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leppott / ContDataQC

Quality control checks on continuous data. Example data is from a HOBO data logger with 30 minute intervals.
https://leppott.github.io/ContDataQC/
MIT License
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Package Build - check() #37

Open leppott opened 7 years ago

leppott commented 7 years ago

Fails on vignette creation. Needs temp data.

image

leppott commented 7 years ago

==> devtools::check()

Updating ContDataQC documentation Loading ContDataQC Loading required package: dataRetrieval Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

as.Date, as.Date.numeric

Loading required package: knitr Loading required package: survival Loading required package: doBy Loading required package: rmarkdown Setting env vars -------------------------------------------------------------- CFLAGS : -Wall -pedantic CXXFLAGS: -Wall -pedantic Building ContDataQC ----------------------------------------------------------- "C:/Programs/R/R-34~1.1/bin/i386/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD build "C:\Users\Erik.Leppo\OneDrive - Tetra Tech, \ Inc\MyDocs_OneDrive\GitHub\ContDataQC" --no-resave-data --no-manual

Setting env vars -------------------------------------------------------------- _R_CHECK_CRANINCOMING : FALSE _R_CHECK_FORCESUGGESTS: FALSE Checking ContDataQC ----------------------------------------------------------- "C:/Programs/R/R-34~1.1/bin/i386/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD check \ "C:\Users\ERIK~1.LEP\AppData\Local\Temp\RtmpYra4XQ/ContDataQC_2.0.1.9042.tar.gz" \ --as-cran --timings --no-manual

Rd file 'ContDataQC.Rd': \examples lines wider than 100 characters: file.copy(file.path(path.package("ContDataQC"),"extdata",myFile),file.path(getwd(),Selection.SUB[1],myFile)) ContDataQC(myData.Operation, myData.SiteID, myData.Type, myData.DateRange.Start, myData.DateRange.End, myDir.import, myDir.export) myConfig <- file.path(getwd(),Selection.SUB[1],"config.TZ.central.R") # include path if not in working directory ContDataQC(myData.Operation, myData.SiteID, myData.Type, myData.DateRange.Start, myData.DateRange.End, myDir.import, myDir.export, myCo ... [TRUNCATED] ContDataQC(myData.Operation, myData.SiteID, myData.Type, myData.DateRange.Start, myData.DateRange.End, myDir.import, myDir.export) ContDataQC(myData.Operation, myData.SiteID, myData.Type, myData.DateRange.Start, myData.DateRange.End, myDir.import, myDir.export) ContDataQC(myData.Operation, myData.SiteID, myData.Type, myData.DateRange.Start, myData.DateRange.End, myDir.import, myDir.export) ContDataQC(myData.Operation, myData.SiteID, myData.Type, myData.DateRange.Start, myData.DateRange.End, myDir.import, myDir.export) myFile <- c("test2_AW_20130426_20130725.csv", "test2_AW_20130725_20131015.csv", "test2_AW_20140901_20140930.csv") ContDataQC(myData.Operation, fun.myDir.import=myDir.import, fun.myDir.export=myDir.export, fun.myFile=myFile) myFile <- c("QC_test2_AW_20130426_20130725.csv", "QC_test2_AW_20130725_20131015.csv", "QC_test2_AW_20140901_20140930.csv") ContDataQC(myData.Operation, fun.myDir.import=myDir.import, fun.myDir.export=myDir.export, fun.myFile=myFile)

myFile <- c("QC_test2_AW_20130426_20130725.csv", "QC_test2_AW_20130725_20131015.csv", "QC_test2_AW_20140901_20140930.csv")

 ContDataQC(myData.Operation, fun.myDir.import=myDir.import, fun.myDir.export=myDir.export, fun.myFile=myFile)

Rd file 'Export.IHA.Rd': \examples lines wider than 100 characters: Notes.Names <- c("Dataset (SiteID)","IHA.Year","Analysis.Date (YYYYMMDD)","Analysis.Time (HHMMSS)","Analysis.User")

Rd file 'Export.StreamThermal.Rd': \examples lines wider than 100 characters: ExUSGSStreamTemp<-readNWISdv("01382310","00010","2011-01-01","2011-12-31",c("00001","00002","00003")) sitedata<-subset(ExUSGSStreamTemp, select=c("site_no","Date","X_00010_00001","X_00010_00002","X_00010_00003"))

Rd file 'fun.AggregateData.File.Rd': \examples lines wider than 100 characters: myFile <- c("QC_test2_AW_20130426_20130725.csv", "QC_test2_AW_20130725_20131015.csv", "QC_test2_AW_20140901_20140930.csv")

Rd file 'fun.QC.File.Rd': \examples lines wider than 100 characters:

myFile <- c("test2_AW_20130426_20130725.csv", "test2_AW_20130725_20131015.csv", "test2_AW_20140901_20140930.csv")

Rd file 'fun.Stats.File.Rd': \examples lines wider than 100 characters:

myFile <- c("QC_test2_Aw_20130426_20130725.csv", "QC_test2_Aw_20130725_20131015.csv", "QC_test2_Aw_20140901_20140930.csv")

Rd file 'rarify.Rd': \examples lines wider than 100 characters: bugs.mysize <- rarify(inbug=DF.biodata, sample.ID="SampRep",abund="Count",subsiz=mySize, mySeed=Seed.MS)

These lines will be truncated in the PDF manual.

Undocumented arguments in documentation object 'fun.Stats' 'fun.myProcedure.Step'

Undocumented arguments in documentation object 'fun.dt.Type2' 'fun2.dt.Type' Documented arguments not in \usage in documentation object 'fun.dt.Type2': 'fun.dt2.Type'

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.

base::assign(".ptime", proc.time(), pos = "CheckExEnv")

Name: CompSiteCDF

Title: CompSiteCDF, compare CDFs of sites

Aliases: CompSiteCDF

Keywords: CDF, comparison continuous data, site

** Examples

load bio data

df.data <- data_CompSiteCDF dim(df.data) [1] 349 6 View(df.data) Error in View(df.data) : View() should not be used in examples etc Execution halted

  • DONE Status: 1 ERROR, 4 WARNINGs, 7 NOTEs checking examples ... ERROR Running examples in 'ContDataQC-Ex.R' failed The error most likely occurred in:

base::assign(".ptime", proc.time(), pos = "CheckExEnv")

Name: CompSiteCDF

Title: CompSiteCDF, compare CDFs of sites

Aliases: CompSiteCDF

Keywords: CDF, comparison continuous data, site

** Examples

load bio data

df.data <- data_CompSiteCDF dim(df.data) [1] 349 6 View(df.data) Error in View(df.data) : View() should not be used in examples etc Execution halted

checking for portable file names ... WARNING Found the following files with non-portable file names: inst/rmd/Report_Aggregate - html.rmd inst/rmd/Report_Aggregate - word.rmd inst/rmd/Report_PeriodStats - word.rmd inst/rmd/Report_QC - html.rmd inst/rmd/Report_QC - word.rmd inst/rmd/Report_Stats - html.rmd inst/rmd/Report_Stats - word.rmd These are not fully portable file names. See section 'Package structure' in the 'Writing R Extensions' manual.

checking Rd \usage sections ... WARNING Documented arguments not in \usage in documentation object 'Export.IHA': 'fun.myDate.Format'

Undocumented arguments in documentation object 'fun.Stats' 'fun.myProcedure.Step'

Undocumented arguments in documentation object 'fun.dt.Type2' 'fun2.dt.Type' Documented arguments not in \usage in documentation object 'fun.dt.Type2': 'fun.dt2.Type'

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 for unstated dependencies in examples ... WARNING 'library' or 'require' calls not declared from: 'IHA' 'StreamThermal' 'XLConnect' 'installr'

checking package dependencies ... NOTE Depends: includes the non-default packages: 'dataRetrieval' 'zoo' 'knitr' 'survival' 'doBy' 'rmarkdown' Adding so many packages to the search path is excessive and importing selectively is preferable.

checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'knitr' 'rmarkdown' A package should be listed in only one of these fields.

checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. Non-standard files/directories found at top level: 'CompSiteCDF_20170922_115723.pdf' 'data-raw'

checking dependencies in R code ... NOTE Packages in Depends field not imported from: 'dataRetrieval' 'doBy' 'knitr' 'rmarkdown' 'survival' 'zoo' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE CompSiteCDF: no visible global function definition for 'read.csv' CompSiteCDF: no visible global function definition for 'View' CompSiteCDF: no visible global function definition for 'ecdf' CompSiteCDF: no visible global function definition for 'plot' CompSiteCDF: no visible global function definition for 'pdf' CompSiteCDF: no visible global function definition for 'par' CompSiteCDF: no visible global function definition for 'hist' CompSiteCDF: no visible global function definition for 'box' CompSiteCDF: no visible global function definition for 'lines' ... 120 lines ... myFile myFormat.Time myName.Date myName.DateTime na.omit par pdf plot polygon quantile read.csv runif sd var write.csv write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "axis", "box", "hist", "legend", "lines", "par", "plot", "polygon") importFrom("stats", "aggregate", "density", "ecdf", "median", "na.omit", "quantile", "runif", "sd", "var") importFrom("utils", "View", "flush.console", "head", "read.csv", "write.csv", "write.table") to your NAMESPACE file.

checking Rd line widths ... NOTE Rd file 'CompSiteCDF.Rd': \examples lines wider than 100 characters: bugs.m See 'C:/Users/Erik.Leppo/OneDrive - Tetra Tech, Inc/MyDocs_OneDrive/GitHub/ContDataQC.Rcheck/00check.log' for details.

R CMD check results 1 error | 3 warnings | 7 notes ysize <- rarify(inbug=DF.biodata, sample.ID="SampRep",abund="Count",subsiz=mySize, mySeed=Seed.MS)

Rd file 'ContDataQC.Rd': \examples lines wider than 100 characters: file.copy(file.path(path.package("ContDataQC"),"extdata",myFile),file.path(getwd(),Selection.SUB[1],myFile)) ContDataQC(myData.Operation, myData.SiteID, myData.Type, myData.DateRange.Start, myData.DateRange.End, myDir.import, myDir.export) myConfig <- file.path(getwd(),Selection.SUB[1],"config.TZ.central.R") # include path if not in working directory ... 28 lines ...

myFile <- c("test2_AW_20130426_20130725.csv", "test2_AW_20130725_20131015.csv", "test2_AW_20140901_20140930.csv")

Rd file 'fun.Stats.File.Rd': \examples lines wider than 100 characters:

myFile <- c("QC_test2_Aw_20130426_20130725.csv", "QC_test2_Aw_20130725_20131015.csv", "QC_test2_Aw_20140901_20140930.csv")

Rd file 'rarify.Rd': \examples lines wider than 100 characters: bugs.mysize <- rarify(inbug=DF.biodata, sample.ID="SampRep",abund="Count",subsiz=mySize, mySeed=Seed.MS)

These lines will be truncated in the PDF manual.

checking for old-style vignette sources ... NOTE Vignette sources only in 'inst/doc': 'ContDataQC_Vignette.Rmd' A 'vignettes' directory is required as from R 3.1.0 and these will not be indexed nor checked

R CMD check succeeded

leppott commented 7 years ago

Moved packages from Depends to Suggests.

v2.0.1.9043

leppott commented 7 years ago

Issues to check:

--1. Bad file names checking for portable file names ... WARNING Found the following files with non-portable file names: inst/rmd/Report_Aggregate - html.rmd inst/rmd/Report_Aggregate - word.rmd inst/rmd/Report_PeriodStats - word.rmd inst/rmd/Report_QC - html.rmd inst/rmd/Report_QC - word.rmd inst/rmd/Report_Stats - html.rmd inst/rmd/Report_Stats - word.rmd These are not fully portable file names. See section 'Package structure' in the 'Writing R Extensions' manual.--

  1. checking R code for possible problems ... NOTE See each function

--3. Line width. checking Rd line widths ... NOTE LOTS--

  1. checking Rd \usage sections ... WARNING check on these.

--5. Vignette may be using packages not declared in DESCRIPTION checking for unstated dependencies in examples ... WARNING 'library' or 'require' calls not declared from: 'IHA' 'StreamThermal' 'XLConnect' 'installr'--

  1. An example failed. checking examples ... ERROR

--7. License not in DESCRIPTION LICENSE is not mentioned in the DESCRIPTION file. Non-standard files/directories found at top level: 'CompSiteCDF_20170922_115723.pdf' 'data-raw'--

--8. Vignette directory.--

leppott commented 7 years ago
  1. Fixed Vignette error on creation. Put demo data into folder. Removed after vignette complete. Store files outside of package and copy into vignette folder.

v2.0.1.9045

leppott commented 7 years ago
  1. Added extra Suggests. XLConnect, installr, IHA, StreamThermal

v2.0.1.9046

leppott commented 7 years ago
  1. License.

v2.0.1.9046

leppott commented 7 years ago
  1. Line widths > 100 characters.

v2.0.1.9046

leppott commented 6 years ago

v2.0.2.9001, 2018-05-10

1 error | 2 warnings | 6 notes