[R] Running sweave automatically using cygwin

Thu Dec 23 11:51:13 CET 2010

On 23.12.2010 02:17, Raquel Rangel de Meireles Guimarães wrote:
> Hi all,
>
> Hope someone could help me.
>
> I am trying to run automatically the conversion of an Rwn file to a tex
> file.
>
> I am using windows 7, and cygwin.
>
> I tried to run automatically the Sweave.sh script, in its the most
> recent version available at R webpage:
>
> http://cran.r-project.org/contrib/extra/scripts/Sweave.sh
>
> Unfortunately, I got this error message:
>
> ===========================
>
> Raquel at Dell-Raquel-PC ~
> $ cd /cygdrive/c/Users/Raquel/Desktop/test_max_planck/test-raquel
>
> Raquel at Dell-Raquel-PC
> /cygdrive/c/Users/Raquel/Desktop/test_max_planck/test-raquel
> $ chmod +x Sweave.sh
>
> Raquel at Dell-Raquel-PC
> /cygdrive/c/Users/Raquel/Desktop/test_max_planck/test-raquel
> $ ./Sweave.sh test-raquel.Rnw
>
> Run Sweave and postprocess with LaTeX directly from the command line
>
> ./Sweave.sh: line 657: R: command not found

Then R is not in your PATH, obviously.

On the other hand, why don't you simply use

  R CMD Sweave yourFIle.Rnw

from your favorite shell (for which you need R in the PATH environment 
variable as well).

Best,
Uwe Ligges

> An error occured after the use of 'R'!
> Quiting.
>
> =========================================
>
> I don't know what is the problem. Could you please help me? Below you
> find my Rnw code and the data for running sweave.
>
> Best regards,
>
> Raquel
>
> ========================================
> Rnw file
>
> \documentclass[12pt,oneside,a4paper]{article}
> \usepackage[latin1]{inputenc}
> \usepackage[brazil]{babel}
> \usepackage{amsthm,amsfonts,bm}
> \usepackage{graphicx}
> \usepackage[T1]{fontenc}
> \usepackage{ae}
> \usepackage[alf,bibjustif,recuo=1cm]{abntcite} %bibliografia da ABNT
> \usepackage{setspace}
> \usepackage[charter]{mathdesign}
> \usepackage{graphicx}
> \usepackage{Sweave}
>
> \bibliographystyle{abnt-alf}
>
> \onehalfspacing
> \setlength\parskip{0.5cm} % espaçamento entre parágrafos
>
> \title{MP 187: Statistical Models with missing values \\Final Test}
> \author{Raquel Rangel de Meireles Guimarães}
> \date{December, 2010}
>
> \begin{document}
>
> \maketitle
>
> <<echo=false,results=hide>>=
> if (require(xtable) == FALSE)
> stop("Pacote xtable() necessário para rodar essa análise.")
> options(digits=3)
> @
>
>
> In this test we were required to analyse data from IQ scores of 250
> subjects, repeated after one month. A large part of the sample dropped
> the second visit.
>
> Using only the complete cases, estimate the parameters of the regression
> line:
>
> <<>>=
> setwd("C:\\Users\\Raquel\\Desktop\\test_max_planck")
> data<-read.table("IQ.txt")
> attach(data)
> @
>
>
> I start here with a scatterplot of the two variables. It is easy to see
> from the figure \ref{fig:scatter} that we have a censored
>
> \begin{figure}[ht!]
> \centering
> <<echo=false,fig=true>>=
> plot(data$IQ1,data$IQ2)
> @
> \caption{Scatterplot of the two measurements of the IQ score, in the
> first and second visit.}
> \label{fig:scatter}
> \end{figure}
>
> \end{document}
>
> =====================================
>
> Data file: IQ.txt
>
> "IQ1" "IQ2"
> "1" 114.71 NA
> "2" 112.84 NA
> "3" 184.88 NA
> "4" 120.03 NA
> "5" 67 85.28
> "6" 75.12 64.24
> "7" 104.87 NA
> "8" 73.07 67.34
> "9" 100.7 NA
> "10" 129.79 NA
> "11" 11.83 109.91
> "12" 139.52 NA
> "13" 130.74 NA
> "14" 111.92 NA
> "15" 83.45 106.15
> "16" 80.33 19.14
> "17" 80.85 146.93
> "18" 65.63 89.09
> "19" 152.95 NA
> "20" 9.84 104.58
> "21" 112.47 NA
> "22" 92.14 NA
> "23" 151.66 NA
> "24" 168.06 NA
> "25" 34.6 47.21
> "26" 120.65 NA
> "27" 112.47 NA
> "28" 80.5 109.71
> "29" 58.46 52.5
> "30" 112.97 NA
> "31" 75.95 55.53
> "32" 58.59 123.95
> "33" 147.19 NA
> "34" 38.98 90.26
> "35" 115.18 NA
> "36" 98.93 NA
> "37" 113.2 NA
> "38" 144.42 NA
> "39" 145.52 NA
> "40" 134.97 NA
> "41" 98.61 NA
> "42" 98.23 NA
> "43" 166.18 NA
> "44" 43.75 95.76
> "45" 77.07 99.5
> "46" 112.2 NA
> "47" -0.03 13.23
> "48" 102.19 NA
> "49" 70.98 74.52
> "50" 80.48 26.61
> "51" 102.87 NA
> "52" 94.22 NA
> "53" 60.33 52.95
> "54" 54.09 95.25
> "55" 60.81 87.87
> "56" 106.98 NA
> "57" 71.18 112.27
> "58" 80.95 53
> "59" 122.56 NA
> "60" 74.22 41.55
> "61" 109.73 NA
> "62" 142.66 NA
> "63" 95.39 NA
> "64" 97.68 NA
> "65" 114.37 NA
> "66" 114.02 NA
> "67" 87.39 NA
> "68" 183.12 NA
> "69" 88.39 NA
> "70" 57.81 99.84
> "71" 133.65 NA
> "72" 78.16 30.84
> "73" 80.52 82.42
> "74" 107.02 NA
> "75" 85.35 NA
> "76" 84.35 NA
> "77" 92.62 NA
> "78" 45.62 100.89
> "79" 79.53 102.13
> "80" 85.11 NA
> "81" 108.72 NA
> "82" 95.55 NA
> "83" 57.17 52.48
> "84" 106.16 NA
> "85" 72.3 109.69
> "86" 88.13 NA
> "87" 117.57 NA
> "88" 86.59 NA
> "89" 65.56 71.14
> "90" 97.76 NA
> "91" 81.91 85.55
> "92" 65.58 78.26
> "93" 109.13 NA
> "94" 92.55 NA
> "95" 112.54 NA
> "96" 66.77 106.92
> "97" 106.69 NA
> "98" 43.65 56.27
> "99" 13.29 14.43
> "100" 108.6 NA
> "101" 111.95 NA
> "102" 62.04 25.49
> "103" 113.79 NA
> "104" 125.43 NA
> "105" 68.13 85.19
> "106" 112.13 NA
> "107" 21.61 83.67
> "108" 49.13 132.66
> "109" 104.61 NA
> "110" 105.9 NA
> "111" 107.7 NA
> "112" 157.83 NA
> "113" 20.3 41.49
> "114" 43.87 -7.62
> "115" 130.19 NA
> "116" 137.28 NA
> "117" 62.99 128.23
> "118" 97.71 NA
> "119" 103.46 NA
> "120" 90.81 NA
> "121" 40.89 51
> "122" 146.28 NA
> "123" 136.18 NA
> "124" 111.93 NA
> "125" 84.19 51.3
> "126" 105.01 NA
> "127" 78.28 44.44
> "128" 74.54 67.52
> "129" 80.92 152.09
> "130" 151.56 NA
> "131" 30.4 147.39
> "132" 62.99 97.48
> "133" 111.86 NA
> "134" 81.48 27.73
> "135" 146.15 NA
> "136" 67.1 102.68
> "137" 143.29 NA
> "138" 96.46 NA
> "139" 68.32 111.41
> "140" 99.3 NA
> "141" 84.19 NA
> "142" 81.72 125.93
> "143" 96.15 NA
> "144" 108.72 NA
> "145" 90.13 NA
> "146" 122.81 NA
> "147" 105.8 NA
> "148" 62.01 74.33
> "149" 119.9 NA
> "150" 106.85 NA
> "151" 122.73 NA
> "152" 165.65 NA
> "153" 102.62 NA
> "154" 104.4 NA
> "155" 164.31 NA
> "156" 131.4 NA
> "157" 63.49 55.07
> "158" 101.66 NA
> "159" 78 112.99
> "160" 123.43 NA
> "161" 57.85 89.96
> "162" 122.07 NA
> "163" 73.16 96.74
> "164" 82.56 80.55
> "165" 83.13 127.28
> "166" 96.86 NA
> "167" 71 105.9
> "168" 87.04 NA
> "169" 111.32 NA
> "170" 81.98 109.89
> "171" 66.82 49.2
> "172" 47.69 69.14
> "173" 125.36 NA
> "174" 102.1 NA
> "175" 135.84 NA
> "176" 113.58 NA
> "177" 58.7 44.42
> "178" 103.84 NA
> "179" 136.15 NA
> "180" 71.53 78.96
> "181" 114.4 NA
> "182" 123.94 NA
> "183" 149.28 NA
> "184" 137.63 NA
> "185" 77.12 89.17
> "186" 96.78 NA
> "187" 124.7 NA
> "188" 36.6 87.75
> "189" 119.91 NA
> "190" 98.61 NA
> "191" 68.51 64.39
> "192" 114.2 NA
> "193" 14.52 103.93
> "194" 140.32 NA
> "195" 41.35 89.9
> "196" 105.18 NA
> "197" 51.7 46.25
> "198" 128.1 NA
> "199" 86.58 NA
> "200" 105.8 NA
> "201" 156.95 NA
> "202" 116.36 NA
> "203" 105.48 NA
> "204" 31.71 78.27
> "205" 99.88 NA
> "206" 99.88 NA
> "207" 44.45 61.91
> "208" 124.56 NA
> "209" 92.08 NA
> "210" 174.38 NA
> "211" 75.18 28.15
> "212" 137.6 NA
> "213" 133.73 NA
> "214" 70.77 116
> "215" 55.07 95.08
> "216" 106.5 NA
> "217" 122.68 NA
> "218" 34.61 99.65
> "219" 53.79 46.15
> "220" 157.05 NA
> "221" 36.79 109.09
> "222" 97.73 NA
> "223" 10.11 104.35
> "224" 87.95 NA
> "225" 72.36 163.16
> "226" 57.72 113.36
> "227" 62.33 26.95
> "228" 122.27 NA
> "229" 49.03 78.68
> "230" 92.04 NA
> "231" 69.14 137.36
> "232" 29.93 138.28
> "233" 60.21 128.74
> "234" 124.81 NA
> "235" 121.18 NA
> "236" 106.76 NA
> "237" 116.47 NA
> "238" 59.32 86.54
> "239" 95.38 NA
> "240" 103.09 NA
> "241" 80.5 77.09
> "242" 56.99 76.54
> "243" 45.43 53.26
> "244" 114.7 NA
> "245" 50.22 144.81
> "246" 107.48 NA
> "247" 165.26 NA
> "248" 67.44 72.73
> "249" 89.46 NA
> "250" 88.88 NA
>
> =======================================
>