AnnBuilder built package not supported in R 2.2.0
2
0
Entering edit mode
Brian Parker ▴ 30
@brian-parker-1623
Last seen 10.2 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 • 1.2k views
ADD COMMENT •
0
Entering edit mode
@james-w-macdonald-5106
Last seen 10 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
ADD COMMENT •
0
Entering edit mode
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 > > >
ADD REPLY •
0
Entering edit mode
John Zhang ★ 2.9k
@john-zhang-6
Last seen 10.2 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
ADD COMMENT •
0
Entering edit mode
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 > > >
ADD REPLY •
0
Entering edit mode
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 >
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 831 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6