Forbid new check warnings

CHANGELOG.md

@@ -18,6 +18,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - The `parse` option to `PEcAn.utils::read_web_config` had no effect when `expand` was TRUE (#2421).
 
 ### Changed
+- Stricter package checking (#2404): `make check` and CI builds will now fail if `R CMD check` returns any ERRORs or any "newly-added" WARNINGs or NOTEs. "Newly-added" is determined by strict string comparison against a check result saved 2019-09-03; messages that exist in the reference result do not break the build but will be fixed as time allows in future refactorings.
 - Updated modules/rtm PROSPECT docs
 - Updated models/sipnet/R/model2netcdf.SIPNET.R to address issues in PR #2254 
 - Improved testing (#2281). Automatic Travis CI builds of PEcAn on are now run using three versions of R in parallel. This should mean fewer issues with new releases and better backwards compatibility, but note that we still only guarantee full compatibility with the current release version of R. The tested versions are:

base/all/data/pecan.packages.csv

@@ -1,4 +1,2 @@
 1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18
-"utils";"common";"db";"modules/meta.analysis";"modules/uncertainty";"modules/emulator";"modules/assim.batch";"modules/assim.sequential";"modules/data.land";"modules/photosythesis";"modules/priors";"modules/rtm";"modules/benchmark";models/c4photo";"models/ed";"models/sipnet";"models/maat";"all"
-
-
+"utils";"common";"db";"modules/meta.analysis";"modules/uncertainty";"modules/emulator";"modules/assim.batch";"modules/assim.sequential";"modules/data.land";"modules/photosythesis";"modules/priors";"modules/rtm";"modules/benchmark";"models/c4photo";"models/ed";"models/sipnet";"models/maat";"all"

base/all/tests/Rcheck_reference.log

@@ -0,0 +1,58 @@
+* using log directory ‘/tmp/Rtmp3UHCCJ/PEcAn.all.Rcheck’
+* using R version 3.5.2 (2018-12-20)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using options ‘--no-tests --no-manual --as-cran’
+* checking for file ‘PEcAn.all/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘PEcAn.all’ version ‘1.7.0’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Depends: includes the non-default packages:
+  ‘PEcAn.DB’ ‘PEcAn.settings’ ‘PEcAn.MA’ ‘PEcAn.logger’ ‘PEcAn.utils’
+  ‘PEcAn.uncertainty’ ‘PEcAn.data.atmosphere’ ‘PEcAn.data.land’
+  ‘PEcAn.data.remote’ ‘PEcAn.assim.batch’ ‘PEcAn.emulator’
+  ‘PEcAn.priors’ ‘PEcAn.benchmark’ ‘PEcAn.remote’ ‘PEcAn.workflow’
+Adding so many packages to the search path is excessive and importing
+selectively is preferable.
+* 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 serialization versions ... OK
+* checking whether package ‘PEcAn.all’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License components with restrictions not permitted:
+  FreeBSD + file LICENSE
+Authors@R field gives no person with name and roles.
+Authors@R field gives no person with maintainer role, valid email
+address and non-empty name.
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... 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 for missing documentation entries ... WARNING
+Undocumented data sets:
+  ‘pecan.packages’
+All user-level objects in a package should have documentation entries.
+See chapter ‘Writing R documentation files’ in the ‘Writing R
+Extensions’ manual.
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking examples ... NONE
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... SKIPPED
+* DONE
+Status: 1 WARNING, 2 NOTEs

base/db/tests/Rcheck_reference.log

@@ -0,0 +1,199 @@
+* using log directory ‘/tmp/RtmpzhxcCR/PEcAn.DB.Rcheck’
+* using R version 3.5.2 (2018-12-20)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using options ‘--no-tests --no-manual --as-cran’
+* checking for file ‘PEcAn.DB/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘PEcAn.DB’ version ‘1.7.0’
+* package encoding: UTF-8
+* 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 executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking serialization versions ... OK
+* checking whether package ‘PEcAn.DB’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License components with restrictions not permitted:
+  FreeBSD + file LICENSE
+* 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 ... WARNING
+'::' or ':::' import not declared from: ‘bit64’
+'loadNamespace' or 'requireNamespace' call not declared from: ‘bit64’
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... NOTE
+clone_pft: no visible binding for global variable ‘name’
+clone_pft: no visible binding for global variable ‘id’
+clone_pft: no visible binding for global variable ‘created_at’
+clone_pft: no visible binding for global variable ‘updated_at’
+clone_pft: no visible binding for global variable ‘pft_id’
+db.exists: no visible binding for '<<-' assignment to ‘user.permission’
+db.exists: no visible binding for global variable ‘user.permission’
+dbfile.check: no visible binding for global variable ‘container_type’
+dbfile.check: no visible binding for global variable ‘container_id’
+dbfile.check: no visible binding for global variable ‘machine_id’
+dbfile.check: no visible binding for global variable ‘updated_at’
+dbHostInfo: no visible binding for global variable ‘sync_host_id’
+dbHostInfo: no visible binding for global variable ‘sync_start’
+dbHostInfo: no visible binding for global variable ‘sync_end’
+get_run_ids: no visible binding for global variable ‘run_id’
+get_users: no visible binding for global variable ‘id’
+get_workflow_ids: no visible binding for global variable ‘workflow_id’
+get.trait.data.pft: no visible binding for global variable ‘pft_id’
+get.trait.data.pft: no visible binding for global variable ‘created_at’
+get.trait.data.pft: no visible global function definition for ‘head’
+get.trait.data.pft: no visible binding for global variable ‘stat’
+get.trait.data.pft: no visible binding for global variable ‘trait’
+insert.format.vars: no visible binding for global variable ‘id’
+insert.format.vars: no visible binding for global variable ‘name’
+insert.format.vars: no visible global function definition for ‘collect’
+load_data_single_run: no visible global function definition for
+  ‘read.output’
+load_data_single_run: no visible binding for global variable ‘var_name’
+load_data_single_run: no visible binding for global variable ‘vals’
+load_data_single_run: no visible binding for global variable ‘posix’
+match_dbcols: no visible global function definition for ‘head’
+match_dbcols: no visible binding for global variable ‘.’
+match_dbcols: no visible binding for global variable ‘as’
+query_pfts: no visible binding for global variable ‘name’
+query.data: no visible binding for global variable ‘settings’
+query.format.vars: no visible binding for global variable ‘variable_id’
+query.format.vars: no visible binding for global variable
+  ‘storage_type’
+query.pft_cultivars: no visible binding for global variable ‘name’
+query.pft_cultivars: no visible binding for global variable ‘pft_type’
+query.pft_cultivars: no visible binding for global variable ‘name.mt’
+query.pft_cultivars: no visible binding for global variable
+  ‘cultivar_id’
+query.pft_cultivars: no visible binding for global variable ‘specie_id’
+query.pft_cultivars: no visible binding for global variable ‘genus’
+query.pft_cultivars: no visible binding for global variable ‘species’
+query.pft_cultivars: no visible binding for global variable
+  ‘scientificname’
+query.pft_cultivars: no visible binding for global variable ‘name.cv’
+query.priors: no visible binding for global variable ‘settings’
+query.traits: no visible binding for global variable ‘settings’
+query.traits: no visible binding for global variable ‘name’
+rename_jags_columns: no visible binding for global variable ‘stat’
+rename_jags_columns: no visible binding for global variable ‘n’
+rename_jags_columns: no visible binding for global variable ‘trt_id’
+rename_jags_columns: no visible binding for global variable ‘site_id’
+rename_jags_columns: no visible binding for global variable
+  ‘citation_id’
+rename_jags_columns: no visible binding for global variable
+  ‘greenhouse’
+runs: no visible binding for global variable ‘folder’
+runs: no visible binding for global variable ‘id’
+runs: no visible binding for global variable ‘ensemble_id’
+search_reference_single: no visible binding for global variable ‘score’
+search_reference_single: no visible binding for global variable
+  ‘author’
+search_reference_single: no visible binding for global variable
+  ‘author_family’
+search_reference_single: no visible binding for global variable
+  ‘author_given’
+search_reference_single: no visible binding for global variable
+  ‘issued’
+symmetric_setdiff: no visible global function definition for ‘:=’
+workflows: no visible binding for global variable ‘workflow_id’
+Undefined global functions or variables:
+  := . as author author_family author_given citation_id collect
+  container_id container_type created_at cultivar_id ensemble_id folder
+  genus greenhouse head id issued machine_id n name name.cv name.mt
+  pft_id pft_type posix read.output run_id scientificname score
+  settings site_id specie_id species stat storage_type sync_end
+  sync_host_id sync_start trait trt_id updated_at user.permission vals
+  var_name variable_id workflow_id
+Consider adding
+  importFrom("methods", "as")
+  importFrom("utils", "head")
+to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
+contains 'methods').
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd line widths ... NOTE
+Rd file 'dbfile.input.insert.Rd':
+  \examples lines wider than 100 characters:
+       dbfile.input.insert('trait.data.Rdata', siteid, startdate, enddate, 'application/x-RData', 'traits', dbcon)
+
+Rd file 'insert.format.vars.Rd':
+  \examples lines wider than 100 characters:
+       insert.format.vars(con = bety$con, format_name = "LTER-HFR-103", mimetype_id = 1090, notes = "NPP from Harvard Forest.", header = FAL ... [TRUNCATED]
+
+Rd file 'query.data.Rd':
+  \usage lines wider than 90 characters:
+       extra.columns = "ST_X(ST_CENTROID(sites.geometry)) AS lon, ST_Y(ST_CENTROID(sites.geometry)) AS lat, ",
+
+These lines will be truncated in the PDF manual.
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... WARNING
+Undocumented arguments in documentation object 'get_workflow_ids'
+  ‘all.ids’
+
+Undocumented arguments in documentation object 'ncdays2date'
+  ‘time’ ‘unit’
+
+Undocumented arguments in documentation object 'query.data'
+  ‘store.unconverted’
+
+Undocumented arguments in documentation object 'query.file.path'
+  ‘input.id’
+Documented arguments not in \usage in documentation object 'query.file.path':
+  ‘input_id’
+
+Undocumented arguments in documentation object 'query.format.vars'
+  ‘input.id’
+Documented arguments not in \usage in documentation object 'query.format.vars':
+  ‘input_id’
+
+Undocumented arguments in documentation object 'query.site'
+  ‘site.id’
+Documented arguments not in \usage in documentation object 'query.site':
+  ‘site_id’
+
+Undocumented arguments in documentation object 'query.trait.data'
+  ‘con’ ‘update.check.only’ ‘...’
+
+Undocumented arguments in documentation object 'query_pfts'
+  ‘strict’
+
+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 'query_pfts':
+  ‘modeltype’
+
+* checking for unstated dependencies in examples ... OK
+* checking files in ‘vignettes’ ... WARNING
+Files in the 'vignettes' directory but no files in 'inst/doc':
+  ‘betydb_access.Rmd’, ‘create_sites.geometry.Rmd’
+Package has no Sweave vignette sources and no VignetteBuilder field.
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... SKIPPED
+* DONE
+Status: 4 WARNINGs, 3 NOTEs

base/logger/tests/Rcheck_reference.log

@@ -0,0 +1,89 @@
+* using log directory ‘/tmp/Rtmp1Q6pph/PEcAn.logger.Rcheck’
+* using R version 3.5.2 (2018-12-20)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using options ‘--no-manual --as-cran’
+* checking for file ‘PEcAn.logger/DESCRIPTION’ ... OK
+* this is package ‘PEcAn.logger’ version ‘1.7.0’
+* package encoding: UTF-8
+* 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 executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking serialization versions ... OK
+* checking whether package ‘PEcAn.logger’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License components with restrictions not permitted:
+  FreeBSD + file LICENSE
+Authors@R field gives no person with name and roles.
+Authors@R field gives no person with maintainer role, valid email
+address and non-empty name.
+* 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 ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... NOTE
+logger.message: no visible global function definition for ‘dump.frames’
+logger.message: no visible binding for global variable ‘dump.log’
+logger.message: no visible global function definition for ‘tail’
+print2string: no visible global function definition for
+  ‘capture.output’
+Undefined global functions or variables:
+  capture.output dump.frames dump.log tail
+Consider adding
+  importFrom("utils", "capture.output", "dump.frames", "tail")
+to your NAMESPACE file.
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd line widths ... NOTE
+Rd file 'severeifnot.Rd':
+  \examples lines wider than 100 characters:
+       severeifnot("I absolutely cannot deal with the fact that something is not a list.", is.list(a), is.list(b))
+
+These lines will be truncated in the PDF manual.
+* checking Rd cross-references ... WARNING
+Missing link or links in documentation object 'logger.severe.Rd':
+  ‘logger.setQuitOnSevere(FALSE)’
+
+See section 'Cross-references' in the 'Writing R Extensions' manual.
+
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... WARNING
+Undocumented arguments in documentation object 'check_conditions'
+  ‘...’
+
+Undocumented arguments in documentation object 'is_definitely_true'
+  ‘x’
+
+Undocumented arguments in documentation object 'logger.getLevelNumber'
+  ‘level’
+
+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 ... OK
+* checking for unstated dependencies in examples ... OK
+* checking examples ... OK
+* DONE
+Status: 2 WARNINGs, 3 NOTEs