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

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.