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

[Jenny Drnevich]

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