf-2 -std=gnu99 -c interpolate.c -o interpolate.o
x86_64-w64-mingw32-gcc -shared -static-libgcc -o climates.dll tmp.def interpolate.o -Lc:/PROGRA~1/r/R-211~1.0-X/bin -lR
installing to c:/tmp/Rinst144844912/climates/libs/x64
... done
** R
** preparing package for lazy loading
** help
Warning: ./man/read.nc.Rd:9: unexpected section header '\usage'
Warning: ./man/read.nc.Rd:19: unexpected section header '\arguments'
Warning: ./man/read.nc.Rd:20: unknown macro '\item'
Warning: ./man/read.nc.Rd:21: unknown macro '\item'
Warning: ./man/read.nc.Rd:22: unknown macro '\item'
Warning: ./man/read.nc.Rd:23: unknown macro '\item'
Warning: ./man/read.nc.Rd:24: unknown macro '\item'
Warning: ./man/read.nc.Rd:25: unknown macro '\item'
Warning: ./man/read.nc.Rd:26: unknown macro '\item'
Warning: ./man/read.nc.Rd:27: unknown macro '\item'
Warning: ./man/read.nc.Rd:28: unknown macro '\item'
Warning: ./man/read.nc.Rd:29: unknown macro '\item'
Warning: ./man/read.nc.Rd:30: unknown macro '\item'
Warning: ./man/read.nc.Rd:31: unknown macro '\item'
Warning: ./man/read.nc.Rd:32: unknown macro '\item'
Warning: ./man/read.nc.Rd:34: unknown macro '\item'
Warning: ./man/read.nc.Rd:35: unknown macro '\item'
Warning: ./man/read.nc.Rd:36: unknown macro '\item'
Warning: ./man/read.nc.Rd:37: unknown macro '\item'
Warning: ./man/read.nc.Rd:38: unknown macro '\item'
Warning: ./man/read.nc.Rd:39: unknown macro '\item'
Warning: ./man/read.nc.Rd:42: unknown macro '\item'
Warning: ./man/read.nc.Rd:46: unexpected section header '\value'
Warning: ./man/read.nc.Rd:67: unexpected section header '\author'
Warning: ./man/read.nc.Rd:68: unexpected section header '\references'
Warning: ./man/read.nc.Rd:69: unexpected section header '\examples'
Warning: ./man/read.nc.Rd:70: unexpected END_OF_INPUT '
'
*** installing help indices
** building package indices ...
** MD5 sums
** testing if installed package can be loaded
packaged installation of 'climates' as climates_0.1-1.zip

* DONE (climates)


Build log for Mac OS X 10.5 (R 2.16.x)

* installing *source* package 'climates' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c interpolate.c -o interpolate.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o climates.so interpolate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/climates/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c interpolate.c -o interpolate.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o climates.so interpolate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/climates/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c interpolate.c -o interpolate.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o climates.so interpolate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/climates/libs/x86_64
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - ppc
*** arch - x86_64
packaged installation of 'climates' as 'climates_0.1-1.2.tgz'

* DONE (climates)

Build log for Windows 7 (R 3.0.x)

(climates 0.1-1.3)
* installing to library 'z:/rforge/Rlib/win7-3.0'
* installing *source* package 'climates' ...
** libs

*** arch - i386
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c interpolate.c -o interpolate.o
gcc -m32 -shared -s -static-libgcc -o climates.dll tmp.def interpolate.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/i386 -lR
installing to z:/rforge/Rlib/win7-3.0/climates/libs/i386

*** arch - x64
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c interpolate.c -o interpolate.o
gcc -m64 -shared -s -static-libgcc -o climates.dll tmp.def interpolate.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/x64 -lR
installing to z:/rforge/Rlib/win7-3.0/climates/libs/x64
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* MD5 sums
packaged installation of 'climates' as climates_0.1-1.3.zip
* DONE (climates)