AnnBuilder built package not supported in R 2.2.0
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Brian Parker ▴ 30
@brian-parker-1623
Last seen 9.6 years ago
Hi, I have tried generating an example annotation file using AnnBuilder following the example in the AnnBuilder vignette. The example package "myPkg" appears to build OK, but when I try to use it I get the following error- > library(myPkg) Error in library(myPkg) : 'myPkg' is not a valid package -- installed < 2.0.0? I have tried R 2.2.0 and 2.2.1 under Windows. Any suggestions? Thanks, Brian Parker
Annotation AnnBuilder Annotation AnnBuilder • 972 views
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@james-w-macdonald-5106
Last seen 5 hours ago
United States
Brian Parker wrote: > Hi, > > I have tried generating an example annotation file using AnnBuilder > following the example in the AnnBuilder vignette. > The example package "myPkg" appears to build OK, but when I try to use > it I get the following error- > > library(myPkg) > Error in library(myPkg) : 'myPkg' is not a valid package -- installed < > 2.0.0? How exactly are you installing this package? From the error, it looks like you are just sticking the package into your R_HOME/library directory, rather than actually installing it. On Windows, you will need to get set up to install packages, as the necessary tools aren't part of Windows. See the R-FAQ for windows: http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install- packages-into-libraries-in-this-version_003f Note that the instructions for getting set up could be characterized as being terse. However, everything you need to do is clearly outlined in these instructions - you just have to pay close attention to what is specified. HTH, Jim > > I have tried R 2.2.0 and 2.2.1 under Windows. > Any suggestions? > > Thanks, > Brian Parker > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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
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Yes, that was the problem and the built package installs OK now, thanks a lot. ,Brian Parker James W. MacDonald wrote: > Brian Parker wrote: > >> Hi, >> >> I have tried generating an example annotation file using AnnBuilder >> following the example in the AnnBuilder vignette. >> The example package "myPkg" appears to build OK, but when I try to >> use it I get the following error- >> > library(myPkg) >> Error in library(myPkg) : 'myPkg' is not a valid package -- installed >> < 2.0.0? > > > How exactly are you installing this package? From the error, it looks > like you are just sticking the package into your R_HOME/library > directory, rather than actually installing it. > > On Windows, you will need to get set up to install packages, as the > necessary tools aren't part of Windows. See the R-FAQ for windows: > > http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I -install-packages-into-libraries-in-this-version_003f > > > Note that the instructions for getting set up could be characterized > as being terse. However, everything you need to do is clearly outlined > in these instructions - you just have to pay close attention to what > is specified. > > HTH, > > Jim > > >> >> I have tried R 2.2.0 and 2.2.1 under Windows. >> Any suggestions? >> >> Thanks, >> Brian Parker >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > >
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 9.6 years ago
You will have to tell us a little bit more about what you have done. Did you built the package and then had the package installed using R 2.2.0 or 2.2.1 or built the package using R < 2.0.0 and tried to install the package using R > 2.0.0? >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >X-Spam-Checker-Version: SpamAssassin 3.1.0 (2005-09-13) on hypatia.math.ethz.ch >X-Spam-Level: >X-Spam-Status: No, score=0.0 required=5.0 tests=BAYES_50 autolearn=no version=3.1.0 >Date: Thu, 23 Feb 2006 11:42:30 +1100 >From: Brian Parker <brian.parker at="" rsise.anu.edu.au=""> >User-Agent: Mozilla Thunderbird 1.0.6 (Windows/20050716) >X-Accept-Language: en-us, en >MIME-Version: 1.0 >To: bioconductor at stat.math.ethz.ch >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] AnnBuilder built package not supported in R 2.2.0 >X-BeenThere: bioconductor at stat.math.ethz.ch >X-Mailman-Version: 2.1.6 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >Content-Transfer-Encoding: 7bit >X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.2.0.0, Antispam-Data: 2006.02.22.152606 >X-PMX-Spam: Probability=7%, Report='__CT 0, __CTE 0, __CTYPE_CHARSET_QUOTED 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, __MIME_VERSION 0, __SANE_MSGID 0, __STOCK_CRUFT 0, __USER_AGENT 0' > >Hi, > >I have tried generating an example annotation file using AnnBuilder >following the example in the AnnBuilder vignette. >The example package "myPkg" appears to build OK, but when I try to use >it I get the following error- > > library(myPkg) >Error in library(myPkg) : 'myPkg' is not a valid package -- installed < >2.0.0? > >I have tried R 2.2.0 and 2.2.1 under Windows. >Any suggestions? > >Thanks, >Brian Parker > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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Hi, Actually, I just wasn't installing the generated package properly using R CMD INSTALL (see my response to James MacDonald above) (...actually, that might be a useful newbie FAQ to add to the AnnBuilder vignette...). The one remaining problem I have now is that I am finding that the KEGG site is unresponsive, and on most runs I get the following error message- " Warning message: Built for UCSC is not valid! in: getUCSCBuilt(organism) Error in parseKEGGGenome() : Faild to obtain KEGG organism code " Is there any simple workaround to skip the KEGG data? BTW, thanks for the AnnBuilder function! Brian Parker John Zhang wrote: >You will have to tell us a little bit more about what you have done. Did you >built the package and then had the package installed using R 2.2.0 or 2.2.1 or >built the package using R < 2.0.0 and tried to install the package using R > >2.0.0? > > > > >>X-Original-To: jzhang at jimmy.harvard.edu >>Delivered-To: jzhang at jimmy.harvard.edu >>X-Spam-Checker-Version: SpamAssassin 3.1.0 (2005-09-13) on hypatia.math.ethz.ch >>X-Spam-Level: >>X-Spam-Status: No, score=0.0 required=5.0 tests=BAYES_50 autolearn=no >> >> >version=3.1.0 > > >>Date: Thu, 23 Feb 2006 11:42:30 +1100 >>From: Brian Parker <brian.parker at="" rsise.anu.edu.au=""> >>User-Agent: Mozilla Thunderbird 1.0.6 (Windows/20050716) >>X-Accept-Language: en-us, en >>MIME-Version: 1.0 >>To: bioconductor at stat.math.ethz.ch >>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >>Subject: [BioC] AnnBuilder built package not supported in R 2.2.0 >>X-BeenThere: bioconductor at stat.math.ethz.ch >>X-Mailman-Version: 2.1.6 >>List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >>List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> >> ><mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> > > >>List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >>List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >>List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >>List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> >> ><mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> > > >>Content-Transfer-Encoding: 7bit >>X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.2.0.0, Antispam- Data: >> >> >2006.02.22.152606 > > >>X-PMX-Spam: Probability=7%, Report='__CT 0, __CTE 0, __CTYPE_CHARSET_QUOTED 0, >> >> >__CT_TEXT_PLAIN 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, __MIME_VERSION 0, >__SANE_MSGID 0, __STOCK_CRUFT 0, __USER_AGENT 0' > > >>Hi, >> >>I have tried generating an example annotation file using AnnBuilder >>following the example in the AnnBuilder vignette. >>The example package "myPkg" appears to build OK, but when I try to use >>it I get the following error- >> >> >>>library(myPkg) >>> >>> >>Error in library(myPkg) : 'myPkg' is not a valid package -- installed < >>2.0.0? >> >>I have tried R 2.2.0 and 2.2.1 under Windows. >>Any suggestions? >> >>Thanks, >>Brian Parker >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > >Jianhua Zhang >Department of Medical Oncology >Dana-Farber Cancer Institute >44 Binney Street >Boston, MA 02115-6084 > > >
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Hi Brian, Could you try again? I believe there are some problems in the KEGG site last week, and I also believe these problems have been solved. You should not get the error in the parseKEGGGenome() function again. HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Fri, 24 Feb 2006, Brian Parker wrote: > Hi, > > Actually, I just wasn't installing the generated package properly using > R CMD INSTALL (see my response to James MacDonald above) (...actually, > that might be a useful newbie FAQ to add to the AnnBuilder vignette...). > > The one remaining problem I have now is that I am finding that the KEGG > site is unresponsive, and on most runs I get the following error message- > " > Warning message: > Built for UCSC is not valid! in: getUCSCBuilt(organism) > Error in parseKEGGGenome() : Faild to obtain KEGG organism code > " > Is there any simple workaround to skip the KEGG data? > > BTW, thanks for the AnnBuilder function! > Brian Parker > > John Zhang wrote: > > >You will have to tell us a little bit more about what you have done. Did you > >built the package and then had the package installed using R 2.2.0 or 2.2.1 or > >built the package using R < 2.0.0 and tried to install the package using R > > >2.0.0? > > > > > > > > > >>X-Original-To: jzhang at jimmy.harvard.edu > >>Delivered-To: jzhang at jimmy.harvard.edu > >>X-Spam-Checker-Version: SpamAssassin 3.1.0 (2005-09-13) on hypatia.math.ethz.ch > >>X-Spam-Level: > >>X-Spam-Status: No, score=0.0 required=5.0 tests=BAYES_50 autolearn=no > >> > >> > >version=3.1.0 > > > > > >>Date: Thu, 23 Feb 2006 11:42:30 +1100 > >>From: Brian Parker <brian.parker at="" rsise.anu.edu.au=""> > >>User-Agent: Mozilla Thunderbird 1.0.6 (Windows/20050716) > >>X-Accept-Language: en-us, en > >>MIME-Version: 1.0 > >>To: bioconductor at stat.math.ethz.ch > >>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch > >>Subject: [BioC] AnnBuilder built package not supported in R 2.2.0 > >>X-BeenThere: bioconductor at stat.math.ethz.ch > >>X-Mailman-Version: 2.1.6 > >>List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> > >>List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > >> > >> > ><mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> > > > > > >>List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> > >>List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> > >>List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> > >>List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > >> > >> > ><mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> > > > > > >>Content-Transfer-Encoding: 7bit > >>X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.2.0.0, Antispam- Data: > >> > >> > >2006.02.22.152606 > > > > > >>X-PMX-Spam: Probability=7%, Report='__CT 0, __CTE 0, __CTYPE_CHARSET_QUOTED 0, > >> > >> > >__CT_TEXT_PLAIN 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, __MIME_VERSION 0, > >__SANE_MSGID 0, __STOCK_CRUFT 0, __USER_AGENT 0' > > > > > >>Hi, > >> > >>I have tried generating an example annotation file using AnnBuilder > >>following the example in the AnnBuilder vignette. > >>The example package "myPkg" appears to build OK, but when I try to use > >>it I get the following error- > >> > >> > >>>library(myPkg) > >>> > >>> > >>Error in library(myPkg) : 'myPkg' is not a valid package -- installed < > >>2.0.0? > >> > >>I have tried R 2.2.0 and 2.2.1 under Windows. > >>Any suggestions? > >> > >>Thanks, > >>Brian Parker > >> > >>_______________________________________________ > >>Bioconductor mailing list > >>Bioconductor at stat.math.ethz.ch > >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >> > > > >Jianhua Zhang > >Department of Medical Oncology > >Dana-Farber Cancer Institute > >44 Binney Street > >Boston, MA 02115-6084 > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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