After reading all the email about KEGGSOAP I think I have the entire thing installed. However, it does not seem to work: list.organisms() Called from: parseArrayType(type) Also, it seems to have changed my prompt from ">" to "Browse[n]" where "n" is an integer which is increasing - but not with every command. This makes me nervous, because I do not know if I have changed something in my R environment. --Naomi Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

Naomi Altman <naomi at="" stat.psu.edu=""> writes: > After reading all the email about KEGGSOAP I think I have the entire > thing installed. However, it does not seem to work: > > list.organisms() > Called from: parseArrayType(type) > > > Also, it seems to have changed my prompt from ">" to > "Browse[n]" where "n" is an integer which is increasing - but not > with every command. This makes me nervous, because I do not know if > I have changed something in my R environment. I think you have a bad version of the SSOAP package [but you didn't give us many details on what software you have installed :-)]. I would suggest getting the latest version of SSOAP here: http://www.omegahat.org/SSOAP/ I think the BioC mirror is out of date and we will make sure it gets updated this week after we do some testing. + seth

Hi Naomi, Sounds like you've loaded a function that has a browser() call in it, often used in debugging functions. Looks like someone forgot to remove the browser call. To get out of browser mode, type a capital Q > myfun <- function(x) {y <- x^2; browser(); return(y)} > myfun(2) Called from: myfun(2) Browse[1]> myfun(3) Called from: myfun(3) Browse[2]> Q > That should get you back to the top-level prompt. lower case c also continues function execution, exiting one level of browser at a time. Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney at bccrc.ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Naomi Altman Sent: Mon 11/27/2006 2:01 PM To: Seth Falcon; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] KEGGSOAP Thanks, Seth, but I am still having problems. Firstly, I cannot seem to get out of the Browser. Some R commands work, but not exit. More importantly, I cannot install SSOAP, possibly because it is a tar.gz file, rather than a zip file. (Yup, I am working on Windows.) Regarding versions: I installed R 2.4.0 yesterday, and then installed everything else using the GUI. However, for KEGGSOAP and SSOAP, I downloaded from BiocLite (which was following a suggestion from the email archive. --Naomi At 03:05 PM 11/27/2006, Seth Falcon wrote: >Naomi Altman <naomi at="" stat.psu.edu=""> writes: > > > After reading all the email about KEGGSOAP I think I have the entire > > thing installed. However, it does not seem to work: > > > > list.organisms() > > Called from: parseArrayType(type) > > > > > > Also, it seems to have changed my prompt from ">" to > > "Browse[n]" where "n" is an integer which is increasing - but not > > with every command. This makes me nervous, because I do not know if > > I have changed something in my R environment. > >I think you have a bad version of the SSOAP package [but you didn't >give us many details on what software you have installed :-)]. > >I would suggest getting the latest version of SSOAP here: >http://www.omegahat.org/SSOAP/ > >I think the BioC mirror is out of date and we will make sure it gets >updated this week after we do some testing. > >+ seth > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111 _______________________________________________ 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

Hi Naomi, I do see a windows binary for SSOAP at http://bioconductor.org/packages/omegahat/html/SSOAP.html Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney at bccrc.ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Naomi Altman Sent: Mon 11/27/2006 2:01 PM To: Seth Falcon; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] KEGGSOAP Thanks, Seth, but I am still having problems. Firstly, I cannot seem to get out of the Browser. Some R commands work, but not exit. More importantly, I cannot install SSOAP, possibly because it is a tar.gz file, rather than a zip file. (Yup, I am working on Windows.) Regarding versions: I installed R 2.4.0 yesterday, and then installed everything else using the GUI. However, for KEGGSOAP and SSOAP, I downloaded from BiocLite (which was following a suggestion from the email archive. --Naomi At 03:05 PM 11/27/2006, Seth Falcon wrote: >Naomi Altman <naomi at="" stat.psu.edu=""> writes: > > > After reading all the email about KEGGSOAP I think I have the entire > > thing installed. However, it does not seem to work: > > > > list.organisms() > > Called from: parseArrayType(type) > > > > > > Also, it seems to have changed my prompt from ">" to > > "Browse[n]" where "n" is an integer which is increasing - but not > > with every command. This makes me nervous, because I do not know if > > I have changed something in my R environment. > >I think you have a bad version of the SSOAP package [but you didn't >give us many details on what software you have installed :-)]. > >I would suggest getting the latest version of SSOAP here: >http://www.omegahat.org/SSOAP/ > >I think the BioC mirror is out of date and we will make sure it gets >updated this week after we do some testing. > >+ seth > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111 _______________________________________________ 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

Naomi Altman <naomi at="" stat.psu.edu=""> writes: > Thanks, Seth, but I am still having problems. > > Firstly, I cannot seem to get out of the Browser. Some R commands > work, but not exit. As Steven posted, use 'Q' to quit the browser. > More importantly, I cannot install SSOAP, possibly because it is a > tar.gz file, rather than a zip file. (Yup, I am working on > Windows.) You are correct, no up-to-date Windows binary is currently available. We are working on updating the version of SSOAP that is available via biocLite. We expect to have an update available by the end of day tomorrow and we'll post to this list when it is available. Sorry for the inconvenience. > Regarding versions: > > I installed R 2.4.0 yesterday, and then installed everything else > using the GUI. However, for KEGGSOAP and SSOAP, I downloaded from > BiocLite (which was following a suggestion from the email archive. Using biocLite is the recommended way. + seth

> > > More importantly, I cannot install SSOAP, possibly because it is a > > > tar.gz file, rather than a zip file. (Yup, I am working on > > > Windows.) > > > >You are correct, no up-to-date Windows binary is currently available. > >We are working on updating the version of SSOAP that is available via > >biocLite. We expect to have an update available by the end of day > >tomorrow and we'll post to this list when it is available. The up-to-date KEGGSOAP and its dependencies are available now: KEGGSOAP SSOAP RCurl XML "1.8.2" "0.4-1" "0.8-0" "1.2-0" http://bioconductor.org/packages/1.9/omegahat/ http://bioconductor.org/packages/1.9/bioc/html/KEGGSOAP.html biocLite should also work. Biocore Team