[BioC] warning from make.cdf.package - FYI

[James W. MacDonald]

Hi Jenny,

You don't really need latex, although it is nice if you actually want to 
build packages that contain vignettes. If you do install it, I would 
recommend MikTex, because it has a nice installer and package management 
system.

The hhc thing is because you haven't installed the Microsoft HTML Help 
Workshop. I didn't think this was critical, but I have always installed 
it, so I don't really know. Anyway, I believe it was a simple install:

http://msdn.microsoft.com/library/default.asp?url=/library/en-us/htmlhelp/html/hwmicrosofthtmlhelpdownloads.asp

Good luck!

Jim

Jenny Drnevich wrote:
> Hi Jim,
> 
> I'm in the process of trying to make a custom cdf package, and I got the 
> warning below:
> 
>  >make.cdf.package("lund-zfa530237N.cdf",species="song_bird",
> +     maintainer="Jenny Drnevich <drnevich at uiuc.edu>")
> Reading CDF file.
> Creating CDF environment
> Wait for about 231 
> dots.......................................................................................................................................................................................................................
> Creating package in C:/Statistics/Clayton/lundzfa530237ncdf
> [1] "lundzfa530237ncdf"
> Warning message:
> incomplete final line found by readLines on 
> 'C:/PROGRA~1/R/R-24~1.0/library/makecdfenv/Code/DESCRIPTION'
>  >
> 
> I haven't been able to build the package yet - I thought I had gotten all 
> the tools I needed, but I've been unsuccessful. I doubt this warning has 
> anything to do with it, but I thought I should send it to you anyway. 
> Actually, here's the error from the terminal, just in case:
> 
> cp: cannot stat 
> 'C:/Statistics/Clayton/lundzfa530237ncdf/chm/lundzfa530237ncdf.chm: No such 
> file or directory
> make[1]: *** [chm-lundzfa530237ncdf ] Error 1
> make: *** [pkg-lundzfa530237ncdf ] Error 2
> *** Installation of lundzfa530237ncdf failed ***
> 
> Removing 'c:/PROGRA~1/R/R-24~1.0/library/lundzfa530237ncdf'
> 
> The output was also saying 'latex: not found' and 'hhc not found'. One of 
> our IT guys is going to get my PC up to speed while I'm gone tomorrow & 
> Monday, so if the problem is on my end, I'll be ready to go next week!
> 
> Cheers,
> Jenny
> 
>  >sessionInfo()
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
> States.1252;LC_MONETARY=English_United 
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"
> 
> other attached packages:
>     makecdfenv  affyQCReport    simpleaffy         made4 scatterplot3d
>       "1.12.0"      "1.12.0"       "2.8.0"       "1.8.0"      "0.3-24"
>           ade4       affyPLM         gcrma   matchprobes      affydata
>        "1.4-2"      "1.10.0"       "2.6.0"       "1.6.0"      "1.10.0"
> affycoretools       biomaRt         RCurl           XML       GOstats
>        "1.6.0"       "1.8.0"       "0.7-0"     "0.99-93"       "2.0.0"
>       Category    genefilter      survival          KEGG          RBGL
>        "2.0.0"      "1.12.0"        "2.29"      "1.14.0"      "1.10.0"
>       annotate            GO         graph         limma          affy
>       "1.12.0"      "1.14.0"      "1.12.0"       "2.9.1"      "1.12.0"
>         affyio       Biobase       RWinEdt
>        "1.2.0"      "1.12.2"       "1.7-5"
> 
> 
> 
> 
> Cheers,
> Jenny
> 
> 
> Jenny Drnevich, Ph.D.
> 
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
> 
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
> 
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.