From b8a91b9a92f84972f0e0a06251c6ad3912670bd1 Mon Sep 17 00:00:00 2001 From: Burgeon_Environment Date: Mon, 16 Oct 2017 21:04:17 +0200 Subject: [PATCH] 1.0.2 --- resp.Rcheck/00check.log | 148 +++++++++++++++ resp.Rcheck/00install.out | 8 + resp.Rcheck/Rdlatex.log | 130 +++++++++++++ resp.Rcheck/resp-Ex.R | 80 ++++++++ resp.Rcheck/resp-Ex.Rout | 133 +++++++++++++ resp.Rcheck/resp-Ex.pdf | Bin 0 -> 3611 bytes resp.Rcheck/resp-manual.pdf | Bin 0 -> 75354 bytes resp.Rcheck/resp-manual.tex | 291 +++++++++++++++++++++++++++++ resp.Rcheck/resp/DESCRIPTION | 12 ++ resp.Rcheck/resp/INDEX | 9 + resp.Rcheck/resp/Meta/Rd.rds | Bin 0 -> 512 bytes resp.Rcheck/resp/Meta/features.rds | Bin 0 -> 112 bytes resp.Rcheck/resp/Meta/hsearch.rds | Bin 0 -> 519 bytes resp.Rcheck/resp/Meta/links.rds | Bin 0 -> 208 bytes resp.Rcheck/resp/Meta/nsInfo.rds | Bin 0 -> 196 bytes resp.Rcheck/resp/Meta/package.rds | Bin 0 -> 750 bytes resp.Rcheck/resp/NAMESPACE | 1 + resp.Rcheck/resp/R/resp | 27 +++ resp.Rcheck/resp/R/resp.rdb | Bin 0 -> 9080 bytes resp.Rcheck/resp/R/resp.rdx | Bin 0 -> 418 bytes resp.Rcheck/resp/help/AnIndex | 8 + resp.Rcheck/resp/help/aliases.rds | Bin 0 -> 151 bytes resp.Rcheck/resp/help/paths.rds | Bin 0 -> 199 bytes resp.Rcheck/resp/help/resp.rdb | Bin 0 -> 12349 bytes resp.Rcheck/resp/help/resp.rdx | Bin 0 -> 334 bytes resp.Rcheck/resp/html/00Index.html | 40 ++++ resp.Rcheck/resp/html/R.css | 97 ++++++++++ resp/R/mod.choose.R | 34 +++- resp/R/mod.resp.R | 30 ++- resp/man/mod.resp.Rd | 41 +++- resp_1.0.2.tar.gz | Bin 0 -> 17249 bytes 31 files changed, 1064 insertions(+), 25 deletions(-) create mode 100644 resp.Rcheck/00check.log create mode 100644 resp.Rcheck/00install.out create mode 100644 resp.Rcheck/Rdlatex.log create mode 100644 resp.Rcheck/resp-Ex.R create mode 100644 resp.Rcheck/resp-Ex.Rout create mode 100644 resp.Rcheck/resp-Ex.pdf create mode 100644 resp.Rcheck/resp-manual.pdf create mode 100644 resp.Rcheck/resp-manual.tex create mode 100644 resp.Rcheck/resp/DESCRIPTION create mode 100644 resp.Rcheck/resp/INDEX create mode 100644 resp.Rcheck/resp/Meta/Rd.rds create mode 100644 resp.Rcheck/resp/Meta/features.rds create mode 100644 resp.Rcheck/resp/Meta/hsearch.rds create mode 100644 resp.Rcheck/resp/Meta/links.rds create mode 100644 resp.Rcheck/resp/Meta/nsInfo.rds create mode 100644 resp.Rcheck/resp/Meta/package.rds create mode 100644 resp.Rcheck/resp/NAMESPACE create mode 100644 resp.Rcheck/resp/R/resp create mode 100644 resp.Rcheck/resp/R/resp.rdb create mode 100644 resp.Rcheck/resp/R/resp.rdx create mode 100644 resp.Rcheck/resp/help/AnIndex create mode 100644 resp.Rcheck/resp/help/aliases.rds create mode 100644 resp.Rcheck/resp/help/paths.rds create mode 100644 resp.Rcheck/resp/help/resp.rdb create mode 100644 resp.Rcheck/resp/help/resp.rdx create mode 100644 resp.Rcheck/resp/html/00Index.html create mode 100644 resp.Rcheck/resp/html/R.css create mode 100644 resp_1.0.2.tar.gz diff --git a/resp.Rcheck/00check.log b/resp.Rcheck/00check.log new file mode 100644 index 0000000..5fbbac1 --- /dev/null +++ b/resp.Rcheck/00check.log @@ -0,0 +1,148 @@ +* using log directory ‘/disk2/Documentos/ProjectesR/resp/resp.Rcheck’ +* using R version 3.4.1 (2017-06-30) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* checking for file ‘resp/DESCRIPTION’ ... OK +* this is package ‘resp’ version ‘1.0.2’ +* 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 ... NOTE +Found the following hidden files and directories: + man/.Rhistory +These were most likely included in error. See section ‘Package +structure’ in the ‘Writing R Extensions’ manual. +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘resp’ can be installed ... OK +* checking installed package size ... OK +* checking package directory ... OK +* checking DESCRIPTION meta-information ... NOTE +Authors@R field gives no person with maintainer role, valid email +address and non-empty name. +Checking should be performed on sources prepared by ‘R CMD build’. +* 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 +'library' or 'require' call not declared from: ‘lme4’ +'library' or 'require' calls in package code: + ‘lme4’ ‘stats’ + Please use :: or requireNamespace() instead. + See section 'Suggested packages' in the 'Writing R Extensions' manual. +Namespaces in Imports field not imported from: + ‘lme4’ ‘stats’ + All declared Imports should be used. +* checking S3 generic/method consistency ... WARNING +log: + function(x, base) +log.dataset: + function(data, columns) + +See section ‘Generic functions and methods’ in the ‘Writing R +Extensions’ manual. +* checking replacement functions ... OK +* checking foreign function calls ... OK +* checking R code for possible problems ... NOTE +formula_from_vec: no visible global function definition for + ‘as.formula’ +mod.check: no visible global function definition for ‘anova’ +mod.check: no visible global function definition for ‘shapiro.test’ +mod.check: no visible global function definition for ‘residuals’ +mod.check: no visible global function definition for ‘cor.test’ +mod.check: no visible global function definition for ‘na.omit’ +mod.check: no visible global function definition for ‘fitted’ +mod.check: no visible global function definition for ‘AIC’ +mod.check: no visible global function definition for ‘BIC’ +mod.check: no visible global function definition for ‘logLik’ +mod.choose: no visible global function definition for ‘named_range’ +mod.choose: no visible binding for global variable ‘n’ +mod.resp : mod.form: no visible global function definition for ‘lmer’ +mod.resp: no visible global function definition for ‘na.omit’ +mod.resp: no visible global function definition for ‘as.formula’ +name_range.default: possible error in which(mid = i): unused argument + (mid = i) +Undefined global functions or variables: + AIC BIC anova as.formula cor.test fitted lmer logLik n na.omit + named_range residuals shapiro.test +Consider adding + importFrom("stats", "AIC", "BIC", "anova", "as.formula", "cor.test", + "fitted", "logLik", "na.omit", "residuals", "shapiro.test") +to your NAMESPACE file. +* checking Rd files ... OK +* checking Rd metadata ... OK +* checking Rd cross-references ... WARNING +Unknown package ‘’ in Rd xrefs +* checking for missing documentation entries ... WARNING +Undocumented code objects: + ‘mod.choose’ ‘name_range.data.frame’ ‘name_range.default’ + ‘name_range.numeric’ +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 ... WARNING +Codoc mismatches from documentation object 'mod.resp': +mod.resp + Code: function(data, fixed, random, r_group, exclude, omit_NA = TRUE, + fixed_interaction = TRUE, check_models = TRUE, + choose_models = TRUE, lmer_warnings = FALSE) + Docs: function(data, fixed, random, r_group, exclude, omit_NA = TRUE, + fixed_interaction = TRUE, check_models = TRUE) + Argument names in code not in docs: + choose_models lmer_warnings + +* checking Rd \usage sections ... WARNING +Documented arguments not in \usage in documentation object 'mod.resp': + ‘lmer_warnings’ + +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. +S3 methods shown with full name in documentation object 'log.dataset': + ‘log.dataset’ + +The \usage entries for S3 methods should use the \method markup and not +their full name. +See chapter ‘Writing R documentation files’ in the ‘Writing R +Extensions’ manual. +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... WARNING +Warning: parse error in file 'resp-Ex.R': +11: unexpected symbol +65: +66: ~~ simple examples + ^ +* checking examples ... ERROR +Running examples in ‘resp-Ex.R’ failed +The error most likely occurred in: + +> ### Name: resp-package +> ### Title: Creates response models for whole datasets +> ### Aliases: resp-package resp +> ### Keywords: package +> +> ### ** Examples +> +> ~~ simple examples of the most important functions ~~ +Error: unexpected symbol in "~~ simple examples" +Execution halted +* checking PDF version of manual ... WARNING +LaTeX errors when creating PDF version. +This typically indicates Rd problems. +* checking PDF version of manual without hyperrefs or index ... OK +* DONE +Status: 1 ERROR, 8 WARNINGs, 3 NOTEs diff --git a/resp.Rcheck/00install.out b/resp.Rcheck/00install.out new file mode 100644 index 0000000..286210d --- /dev/null +++ b/resp.Rcheck/00install.out @@ -0,0 +1,8 @@ +* installing *source* package ‘resp’ ... +** R +** preparing package for lazy loading +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded +* DONE (resp) diff --git a/resp.Rcheck/Rdlatex.log b/resp.Rcheck/Rdlatex.log new file mode 100644 index 0000000..25563ee --- /dev/null +++ b/resp.Rcheck/Rdlatex.log @@ -0,0 +1,130 @@ +Hmm ... looks like a package +This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) + restricted \write18 enabled. +entering extended mode +(./Rd2.tex +LaTeX2e <2017/01/01> patch level 3 +Babel <3.9r> and hyphenation patterns for 83 language(s) loaded. + +(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls +Document Class: book 2014/09/29 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+(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) +(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu) +(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) +No file Rd2.aux. +(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) +No file Rd2.toc. +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) +Underfull \hbox (badness 10000) in paragraph at lines 37--39 + +[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) +Overfull \hbox (12.78088pt too wide) in paragraph at lines 73--73 + []\T1/pcr/m/n/10 formula_from_vec(x, start=\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ~ \ +TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , mid=\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 + \TS1/pc +r/m/n/10 '\T1/pcr/m/n/10 , end=\TS1/pcr/m/n/10 ''\T1/pcr/m/n/10 , as_formula=FA +LSE)[] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) +Overfull \hbox (12.00732pt too wide) in paragraph at lines 132--134 +[]\T1/ptm/m/n/10 After a \T1/pcr/m/n/10 mresp \T1/ptm/m/n/10 ob-ject is cre-ate +d, check for fixed fac-tors sig-nif-i-cance and un-val-i-dated re-sults, mod.ch +eck +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [3] [4] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6] (./Rd2.aux) ) +(see the transcript file for additional information){/usr/share/texlive/texmf-d +ist/fonts/enc/dvips/base/8r.enc} +Output written on Rd2.pdf (6 pages, 75167 bytes). +Transcript written on Rd2.log. +This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) + restricted \write18 enabled. +entering extended mode +(./Rd2.tex +LaTeX2e <2017/01/01> patch level 3 +Babel <3.9r> and hyphenation patterns for 83 language(s) loaded. + +(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls +Document Class: book 2014/09/29 v1.4h Standard LaTeX document class +(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) +(/usr/share/R/share/texmf/tex/latex/Rd.sty +(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) +(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) +(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) +(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) +(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) +(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) +(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty +(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def)) +(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty +(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)) +(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def +(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) +(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) +(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu) +(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))) (./Rd2.aux) +(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc) +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) +Underfull \hbox (badness 10000) in paragraph at lines 37--39 + +[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) +(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) +Overfull \hbox (12.78088pt too wide) in paragraph at lines 73--73 + []\T1/pcr/m/n/10 formula_from_vec(x, start=\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ~ \ +TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , mid=\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 + \TS1/pc +r/m/n/10 '\T1/pcr/m/n/10 , end=\TS1/pcr/m/n/10 ''\T1/pcr/m/n/10 , as_formula=FA +LSE)[] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) +Overfull \hbox (12.00732pt too wide) in paragraph at lines 132--134 +[]\T1/ptm/m/n/10 After a \T1/pcr/m/n/10 mresp \T1/ptm/m/n/10 ob-ject is cre-ate +d, check for fixed fac-tors sig-nif-i-cance and un-val-i-dated re-sults, mod.ch +eck +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [3] [4] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5] +(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6] (./Rd2.aux) ) +(see the transcript file for additional information){/usr/share/texlive/texmf-d +ist/fonts/enc/dvips/base/8r.enc} +Output written on Rd2.pdf (6 pages, 75354 bytes). +Transcript written on Rd2.log. +Saving output to ‘resp-manual.pdf’ ... +Done +You may want to clean up by 'rm -rf /tmp/RtmpyYqho2/Rd2pdf7fab2e28e890' diff --git a/resp.Rcheck/resp-Ex.R b/resp.Rcheck/resp-Ex.R new file mode 100644 index 0000000..360e1b4 --- /dev/null +++ b/resp.Rcheck/resp-Ex.R @@ -0,0 +1,80 @@ +pkgname <- "resp" +source(file.path(R.home("share"), "R", "examples-header.R")) +options(warn = 1) +library('resp') + +base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') +cleanEx() +nameEx("mod.resp") +### * mod.resp + +flush(stderr()); flush(stdout()) + +### Name: mod.resp +### Title: Create response lmer models for a whole data.frame +### Aliases: mod.resp + +### ** Examples + +n <- 500L +tr <- c('T1','T2','T3') +sp <- c('S1','S2','S3') +gr <- c('A','B') +F1 <- c();F2 <- c();F3 <- c() +R1 <- c();R2 <- c();R3 <- c() +for (i in 1:n) { + F1[i] <- tr[round(i/n*3,0)] + F2[i] <- sp[round(runif(1L,1L,3L),0)] + F3[i] <- gr[round(runif(1L,1L,2L),0)] + R1[i] <- rnorm(1,10,2)+runif(1L)+(which(tr==F1[i])*3) + R2[i] <- rnorm(1,10,2)+runif(1L)+(which(sp==F2[i])*10) + R3[i] <- rnorm(1,600,20)+runif(1L)+(which(tr==F1[i])*20) +} +table(F1,F2) + +x <- data.frame( + Treatment=F1, + Specie=F2, + Group=F3, + Rand=runif(n), + Heigth=R1, + Diameter=R2, + Number_leaves=R3, + other=runif(n) +) +# rm(n,tr,sp,gr,F1,F2,F3) +a <- mod.resp(data = x, fixed = c('Treatment','Specie'), random='Rand', + r_group = c('Group'),exclude='other',lmer_warnings=TRUE, + choose_models=FALSE,check_models=FALSE) +print(a) + + + +cleanEx() +nameEx("resp-package") +### * resp-package + +flush(stderr()); flush(stdout()) + +### Name: resp-package +### Title: Creates response models for whole datasets +### Aliases: resp-package resp +### Keywords: package + +### ** Examples + +~~ simple examples of the most important functions ~~ + + + +### *