We should provide an official CRAN release. Before that a list of building notes and warning should be fixed.
echo $JAVA_HOME
sh tools/package.sh
--
❯ checking top-level files ... WARNING
A complete check needs the 'checkbashisms' script.
See section ‘Configure and cleanup’ in the ‘Writing R Extensions’
manual.
Non-standard file/directory found at top level:
‘build.log’
❯ checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
‘mda’ ‘rpart’
'library' or 'require' calls to packages already attached by Depends:
‘DBI’ ‘rJava’ ‘RSQLite’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘mda’ ‘rpart’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘DBI’ ‘RSQLite’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
summary:
function(object, ...)
summary.rodps.data:
function(rd)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
❯ checking for missing documentation entries ... WARNING
Undocumented code objects:
‘init.odps.ext’ ‘str.rodps.data’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undocumented arguments in documentation object 'head.rodps.data'
‘rd’ ‘n’
Undocumented arguments in documentation object 'na.omit.rodps.data'
‘rd’
Undocumented arguments in documentation object 'rodps.change.types'
‘types’
Undocumented arguments in documentation object 'rodps.data'
‘tblname’
Undocumented arguments in documentation object 'rodps.predict'
‘x’ ‘...’
Undocumented arguments in documentation object 'rodps.predict.fda'
‘prior’ ‘type’ ‘dimension’
Documented arguments not in \usage in documentation object 'rodps.predict.fda':
‘dryrun’
Undocumented arguments in documentation object 'rodps.predict.rpart'
‘inc.col’
Undocumented arguments in documentation object 'rodps.table.summary'
‘tbl’
Undocumented arguments in documentation object 'rodps.vector'
‘tblname’ ‘colname’
Undocumented arguments in documentation object 'summary.rodps.data'
‘rd’
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 installed package size ... NOTE
installed size is 52.5Mb
sub-directories of 1Mb or more:
java 52.2Mb
❯ checking startup messages can be suppressed ... NOTE
checking RODPS_CONFIG ...
checking ODPS_CONFIG ...
checking /Users/xiaming.cxm/odps_config.ini ...
checking /Users/xiaming.cxm/.odpscmd/odps_config.ini ...
RODPS_CONFIG environment variable is not set or the configuration file does not exist.
rodps.init(path) to manually init RODPS
add RODPS_CONFIG as environment variable
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
❯ checking R code for possible problems ... NOTE
checking RODPS_CONFIG ...
checking ODPS_CONFIG ...
checking /Users/xiaming.cxm/odps_config.ini ...
checking /Users/xiaming.cxm/.odpscmd/odps_config.ini ...
RODPS_CONFIG environment variable is not set or the configuration file does not exist.
rodps.init(path) to manually init RODPS
add RODPS_CONFIG as environment variable
.change.type: no visible binding for global variable
‘rodps.type.java2r’
.change.value: no visible binding for global variable
‘rodps.type.java2r’
.dataframe.to.sqlite: no visible global function definition for
‘dbConnect’
.dataframe.to.sqlite: no visible global function definition for
‘SQLite’
.dataframe.to.sqlite: no visible global function definition for
‘dbWriteTable’
.dataframe.to.sqlite: no visible global function definition for
‘dbDisconnect’
.get.object.type: no visible binding for global variable
‘rodps.type.r2java’
.sqlite.to.dataframe: no visible global function definition for
‘dbConnect’
.sqlite.to.dataframe: no visible global function definition for
‘SQLite’
.sqlite.to.dataframe: no visible global function definition for
‘dbGetQuery’
.sqlite.to.dataframe: no visible global function definition for
‘dbDisconnect’
rodps.change.types: no visible binding for global variable
‘rodps.type.java2r’
rodps.init.type: no visible binding for '<<-' assignment to
‘rodps.type.r2java’
rodps.init.type: no visible binding for '<<-' assignment to
‘rodps.type.java2r’
Undefined global functions or variables:
dbConnect dbDisconnect dbGetQuery dbWriteTable rodps.type.java2r
rodps.type.r2java SQLite
Found if() conditions comparing class() to string:
File ‘RODPS/R/rodps_predict.R’: if (class(object) != "rpart") ...
File ‘RODPS/R/rodps_predict.R’: if (class(object) != "fda") ...
File ‘RODPS/R/rodps_str.R’: if (class(names(d)[i]) == "character") ...
Use inherits() (or maybe is()) instead.
0 errors ✔ | 5 warnings ✖ | 3 notes ✖
Error: R CMD check found WARNINGs
We should provide an official CRAN release. Before that a list of building notes and warning should be fixed.
--
❯ checking top-level files ... WARNING A complete check needs the 'checkbashisms' script. See section ‘Configure and cleanup’ in the ‘Writing R Extensions’ manual. Non-standard file/directory found at top level: ‘build.log’
❯ checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: ‘mda’ ‘rpart’ 'library' or 'require' calls to packages already attached by Depends: ‘DBI’ ‘rJava’ ‘RSQLite’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘mda’ ‘rpart’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used. Packages in Depends field not imported from: ‘DBI’ ‘RSQLite’ 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 ... WARNING rodps.predict: function(x, ...) rodps.predict.rpart: function(object, srctbl, tgttbl, inc.col, dryrun)
rodps.predict: function(x, ...) rodps.predict.fda: function(object, srctbl, tgttbl, prior, type, dimension)
na.omit: function(object, ...) na.omit.rodps.data: function(rd)
summary: function(object, ...) summary.rodps.data: function(rd) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual.
❯ checking for missing documentation entries ... WARNING Undocumented code objects: ‘init.odps.ext’ ‘str.rodps.data’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
❯ checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'error' ‘error_name’ ‘msg’
Undocumented arguments in documentation object 'head.rodps.data' ‘rd’ ‘n’
Undocumented arguments in documentation object 'na.omit.rodps.data' ‘rd’
Undocumented arguments in documentation object 'rodps.change.types' ‘types’
Undocumented arguments in documentation object 'rodps.data' ‘tblname’
Undocumented arguments in documentation object 'rodps.predict' ‘x’ ‘...’
Undocumented arguments in documentation object 'rodps.predict.fda' ‘prior’ ‘type’ ‘dimension’ Documented arguments not in \usage in documentation object 'rodps.predict.fda': ‘dryrun’
Undocumented arguments in documentation object 'rodps.predict.rpart' ‘inc.col’
Undocumented arguments in documentation object 'rodps.table.hist' ‘tblname’ ‘colname’ ‘breaks’ ‘freq’ ‘include.lowest’ ‘right’ ‘main’ ‘xlab’ ‘...’
Undocumented arguments in documentation object 'rodps.table.na.omit' ‘tbl’ ‘tgttbl’
Undocumented arguments in documentation object 'rodps.table.sample.srs' ‘srctable’ ‘tgttable’ ‘samplerate’ ‘cond’ ‘select’
Undocumented arguments in documentation object 'rodps.table.sample.strat' ‘srctable’ ‘tgttable’ ‘samplerate’ ‘strat’ ‘select’
Undocumented arguments in documentation object 'rodps.table.summary' ‘tbl’
Undocumented arguments in documentation object 'rodps.vector' ‘tblname’ ‘colname’
Undocumented arguments in documentation object 'summary.rodps.data' ‘rd’
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 installed package size ... NOTE installed size is 52.5Mb sub-directories of 1Mb or more: java 52.2Mb
❯ checking startup messages can be suppressed ... NOTE checking RODPS_CONFIG ... checking ODPS_CONFIG ... checking /Users/xiaming.cxm/odps_config.ini ... checking /Users/xiaming.cxm/.odpscmd/odps_config.ini ... RODPS_CONFIG environment variable is not set or the configuration file does not exist.
add RODPS_CONFIG as environment variable
It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage.
❯ checking R code for possible problems ... NOTE checking RODPS_CONFIG ... checking ODPS_CONFIG ... checking /Users/xiaming.cxm/odps_config.ini ... checking /Users/xiaming.cxm/.odpscmd/odps_config.ini ... RODPS_CONFIG environment variable is not set or the configuration file does not exist.
add RODPS_CONFIG as environment variable .change.type: no visible binding for global variable ‘rodps.type.java2r’ .change.value: no visible binding for global variable ‘rodps.type.java2r’ .dataframe.to.sqlite: no visible global function definition for ‘dbConnect’ .dataframe.to.sqlite: no visible global function definition for ‘SQLite’ .dataframe.to.sqlite: no visible global function definition for ‘dbWriteTable’ .dataframe.to.sqlite: no visible global function definition for ‘dbDisconnect’ .get.object.type: no visible binding for global variable ‘rodps.type.r2java’ .sqlite.to.dataframe: no visible global function definition for ‘dbConnect’ .sqlite.to.dataframe: no visible global function definition for ‘SQLite’ .sqlite.to.dataframe: no visible global function definition for ‘dbGetQuery’ .sqlite.to.dataframe: no visible global function definition for ‘dbDisconnect’ rodps.change.types: no visible binding for global variable ‘rodps.type.java2r’ rodps.init.type: no visible binding for '<<-' assignment to ‘rodps.type.r2java’ rodps.init.type: no visible binding for '<<-' assignment to ‘rodps.type.java2r’ Undefined global functions or variables: dbConnect dbDisconnect dbGetQuery dbWriteTable rodps.type.java2r rodps.type.r2java SQLite
Found if() conditions comparing class() to string: File ‘RODPS/R/rodps_predict.R’: if (class(object) != "rpart") ... File ‘RODPS/R/rodps_predict.R’: if (class(object) != "fda") ... File ‘RODPS/R/rodps_str.R’: if (class(names(d)[i]) == "character") ... Use inherits() (or maybe is()) instead.
0 errors ✔ | 5 warnings ✖ | 3 notes ✖ Error: R CMD check found WARNINGs