MacOS Package installation problems
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Paulo Nuin ▴ 200
@paulo-nuin-3012
Last seen 6.9 years ago
Canada
It is some type of Mac-only problem that happened in Seattle at the source. Just google for the term and you should get in the first two hits a good answer about it. Cheers Paulo On 2012-05-31, at 10:48 AM, Chinedu Orekie wrote: > I am having the same problem installing packages (Line starting ' PUBLI ...' is malformed). It has not mattered which repoistory I cite, CRAN or > BioC. I first observed this yesterday, 30 Jun 2012. This all seems quite recent > since I was able to access packages only two weeks ago. My computer is Windows > based by the way. > > Could this be some generic systems error? > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
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Hi Chinedu, On Thu, May 31, 2012 at 7:48 AM, Chinedu Orekie <chinedu at="" tntcmedia.us=""> wrote: > I am having the same problem installing packages (Line starting ' PUBLI ...' is malformed). It has not mattered which repoistory I cite, CRAN or > BioC. I first observed this yesterday, 30 Jun 2012. This all seems quite recent > since I was able to access packages only two weeks ago. My computer is Windows > based by the way. > > Could this be some generic systems error? > This is the first I have heard of this happening on windows systems. Can you send the command that caused the error, as well as the full error code and the output of sessionInfo()? Thanks, Dan > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 9 months ago
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On Thu, May 31, 2012 at 7:48 AM, Chinedu Orekie <chinedu at="" tntcmedia.us=""> wrote: > I am having the same problem installing packages (Line starting ' PUBLI ...' is malformed). It has not mattered which repoistory I cite, CRAN or > BioC. I first observed this yesterday, 30 Jun 2012. This all seems quite recent > since I was able to access packages only two weeks ago. My computer is Windows > based by the way. > > Could this be some generic systems error? > I wonder if this is unrelated to the Mac OS problem and is instead a problem with a firewall or proxy at your location. What if you try this command: download.file("http://google.com", tempfile()) Does it work, or produce an error? If it produces an error, try starting R as follows: R --internet2 And then try biocLite() again. Let us know what happens. Thanks, Dan > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
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Hi, On Thu, May 31, 2012 at 6:36 PM, Chinedu Orekie <chinedu at="" tntcmedia.us=""> wrote: > Dan: > > I get the same error at separate internet connections (at home and at work). Now these are locations that worked in the past. So I am doubtful that a change in net connection is explanation. > > The sequence to seeing that error was: utils:::menuInstallPkgs() at the console and then on selecting a mirror site. Which mirror site did you select? Did you try to install a package? Which one? Was there any output besides the error message you sent? > Your thoughts. I don't know what could cause this. The recommended way to install Bioconductor packages, and the only method we support and can troubleshoot, is: source("http://bioconductor.org/biocLite.R") biocLite("pkgName") Also, to rule out any problems with mirrors, you should run chooseCRANmirror() and chooseBioCmirror() and choose Switzerland and USA (WA 1) respectively. Dan > > Chinedu > "TNTC: The need to connect" | P: (908) 514-TNTC > > On May 31, 2012, at 6:57 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > >> Hi Chinedu, >> >> On Thu, May 31, 2012 at 7:48 AM, Chinedu Orekie <chinedu at="" tntcmedia.us=""> wrote: >>> I am having the same problem installing packages (Line starting '>> PUBLI ...' is malformed). It has not mattered which repoistory I cite, CRAN or >>> BioC. I first observed this yesterday, 30 Jun 2012. This all seems quite recent >>> since I was able to access packages only two weeks ago. My computer is Windows >>> based by the way. >>> >>> Could this be some generic systems error? >>> >> >> This is the first I have heard of this happening on windows systems. >> Can you send the command that caused the error, as well as the full >> error code and the output of sessionInfo()? >> >> Thanks, >> Dan >> >> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>
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Dan Tenenbaum ★ 8.2k
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On Fri, Jun 1, 2012 at 8:35 AM, Chinedu Orekie <chinedu at="" tntcmedia.us=""> wrote: > Working from the drop down menu, I pointed to the CRAN mirror and on selecting "Install Packages" I get the error "Error in read.dcf(file = tmpf): ?Line starting '<doctype html="" publi...'="" is="" malformed".=""> > I see the same error when I select "Update Packages" as well. > > This is bug is certainly not package specific since i never get to where I can request one. > I am not sure if this is a Bioconductor issue, but what happens if you try biocLite() as suggested earlier? Dan > Chinedu > "TNTC: The need to connect" | P: (908) 514-TNTC > > On May 31, 2012, at 10:00 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > >> Hi, >> >> >> On Thu, May 31, 2012 at 6:36 PM, Chinedu Orekie <chinedu at="" tntcmedia.us=""> wrote: >>> Dan: >>> >>> I get the same error at separate internet connections (at home and at work). Now these are locations that worked in the past. So I am doubtful that a change in net connection is explanation. >>> >>> The sequence to seeing that error was: utils:::menuInstallPkgs() at the console and then on selecting a mirror site. >> >> >> Which mirror site did you select? Did you try to install a package? >> Which one? Was there any output besides the error message you sent? >> >>> Your thoughts. >> >> I don't know what could cause this. >> The recommended way to install Bioconductor packages, and the only >> method we support and can troubleshoot, is: >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("pkgName") >> >> Also, to rule out any problems with mirrors, you should run >> chooseCRANmirror() >> and >> chooseBioCmirror() >> and choose Switzerland >> and >> USA (WA 1) >> respectively. >> >> Dan >> >> >>> >>> Chinedu >>> "TNTC: The need to connect" | P: (908) 514-TNTC >>> >>> On May 31, 2012, at 6:57 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >>> >>>> Hi Chinedu, >>>> >>>> On Thu, May 31, 2012 at 7:48 AM, Chinedu Orekie <chinedu at="" tntcmedia.us=""> wrote: >>>>> I am having the same problem installing packages (Line starting '>>>> PUBLI ...' is malformed). It has not mattered which repoistory I cite, CRAN or >>>>> BioC. I first observed this yesterday, 30 Jun 2012. This all seems quite recent >>>>> since I was able to access packages only two weeks ago. My computer is Windows >>>>> based by the way. >>>>> >>>>> Could this be some generic systems error? >>>>> >>>> >>>> This is the first I have heard of this happening on windows systems. >>>> Can you send the command that caused the error, as well as the full >>>> error code and the output of sessionInfo()? >>>> >>>> Thanks, >>>> Dan >>>> >>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>
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Hello Where and what should I download a table containing human HUGO gene names and exon_id such as 2372, 2371. I used GenomicFeatures, but it seemed not include the HUGO names. Thanks. John ________________________________ From: Dan Tenenbaum <dtenenba@fhcrc.org> To: Chinedu Orekie <chinedu@tntcmedia.us> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> Sent: Friday, June 1, 2012 11:39 AM Subject: Re: [BioC] MacOS Package installation problems On Fri, Jun 1, 2012 at 8:35 AM, Chinedu Orekie <chinedu@tntcmedia.us> wrote: > Working from the drop down menu, I pointed to the CRAN mirror and on selecting "Install Packages" I get the error "Error in read.dcf(file = tmpf):  Line starting '<doctype html="" publi...'="" is="" malformed".=""> > I see the same error when I select "Update Packages" as well. > > This is bug is certainly not package specific since i never get to where I can request one. > I am not sure if this is a Bioconductor issue, but what happens if you try biocLite() as suggested earlier? Dan > Chinedu > "TNTC: The need to connect" | P: (908) 514-TNTC > > On May 31, 2012, at 10:00 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > >> Hi, >> >> >> On Thu, May 31, 2012 at 6:36 PM, Chinedu Orekie <chinedu@tntcmedia.us> wrote: >>> Dan: >>> >>> I get the same error at separate internet connections (at home and at work). Now these are locations that worked in the past. So I am doubtful that a change in net connection is explanation. >>> >>> The sequence to seeing that error was: utils:::menuInstallPkgs() at the console and then on selecting a mirror site. >> >> >> Which mirror site did you select? Did you try to install a package? >> Which one? Was there any output besides the error message you sent? >> >>> Your thoughts. >> >> I don't know what could cause this. >> The recommended way to install Bioconductor packages, and the only >> method we support and can troubleshoot, is: >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("pkgName") >> >> Also, to rule out any problems with mirrors, you should run >> chooseCRANmirror() >> and >> chooseBioCmirror() >> and choose Switzerland >> and >> USA (WA 1) >> respectively. >> >> Dan >> >> >>> >>> Chinedu >>> "TNTC: The need to connect" | P: (908) 514-TNTC >>> >>> On May 31, 2012, at 6:57 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: >>> >>>> Hi Chinedu, >>>> >>>> On Thu, May 31, 2012 at 7:48 AM, Chinedu Orekie <chinedu@tntcmedia.us> wrote: >>>>> I am having the same problem installing packages (Line starting '>>>> PUBLI ...' is malformed). It has not mattered which repoistory I cite, CRAN or >>>>> BioC. I first observed this yesterday, 30 Jun 2012. This all seems quite recent >>>>> since I was able to access packages only two weeks ago. My computer is Windows >>>>> based by the way. >>>>> >>>>> Could this be some generic systems error? >>>>> >>>> >>>> This is the first I have heard of this happening on windows systems. >>>> Can you send the command that caused the error, as well as the full >>>> error code and the output of sessionInfo()? >>>> >>>> Thanks, >>>> Dan >>>> >>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >> _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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Hi John, If you want to get your questions answered, a good strategy is to put new questions into a new thread. That way the rest of us can tell that there is a new question even if we are not following this particular thread. To answer your question, you can get HUGO gene symbols from the org packages as SYMBOL mappings or by requesting the SYMBOL column from a call to the select() method. If you are using the GenomicFeatures package and the gene names are entrez gene IDs (something that is typical but NOT guaranteed for all tracks since it ulitmately depends on the track that the annotation is based on), then you could get the HUGO symbols like this: geneIDs = c(2372, 2371) library("org.Hs.eg.db") select(org.Hs.eg.db, keys=geneIDs, cols="SYMBOL", keytype="ENTREZID") Marc On 06/01/2012 09:02 AM, John linux-user wrote: > Hello > > Where and what should I download a table containing human HUGO gene names and exon_id such as 2372, 2371. I used GenomicFeatures, but it seemed not include the HUGO names. Thanks. > > John > > > > ________________________________ > From: Dan Tenenbaum<dtenenba@fhcrc.org> > To: Chinedu Orekie<chinedu@tntcmedia.us> > Cc: "bioconductor@stat.math.ethz.ch"<bioconductor@stat.math.ethz.ch> > Sent: Friday, June 1, 2012 11:39 AM > Subject: Re: [BioC] MacOS Package installation problems > > On Fri, Jun 1, 2012 at 8:35 AM, Chinedu Orekie<chinedu@tntcmedia.us> wrote: >> Working from the drop down menu, I pointed to the CRAN mirror and on selecting "Install Packages" I get the error "Error in read.dcf(file = tmpf): Line starting '<doctype html="" publi...'="" is="" malformed".="">> >> I see the same error when I select "Update Packages" as well. >> >> This is bug is certainly not package specific since i never get to where I can request one. >> > I am not sure if this is a Bioconductor issue, but what happens if you > try biocLite() as suggested earlier? > Dan > > >> Chinedu >> "TNTC: The need to connect" | P: (908) 514-TNTC >> >> On May 31, 2012, at 10:00 PM, Dan Tenenbaum<dtenenba@fhcrc.org> wrote: >> >>> Hi, >>> >>> >>> On Thu, May 31, 2012 at 6:36 PM, Chinedu Orekie<chinedu@tntcmedia.us> wrote: >>>> Dan: >>>> >>>> I get the same error at separate internet connections (at home and at work). Now these are locations that worked in the past. So I am doubtful that a change in net connection is explanation. >>>> >>>> The sequence to seeing that error was: utils:::menuInstallPkgs() at the console and then on selecting a mirror site. >>> >>> Which mirror site did you select? Did you try to install a package? >>> Which one? Was there any output besides the error message you sent? >>> >>>> Your thoughts. >>> I don't know what could cause this. >>> The recommended way to install Bioconductor packages, and the only >>> method we support and can troubleshoot, is: >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("pkgName") >>> >>> Also, to rule out any problems with mirrors, you should run >>> chooseCRANmirror() >>> and >>> chooseBioCmirror() >>> and choose Switzerland >>> and >>> USA (WA 1) >>> respectively. >>> >>> Dan >>> >>> >>>> Chinedu >>>> "TNTC: The need to connect" | P: (908) 514-TNTC >>>> >>>> On May 31, 2012, at 6:57 PM, Dan Tenenbaum<dtenenba@fhcrc.org> wrote: >>>> >>>>> Hi Chinedu, >>>>> >>>>> On Thu, May 31, 2012 at 7:48 AM, Chinedu Orekie<chinedu@tntcmedia.us> wrote: >>>>>> I am having the same problem installing packages (Line starting '>>>>> PUBLI ...' is malformed). It has not mattered which repoistory I cite, CRAN or >>>>>> BioC. I first observed this yesterday, 30 Jun 2012. This all seems quite recent >>>>>> since I was able to access packages only two weeks ago. My computer is Windows >>>>>> based by the way. >>>>>> >>>>>> Could this be some generic systems error? >>>>>> >>>>> This is the first I have heard of this happening on windows systems. >>>>> Can you send the command that caused the error, as well as the full >>>>> error code and the output of sessionInfo()? >>>>> >>>>> Thanks, >>>>> Dan >>>>> >>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor@r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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Hi Marc, Thanks. John ________________________________ From: Marc Carlson <mcarlson@fhcrc.org> To: bioconductor@r-project.org Sent: Friday, June 1, 2012 3:18 PM Subject: Re: [BioC] HUGO EXON_ID Hi John, If you want to get your questions answered, a good strategy is to put new questions into a new thread.  That way the rest of us can tell that there is a new question even if we are not following this particular thread. To answer your question, you can get HUGO gene symbols from the org packages as SYMBOL mappings or by requesting the SYMBOL column from a call to the select() method.  If you are using the GenomicFeatures package and the gene names are entrez gene IDs (something that is typical but NOT guaranteed for all tracks since it ulitmately depends on the track that the annotation is based on), then you could get the HUGO symbols like this: geneIDs = c(2372, 2371) library("org.Hs.eg.db") select(org.Hs.eg.db, keys=geneIDs, cols="SYMBOL", keytype="ENTREZID")   Marc On 06/01/2012 09:02 AM, John linux-user wrote: > Hello > > Where and what should I download a table containing human HUGO gene names and exon_id such as 2372, 2371. I used GenomicFeatures, but it seemed not include the HUGO names. Thanks. > > John > > > > ________________________________ >  From: Dan Tenenbaum<dtenenba@fhcrc.org> > To: Chinedu Orekie<chinedu@tntcmedia.us> > Cc: "bioconductor@stat.math.ethz.ch"<bioconductor@stat.math.ethz.ch> > Sent: Friday, June 1, 2012 11:39 AM > Subject: Re: [BioC] MacOS Package installation problems > > On Fri, Jun 1, 2012 at 8:35 AM, Chinedu Orekie<chinedu@tntcmedia.us> wrote: >> Working from the drop down menu, I pointed to the CRAN mirror and on selecting "Install Packages" I get the error "Error in read.dcf(file = tmpf):  Line starting '<doctype html="" publi...'="" is="" malformed".="">> >> I see the same error when I select "Update Packages" as well. >> >> This is bug is certainly not package specific since i never get to where I can request one. >> > I am not sure if this is a Bioconductor issue, but what happens if you > try biocLite() as suggested earlier? > Dan > > >> Chinedu >> "TNTC: The need to connect" | P: (908) 514-TNTC >> >> On May 31, 2012, at 10:00 PM, Dan Tenenbaum<dtenenba@fhcrc.org> wrote: >> >>> Hi, >>> >>> >>> On Thu, May 31, 2012 at 6:36 PM, Chinedu Orekie<chinedu@tntcmedia.us>  wrote: >>>> Dan: >>>> >>>> I get the same error at separate internet connections (at home and at work). Now these are locations that worked in the past. So I am doubtful that a change in net connection is explanation. >>>> >>>> The sequence to seeing that error was: utils:::menuInstallPkgs() at the console and then on selecting a mirror site. >>> >>> Which mirror site did you select? Did you try to install a package? >>> Which one? Was there any output besides the error message you sent? >>> >>>> Your thoughts. >>> I don't know what could cause this. >>> The recommended way to install Bioconductor packages, and the only >>> method we support and can troubleshoot, is: >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("pkgName") >>> >>> Also, to rule out any problems with mirrors, you should run >>> chooseCRANmirror() >>> and >>> chooseBioCmirror() >>> and choose Switzerland >>> and >>> USA (WA 1) >>> respectively. >>> >>> Dan >>> >>> >>>> Chinedu >>>> "TNTC: The need to connect" | P: (908) 514-TNTC >>>> >>>> On May 31, 2012, at 6:57 PM, Dan Tenenbaum<dtenenba@fhcrc.org> wrote: >>>> >>>>> Hi Chinedu, >>>>> >>>>> On Thu, May 31, 2012 at 7:48 AM, Chinedu Orekie<chinedu@tntcmedia.us>  wrote: >>>>>> I am having the same problem installing packages (Line starting '>>>>> PUBLI ...' is malformed). It has not mattered which repoistory I cite, CRAN or >>>>>> BioC. I first observed this yesterday, 30 Jun 2012. This all seems quite recent >>>>>> since I was able to access packages only two weeks ago. My computer is Windows >>>>>> based by the way. >>>>>> >>>>>> Could this be some generic systems error? >>>>>> >>>>> This is the first I have heard of this happening on windows systems. >>>>> Can you send the command that caused the error, as well as the full >>>>> error code and the output of sessionInfo()? >>>>> >>>>> Thanks, >>>>> Dan >>>>> >>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor@r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >     [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor     [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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