Question: PWMscoreStartingAt and ambiguous subject seqs
0
gravatar for Janet Young
7.3 years ago by
Janet Young730
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Janet Young730 wrote:
Hi there, I'm using PWMscoreStartingAt from Biostrings - it's VERY useful for me - thanks! Some of the sequences I'm scanning include ambiguities (some N, some Y, etc - uses IUPAC codes). I'm really glad that PWMscoreStartingAt works on these sequences, but I'd like to understand how scores are calculated when an N (or whatever) is present - would it be easy for you to add that to the documentation? (or just an email response would be fine too, but seems useful to add it to the docs) thanks very much, Janet ------------------------------------------------------------------- Dr. Janet Young Tapscott and Malik labs Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA. tel: (206) 667 1471 fax: (206) 667 6524 email: jayoung ...at... fhcrc.org -------------------------------------------------------------------
cancer biostrings glad • 854 views
ADD COMMENTlink modified 7.3 years ago by Hervé Pagès ♦♦ 14k • written 7.3 years ago by Janet Young730
Answer: PWMscoreStartingAt and ambiguous subject seqs
0
gravatar for Hervé Pagès
7.3 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:
Hi Janet, On 05/21/2012 06:34 PM, Janet Young wrote: > Hi there, > > I'm using PWMscoreStartingAt from Biostrings - it's VERY useful for me - thanks! > > Some of the sequences I'm scanning include ambiguities (some N, some Y, etc - uses IUPAC codes). I'm really glad that PWMscoreStartingAt works on these sequences, but I'd like to understand how scores are calculated when an N (or whatever) is present - would it be easy for you to add that to the documentation? (or just an email response would be fine too, but seems useful to add it to the docs) It seems that IUPAC ambiguity codes are simply ignored in the calculation of the score. For example with the 'pwm' used in the man page for PWMscoreStartingAt(): > dim(pwm) [1] 4 13 > PWMscoreStartingAt(pwm, DNAString("AAAAAAAAAAAAA")) [1] 0.4960267 > sum(pwm["A", ]) [1] 0.4960267 > PWMscoreStartingAt(pwm, DNAString("NNNNNNNNNNNNN")) [1] 0 This is probably not very satisfying. Maybe the contribution of an ambiguity to the score should be the average of the contributions of the individual bases represented by the ambiguity? I could implement this if that sounds reasonable. Feedback on this is welcome, and, in particular, it would be good to know how other tools handle this. Thanks! H. > > thanks very much, > > Janet > > > ------------------------------------------------------------------- > > Dr. Janet Young > > Tapscott and Malik labs > > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., C3-168, > P.O. Box 19024, Seattle, WA 98109-1024, USA. > > tel: (206) 667 1471 fax: (206) 667 6524 > email: jayoung ...at... fhcrc.org > > > ------------------------------------------------------------------- > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD COMMENTlink written 7.3 years ago by Hervé Pagès ♦♦ 14k
Hi Herve, Thanks for checking that out - interesting. I'm a little naive about these things, but your idea of averaging sounds reasonable to me. I'm copying Zizhen here - she's worked with PWMs much more than I have, and might have some helpful thoughts. Janet On May 21, 2012, at 10:33 PM, Hervé Pagès wrote: > Hi Janet, > > On 05/21/2012 06:34 PM, Janet Young wrote: >> Hi there, >> >> I'm using PWMscoreStartingAt from Biostrings - it's VERY useful for me - thanks! >> >> Some of the sequences I'm scanning include ambiguities (some N, some Y, etc - uses IUPAC codes). I'm really glad that PWMscoreStartingAt works on these sequences, but I'd like to understand how scores are calculated when an N (or whatever) is present - would it be easy for you to add that to the documentation? (or just an email response would be fine too, but seems useful to add it to the docs) > > It seems that IUPAC ambiguity codes are simply ignored in the > calculation of the score. For example with the 'pwm' used in the > man page for PWMscoreStartingAt(): > > > dim(pwm) > [1] 4 13 > > PWMscoreStartingAt(pwm, DNAString("AAAAAAAAAAAAA")) > [1] 0.4960267 > > sum(pwm["A", ]) > [1] 0.4960267 > > PWMscoreStartingAt(pwm, DNAString("NNNNNNNNNNNNN")) > [1] 0 > > This is probably not very satisfying. Maybe the contribution of an > ambiguity to the score should be the average of the contributions > of the individual bases represented by the ambiguity? I could implement > this if that sounds reasonable. Feedback on this is welcome, and, in > particular, it would be good to know how other tools handle this. > > Thanks! > H. > >> >> thanks very much, >> >> Janet >> >> >> ------------------------------------------------------------------- >> >> Dr. Janet Young >> >> Tapscott and Malik labs >> >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Avenue N., C3-168, >> P.O. Box 19024, Seattle, WA 98109-1024, USA. >> >> tel: (206) 667 1471 fax: (206) 667 6524 >> email: jayoung ...at... fhcrc.org >> >> >> ------------------------------------------------------------------- >> >> _______________________________________________ >> 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 > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319
ADD REPLYlink written 7.2 years ago by Janet Young730
Hi again, Yes, Zizhen agrees that averaging is a good choice. You're right - might be good to know what other tools do (I wish I had a little more time to look into that, but don't). Maybe others on the list have some experience? Janet On May 22, 2012, at 11:33 AM, Janet Young wrote: > Hi Herve, > > Thanks for checking that out - interesting. I'm a little naive about these things, but your idea of averaging sounds reasonable to me. I'm copying Zizhen here - she's worked with PWMs much more than I have, and might have some helpful thoughts. > > Janet > > > On May 21, 2012, at 10:33 PM, Hervé Pagès wrote: > >> Hi Janet, >> >> On 05/21/2012 06:34 PM, Janet Young wrote: >>> Hi there, >>> >>> I'm using PWMscoreStartingAt from Biostrings - it's VERY useful for me - thanks! >>> >>> Some of the sequences I'm scanning include ambiguities (some N, some Y, etc - uses IUPAC codes). I'm really glad that PWMscoreStartingAt works on these sequences, but I'd like to understand how scores are calculated when an N (or whatever) is present - would it be easy for you to add that to the documentation? (or just an email response would be fine too, but seems useful to add it to the docs) >> >> It seems that IUPAC ambiguity codes are simply ignored in the >> calculation of the score. For example with the 'pwm' used in the >> man page for PWMscoreStartingAt(): >> >>> dim(pwm) >> [1] 4 13 >>> PWMscoreStartingAt(pwm, DNAString("AAAAAAAAAAAAA")) >> [1] 0.4960267 >>> sum(pwm["A", ]) >> [1] 0.4960267 >>> PWMscoreStartingAt(pwm, DNAString("NNNNNNNNNNNNN")) >> [1] 0 >> >> This is probably not very satisfying. Maybe the contribution of an >> ambiguity to the score should be the average of the contributions >> of the individual bases represented by the ambiguity? I could implement >> this if that sounds reasonable. Feedback on this is welcome, and, in >> particular, it would be good to know how other tools handle this. >> >> Thanks! >> H. >> >>> >>> thanks very much, >>> >>> Janet >>> >>> >>> ------------------------------------------------------------------- >>> >>> Dr. Janet Young >>> >>> Tapscott and Malik labs >>> >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Avenue N., C3-168, >>> P.O. Box 19024, Seattle, WA 98109-1024, USA. >>> >>> tel: (206) 667 1471 fax: (206) 667 6524 >>> email: jayoung ...at... fhcrc.org >>> >>> >>> ------------------------------------------------------------------- >>> >>> _______________________________________________ >>> 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 >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages at fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >
ADD REPLYlink written 7.2 years ago by Janet Young730
Hello, Can anybody help me to solve this error? I can not understand it :( library(org.Sc.sgd.db) frame <- toTable(org.Sc.sgdGO) goframeData <- data.frame(frame$go_id, frame$Evidence, frame$systematic_name) goFrame <- GOFrame(goframeData, organism = "Saccharomyces cerevisiae") Loading required package: GO.db Error in .testGOFrame(x, organism) : All of the Evidence codes in your data.frame object must be legitimate Evidence Codes. Thanks a lot. Nooshin
ADD REPLYlink written 7.2 years ago by nooshin290
On 05/25/2012 02:35 AM, omranian wrote: > Hello, > > Can anybody help me to solve this error? I can not understand it :( > > library(org.Sc.sgd.db) > frame <- toTable(org.Sc.sgdGO) > goframeData <- data.frame(frame$go_id, frame$Evidence, > frame$systematic_name) > goFrame <- GOFrame(goframeData, organism = "Saccharomyces cerevisiae") > Loading required package: GO.db > > Error in .testGOFrame(x, organism) : > All of the Evidence codes in your data.frame object must be legitimate > Evidence Codes. Hi Nooshin -- the AnnotationDbi package is slightly out of date with respect to Evidence codes it selects; this is fixed in AnnotationDbi 1.18.1, which will be available for download via biocLite in a day or so. A work-around is to drop the 13 'IRD' evidence codes, > idx = goframeData$frame.Evidence != "IRD" > table(idx) idx FALSE TRUE 13 73735 > goframeData = goframeData[idx,] Martin > > Thanks a lot. > Nooshin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 7.2 years ago by Martin Morgan ♦♦ 23k
On 05/25/2012 03:09 PM, Martin Morgan wrote: > On 05/25/2012 02:35 AM, omranian wrote: >> Hello, >> >> Can anybody help me to solve this error? I can not understand it :( >> >> library(org.Sc.sgd.db) >> frame <- toTable(org.Sc.sgdGO) >> goframeData <- data.frame(frame$go_id, frame$Evidence, >> frame$systematic_name) >> goFrame <- GOFrame(goframeData, organism = "Saccharomyces cerevisiae") >> Loading required package: GO.db >> >> Error in .testGOFrame(x, organism) : >> All of the Evidence codes in your data.frame object must be legitimate >> Evidence Codes. > > Hi Nooshin -- the AnnotationDbi package is slightly out of date with > respect to Evidence codes it selects; this is fixed in AnnotationDbi > 1.18.1, which will be available for download via biocLite in a day or > so. A work-around is to drop the 13 'IRD' evidence codes, > > > idx = goframeData$frame.Evidence != "IRD" > > table(idx) > idx > FALSE TRUE > 13 73735 > > goframeData = goframeData[idx,] > > Martin > >> >> Thanks a lot. >> Nooshin >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hi Martin, Thanks for the reply! I removed the package and reinstalled it many times, but doesn't help :( I used biocLite to install and hope it installed the latest version. Now, I really don't know what should I do?! Best, Nooshin
ADD REPLYlink written 7.2 years ago by nooshin290
On 05/25/2012 06:13 AM, omranian wrote: > On 05/25/2012 03:09 PM, Martin Morgan wrote: >> On 05/25/2012 02:35 AM, omranian wrote: >>> Hello, >>> >>> Can anybody help me to solve this error? I can not understand it :( >>> >>> library(org.Sc.sgd.db) >>> frame <- toTable(org.Sc.sgdGO) >>> goframeData <- data.frame(frame$go_id, frame$Evidence, >>> frame$systematic_name) >>> goFrame <- GOFrame(goframeData, organism = "Saccharomyces cerevisiae") >>> Loading required package: GO.db >>> >>> Error in .testGOFrame(x, organism) : >>> All of the Evidence codes in your data.frame object must be legitimate >>> Evidence Codes. >> >> Hi Nooshin -- the AnnotationDbi package is slightly out of date with >> respect to Evidence codes it selects; this is fixed in AnnotationDbi >> 1.18.1, which will be available for download via biocLite in a day or >> so. A work-around is to drop the 13 'IRD' evidence codes, >> >> > idx = goframeData$frame.Evidence != "IRD" >> > table(idx) >> idx >> FALSE TRUE >> 13 73735 >> > goframeData = goframeData[idx,] >> >> Martin >> >>> >>> Thanks a lot. >>> Nooshin >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > Hi Martin, > Thanks for the reply! > I removed the package and reinstalled it many times, but doesn't help :( > > I used biocLite to install and hope it installed the latest version. > Now, I really don't know what should I do?! wait two days and try again; the package had a bug, the bug has been fixed (a few minutes ago); it takes a couple of days for the package to be checked and made available to you. When it is ready, using biocLite will download and install AnnotationDbi version 1.18.1. You must be using R version 2.15.0. Martin > > Best, > Nooshin -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 7.2 years ago by Martin Morgan ♦♦ 23k
On 05/25/2012 03:20 PM, Martin Morgan wrote: > On 05/25/2012 06:13 AM, omranian wrote: >> On 05/25/2012 03:09 PM, Martin Morgan wrote: >>> On 05/25/2012 02:35 AM, omranian wrote: >>>> Hello, >>>> >>>> Can anybody help me to solve this error? I can not understand it :( >>>> >>>> library(org.Sc.sgd.db) >>>> frame <- toTable(org.Sc.sgdGO) >>>> goframeData <- data.frame(frame$go_id, frame$Evidence, >>>> frame$systematic_name) >>>> goFrame <- GOFrame(goframeData, organism = "Saccharomyces cerevisiae") >>>> Loading required package: GO.db >>>> >>>> Error in .testGOFrame(x, organism) : >>>> All of the Evidence codes in your data.frame object must be legitimate >>>> Evidence Codes. >>> >>> Hi Nooshin -- the AnnotationDbi package is slightly out of date with >>> respect to Evidence codes it selects; this is fixed in AnnotationDbi >>> 1.18.1, which will be available for download via biocLite in a day or >>> so. A work-around is to drop the 13 'IRD' evidence codes, >>> >>> > idx = goframeData$frame.Evidence != "IRD" >>> > table(idx) >>> idx >>> FALSE TRUE >>> 13 73735 >>> > goframeData = goframeData[idx,] >>> >>> Martin >>> >>>> >>>> Thanks a lot. >>>> Nooshin >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> Hi Martin, >> Thanks for the reply! >> I removed the package and reinstalled it many times, but doesn't help :( >> >> I used biocLite to install and hope it installed the latest version. >> Now, I really don't know what should I do?! > > wait two days and try again; the package had a bug, the bug has been > fixed (a few minutes ago); it takes a couple of days for the package > to be checked and made available to you. When it is ready, using > biocLite will download and install AnnotationDbi version 1.18.1. You > must be using R version 2.15.0. > > Martin > >> >> Best, >> Nooshin > > Thanks a lot. So, you believe if I wait it would work! I have R version 2.15.0 but the version of AnnotationDbi is 1.14.1 even when I uninstall and install it again. So I'll wait for two days and try it again. I hope it works by then. Best, Nooshin
ADD REPLYlink written 7.2 years ago by nooshin290
On 05/25/2012 06:33 AM, omranian wrote: > On 05/25/2012 03:20 PM, Martin Morgan wrote: >> On 05/25/2012 06:13 AM, omranian wrote: >>> On 05/25/2012 03:09 PM, Martin Morgan wrote: >>>> On 05/25/2012 02:35 AM, omranian wrote: >>>>> Hello, >>>>> >>>>> Can anybody help me to solve this error? I can not understand it :( >>>>> >>>>> library(org.Sc.sgd.db) >>>>> frame <- toTable(org.Sc.sgdGO) >>>>> goframeData <- data.frame(frame$go_id, frame$Evidence, >>>>> frame$systematic_name) >>>>> goFrame <- GOFrame(goframeData, organism = "Saccharomyces cerevisiae") >>>>> Loading required package: GO.db >>>>> >>>>> Error in .testGOFrame(x, organism) : >>>>> All of the Evidence codes in your data.frame object must be legitimate >>>>> Evidence Codes. >>>> >>>> Hi Nooshin -- the AnnotationDbi package is slightly out of date with >>>> respect to Evidence codes it selects; this is fixed in AnnotationDbi >>>> 1.18.1, which will be available for download via biocLite in a day or >>>> so. A work-around is to drop the 13 'IRD' evidence codes, >>>> >>>> > idx = goframeData$frame.Evidence != "IRD" >>>> > table(idx) >>>> idx >>>> FALSE TRUE >>>> 13 73735 >>>> > goframeData = goframeData[idx,] >>>> >>>> Martin >>>> >>>>> >>>>> Thanks a lot. >>>>> Nooshin >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>> Hi Martin, >>> Thanks for the reply! >>> I removed the package and reinstalled it many times, but doesn't help :( >>> >>> I used biocLite to install and hope it installed the latest version. >>> Now, I really don't know what should I do?! >> >> wait two days and try again; the package had a bug, the bug has been >> fixed (a few minutes ago); it takes a couple of days for the package >> to be checked and made available to you. When it is ready, using >> biocLite will download and install AnnotationDbi version 1.18.1. You >> must be using R version 2.15.0. >> >> Martin >> >>> >>> Best, >>> Nooshin >> >> > Thanks a lot. > So, you believe if I wait it would work! > I have R version 2.15.0 but the version of AnnotationDbi is 1.14.1 even > when I uninstall and install it again. > So I'll wait for two days and try it again. > I hope it works by then. biocLite should not be installing AnnotationDbi 1.14.1 when using R 2.15. If that is really the case, then please report (copy and paste) the result of running the following commands in a new R session. source("http://bioconductor.org/biocLite.R") biocLite("AnnotationDbi") sessionInfo() Martin > > Best, > Nooshin -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 7.2 years ago by Martin Morgan ♦♦ 23k
On 05/25/2012 05:29 PM, Martin Morgan wrote: > On 05/25/2012 06:33 AM, omranian wrote: >> On 05/25/2012 03:20 PM, Martin Morgan wrote: >>> On 05/25/2012 06:13 AM, omranian wrote: >>>> On 05/25/2012 03:09 PM, Martin Morgan wrote: >>>>> On 05/25/2012 02:35 AM, omranian wrote: >>>>>> Hello, >>>>>> >>>>>> Can anybody help me to solve this error? I can not understand it :( >>>>>> >>>>>> library(org.Sc.sgd.db) >>>>>> frame <- toTable(org.Sc.sgdGO) >>>>>> goframeData <- data.frame(frame$go_id, frame$Evidence, >>>>>> frame$systematic_name) >>>>>> goFrame <- GOFrame(goframeData, organism = "Saccharomyces >>>>>> cerevisiae") >>>>>> Loading required package: GO.db >>>>>> >>>>>> Error in .testGOFrame(x, organism) : >>>>>> All of the Evidence codes in your data.frame object must be >>>>>> legitimate >>>>>> Evidence Codes. >>>>> >>>>> Hi Nooshin -- the AnnotationDbi package is slightly out of date with >>>>> respect to Evidence codes it selects; this is fixed in AnnotationDbi >>>>> 1.18.1, which will be available for download via biocLite in a day or >>>>> so. A work-around is to drop the 13 'IRD' evidence codes, >>>>> >>>>> > idx = goframeData$frame.Evidence != "IRD" >>>>> > table(idx) >>>>> idx >>>>> FALSE TRUE >>>>> 13 73735 >>>>> > goframeData = goframeData[idx,] >>>>> >>>>> Martin >>>>> >>>>>> >>>>>> Thanks a lot. >>>>>> Nooshin >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>> Hi Martin, >>>> Thanks for the reply! >>>> I removed the package and reinstalled it many times, but doesn't >>>> help :( >>>> >>>> I used biocLite to install and hope it installed the latest version. >>>> Now, I really don't know what should I do?! >>> >>> wait two days and try again; the package had a bug, the bug has been >>> fixed (a few minutes ago); it takes a couple of days for the package >>> to be checked and made available to you. When it is ready, using >>> biocLite will download and install AnnotationDbi version 1.18.1. You >>> must be using R version 2.15.0. >>> >>> Martin >>> >>>> >>>> Best, >>>> Nooshin >>> >>> >> Thanks a lot. >> So, you believe if I wait it would work! >> I have R version 2.15.0 but the version of AnnotationDbi is 1.14.1 even >> when I uninstall and install it again. >> So I'll wait for two days and try it again. >> I hope it works by then. > > biocLite should not be installing AnnotationDbi 1.14.1 when using R > 2.15. If that is really the case, then please report (copy and paste) > the result of running the following commands in a new R session. > > source("http://bioconductor.org/biocLite.R") > biocLite("AnnotationDbi") > sessionInfo() > > Martin > >> >> Best, >> Nooshin > > I think I made a mistake by the version. But still is not working and I have to wait for another 2 days as you said! Nooshin > source("http://bioconductor.org/biocLite.R") > biocLite("AnnotationDbi") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Installing package(s) 'AnnotationDbi' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotation Dbi_1.18.0.tar.gz' Content type 'application/x-gzip' length 4609048 bytes (4.4 Mb) opened URL ================================================== downloaded 4.4 Mb * installing *source* package ?AnnotationDbi? ... ** R ** inst ** preparing package for lazy loading Creating a generic function for ?toString? from package ?base? in package ?AnnotationDbi? Creating a generic function for ?rev? from package ?base? in package ?AnnotationDbi? Creating a generic function for ?subset? from package ?base? in package ?AnnotationDbi? Creating a generic function for ?as.data.frame? from package ?base? in package ?AnnotationDbi? Creating a generic function for ?head? from package ?utils? in package ?AnnotationDbi? Creating a generic function for ?tail? from package ?utils? in package ?AnnotationDbi? Creating a generic function for ?as.list? from package ?base? in package ?AnnotationDbi? Creating a generic function for ?ls? from package ?base? in package ?AnnotationDbi? Creating a generic function for ?eapply? from package ?base? in package ?AnnotationDbi? Creating a generic function for ?exists? from package ?base? in package ?AnnotationDbi? Creating a generic function for ?sample? from package ?base? in package ?AnnotationDbi? ** help *** installing help indices converting help for package ?AnnotationDbi? finding HTML links ... done AnnDbBimap-envirAPI html AnnDbObj-class html AnnDbPkg-checker html AnnDbPkg-maker html AnnotationDb-class html AnnotationDbi-internals html Bimap-direction html Bimap-keys html Bimap-toTable html Bimap html BimapFiltering html BimapFormatting html GOFrame html GOTerms-class html KEGGFrame html NCBI_getters html available.db0pkgs html createSimpleBimap html getProbeDataAffy html getProbeData_1lq html inpIDMapper html makeOrgPackage html makeProbePackage html make_eg_to_go_map html print.probetable html sqlForge-makeCHIPDB html sqlForge-popDB html sqlForge-wrapDBPackages html toSQLStringSet html unlist2 html ** building package indices ** installing vignettes ?AnnotationDbi.Rnw? ?IntroToAnnotationPackages.Rnw? ?NewSchema.Rnw? ?SQLForge.Rnw? ?makeProbePackage.Rnw? ** testing if installed package can be loaded * DONE (AnnotationDbi) The downloaded source packages are in ?/tmp/RtmpGs7sqo/downloaded_packages? > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods base other attached packages: [1] feature_1.2.8 ks_1.8.7 misc3d_0.8-2 rgl_0.92.880 mvtnorm_0.9-9992 KernSmooth_2.23-7 [7] limma_3.12.0 fields_6.6.3 spam_0.29-1 igraph_0.5.5-4 BiocInstaller_1.4.4 loaded via a namespace (and not attached): [1] tools_2.15.0
ADD REPLYlink written 7.2 years ago by nooshin290
Hi, No I have again another problem: biocLite("AnnotationDbi") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Installing package(s) 'AnnotationDbi' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotation Dbi_1.18.0.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotation Dbi_1.18.0.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open: HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ?AnnotationDbi? failed Would you please help me? On 05/25/2012 06:36 PM, omranian wrote: > On 05/25/2012 05:29 PM, Martin Morgan wrote: >> On 05/25/2012 06:33 AM, omranian wrote: >>> On 05/25/2012 03:20 PM, Martin Morgan wrote: >>>> On 05/25/2012 06:13 AM, omranian wrote: >>>>> On 05/25/2012 03:09 PM, Martin Morgan wrote: >>>>>> On 05/25/2012 02:35 AM, omranian wrote: >>>>>>> Hello, >>>>>>> >>>>>>> Can anybody help me to solve this error? I can not understand it :( >>>>>>> >>>>>>> library(org.Sc.sgd.db) >>>>>>> frame <- toTable(org.Sc.sgdGO) >>>>>>> goframeData <- data.frame(frame$go_id, frame$Evidence, >>>>>>> frame$systematic_name) >>>>>>> goFrame <- GOFrame(goframeData, organism = "Saccharomyces >>>>>>> cerevisiae") >>>>>>> Loading required package: GO.db >>>>>>> >>>>>>> Error in .testGOFrame(x, organism) : >>>>>>> All of the Evidence codes in your data.frame object must be >>>>>>> legitimate >>>>>>> Evidence Codes. >>>>>> >>>>>> Hi Nooshin -- the AnnotationDbi package is slightly out of date with >>>>>> respect to Evidence codes it selects; this is fixed in AnnotationDbi >>>>>> 1.18.1, which will be available for download via biocLite in a >>>>>> day or >>>>>> so. A work-around is to drop the 13 'IRD' evidence codes, >>>>>> >>>>>> > idx = goframeData$frame.Evidence != "IRD" >>>>>> > table(idx) >>>>>> idx >>>>>> FALSE TRUE >>>>>> 13 73735 >>>>>> > goframeData = goframeData[idx,] >>>>>> >>>>>> Martin >>>>>> >>>>>>> >>>>>>> Thanks a lot. >>>>>>> Nooshin >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> >>>>> Hi Martin, >>>>> Thanks for the reply! >>>>> I removed the package and reinstalled it many times, but doesn't >>>>> help :( >>>>> >>>>> I used biocLite to install and hope it installed the latest version. >>>>> Now, I really don't know what should I do?! >>>> >>>> wait two days and try again; the package had a bug, the bug has been >>>> fixed (a few minutes ago); it takes a couple of days for the package >>>> to be checked and made available to you. When it is ready, using >>>> biocLite will download and install AnnotationDbi version 1.18.1. You >>>> must be using R version 2.15.0. >>>> >>>> Martin >>>> >>>>> >>>>> Best, >>>>> Nooshin >>>> >>>> >>> Thanks a lot. >>> So, you believe if I wait it would work! >>> I have R version 2.15.0 but the version of AnnotationDbi is 1.14.1 even >>> when I uninstall and install it again. >>> So I'll wait for two days and try it again. >>> I hope it works by then. >> >> biocLite should not be installing AnnotationDbi 1.14.1 when using R >> 2.15. If that is really the case, then please report (copy and paste) >> the result of running the following commands in a new R session. >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("AnnotationDbi") >> sessionInfo() >> >> Martin >> >>> >>> Best, >>> Nooshin >> >> > > I think I made a mistake by the version. But still is not working and > I have to wait for another 2 days as you said! > Nooshin > > > source("http://bioconductor.org/biocLite.R") > > biocLite("AnnotationDbi") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.4. > Installing package(s) 'AnnotationDbi' > trying URL > 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotati onDbi_1.18.0.tar.gz' > Content type 'application/x-gzip' length 4609048 bytes (4.4 Mb) > opened URL > ================================================== > downloaded 4.4 Mb > > * installing *source* package ?AnnotationDbi? ... > ** R > ** inst > ** preparing package for lazy loading > Creating a generic function for ?toString? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?rev? from package ?base? in package > ?AnnotationDbi? > Creating a generic function for ?subset? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?as.data.frame? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?head? from package ?utils? in package > ?AnnotationDbi? > Creating a generic function for ?tail? from package ?utils? in package > ?AnnotationDbi? > Creating a generic function for ?as.list? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?ls? from package ?base? in package > ?AnnotationDbi? > Creating a generic function for ?eapply? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?exists? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?sample? from package ?base? in > package ?AnnotationDbi? > ** help > *** installing help indices > converting help for package ?AnnotationDbi? > finding HTML links ... done > AnnDbBimap-envirAPI html > AnnDbObj-class html > AnnDbPkg-checker html > AnnDbPkg-maker html > AnnotationDb-class html > AnnotationDbi-internals html > Bimap-direction html > Bimap-keys html > Bimap-toTable html > Bimap html > BimapFiltering html > BimapFormatting html > GOFrame html > GOTerms-class html > KEGGFrame html > NCBI_getters html > available.db0pkgs html > createSimpleBimap html > getProbeDataAffy html > getProbeData_1lq html > inpIDMapper html > makeOrgPackage html > makeProbePackage html > make_eg_to_go_map html > print.probetable html > sqlForge-makeCHIPDB html > sqlForge-popDB html > sqlForge-wrapDBPackages html > toSQLStringSet html > unlist2 html > ** building package indices > ** installing vignettes > ?AnnotationDbi.Rnw? > ?IntroToAnnotationPackages.Rnw? > ?NewSchema.Rnw? > ?SQLForge.Rnw? > ?makeProbePackage.Rnw? > ** testing if installed package can be loaded > > * DONE (AnnotationDbi) > > The downloaded source packages are in > ?/tmp/RtmpGs7sqo/downloaded_packages? > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 > LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 > [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C > LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tcltk stats graphics grDevices utils datasets methods base > > other attached packages: > [1] feature_1.2.8 ks_1.8.7 misc3d_0.8-2 rgl_0.92.880 mvtnorm_0.9-9992 > KernSmooth_2.23-7 > [7] limma_3.12.0 fields_6.6.3 spam_0.29-1 igraph_0.5.5-4 > BiocInstaller_1.4.4 > > loaded via a namespace (and not attached): > [1] tools_2.15.0 > > _______________________________________________ > 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
ADD REPLYlink written 7.2 years ago by nooshin290
Hi, No I have again another problem: biocLite("AnnotationDbi") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Installing package(s) 'AnnotationDbi' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotation Dbi_1.18.0.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotation Dbi_1.18.0.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open: HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ?AnnotationDbi? failed Would you please help me? On 05/25/2012 06:36 PM, omranian wrote: > On 05/25/2012 05:29 PM, Martin Morgan wrote: >> On 05/25/2012 06:33 AM, omranian wrote: >>> On 05/25/2012 03:20 PM, Martin Morgan wrote: >>>> On 05/25/2012 06:13 AM, omranian wrote: >>>>> On 05/25/2012 03:09 PM, Martin Morgan wrote: >>>>>> On 05/25/2012 02:35 AM, omranian wrote: >>>>>>> Hello, >>>>>>> >>>>>>> Can anybody help me to solve this error? I can not understand it :( >>>>>>> >>>>>>> library(org.Sc.sgd.db) >>>>>>> frame <- toTable(org.Sc.sgdGO) >>>>>>> goframeData <- data.frame(frame$go_id, frame$Evidence, >>>>>>> frame$systematic_name) >>>>>>> goFrame <- GOFrame(goframeData, organism = "Saccharomyces >>>>>>> cerevisiae") >>>>>>> Loading required package: GO.db >>>>>>> >>>>>>> Error in .testGOFrame(x, organism) : >>>>>>> All of the Evidence codes in your data.frame object must be >>>>>>> legitimate >>>>>>> Evidence Codes. >>>>>> >>>>>> Hi Nooshin -- the AnnotationDbi package is slightly out of date with >>>>>> respect to Evidence codes it selects; this is fixed in AnnotationDbi >>>>>> 1.18.1, which will be available for download via biocLite in a >>>>>> day or >>>>>> so. A work-around is to drop the 13 'IRD' evidence codes, >>>>>> >>>>>> > idx = goframeData$frame.Evidence != "IRD" >>>>>> > table(idx) >>>>>> idx >>>>>> FALSE TRUE >>>>>> 13 73735 >>>>>> > goframeData = goframeData[idx,] >>>>>> >>>>>> Martin >>>>>> >>>>>>> >>>>>>> Thanks a lot. >>>>>>> Nooshin >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> >>>>> Hi Martin, >>>>> Thanks for the reply! >>>>> I removed the package and reinstalled it many times, but doesn't >>>>> help :( >>>>> >>>>> I used biocLite to install and hope it installed the latest version. >>>>> Now, I really don't know what should I do?! >>>> >>>> wait two days and try again; the package had a bug, the bug has been >>>> fixed (a few minutes ago); it takes a couple of days for the package >>>> to be checked and made available to you. When it is ready, using >>>> biocLite will download and install AnnotationDbi version 1.18.1. You >>>> must be using R version 2.15.0. >>>> >>>> Martin >>>> >>>>> >>>>> Best, >>>>> Nooshin >>>> >>>> >>> Thanks a lot. >>> So, you believe if I wait it would work! >>> I have R version 2.15.0 but the version of AnnotationDbi is 1.14.1 even >>> when I uninstall and install it again. >>> So I'll wait for two days and try it again. >>> I hope it works by then. >> >> biocLite should not be installing AnnotationDbi 1.14.1 when using R >> 2.15. If that is really the case, then please report (copy and paste) >> the result of running the following commands in a new R session. >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("AnnotationDbi") >> sessionInfo() >> >> Martin >> >>> >>> Best, >>> Nooshin >> >> > > I think I made a mistake by the version. But still is not working and > I have to wait for another 2 days as you said! > Nooshin > > > source("http://bioconductor.org/biocLite.R") > > biocLite("AnnotationDbi") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.4. > Installing package(s) 'AnnotationDbi' > trying URL > 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotati onDbi_1.18.0.tar.gz' > Content type 'application/x-gzip' length 4609048 bytes (4.4 Mb) > opened URL > ================================================== > downloaded 4.4 Mb > > * installing *source* package ?AnnotationDbi? ... > ** R > ** inst > ** preparing package for lazy loading > Creating a generic function for ?toString? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?rev? from package ?base? in package > ?AnnotationDbi? > Creating a generic function for ?subset? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?as.data.frame? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?head? from package ?utils? in package > ?AnnotationDbi? > Creating a generic function for ?tail? from package ?utils? in package > ?AnnotationDbi? > Creating a generic function for ?as.list? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?ls? from package ?base? in package > ?AnnotationDbi? > Creating a generic function for ?eapply? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?exists? from package ?base? in > package ?AnnotationDbi? > Creating a generic function for ?sample? from package ?base? in > package ?AnnotationDbi? > ** help > *** installing help indices > converting help for package ?AnnotationDbi? > finding HTML links ... done > AnnDbBimap-envirAPI html > AnnDbObj-class html > AnnDbPkg-checker html > AnnDbPkg-maker html > AnnotationDb-class html > AnnotationDbi-internals html > Bimap-direction html > Bimap-keys html > Bimap-toTable html > Bimap html > BimapFiltering html > BimapFormatting html > GOFrame html > GOTerms-class html > KEGGFrame html > NCBI_getters html > available.db0pkgs html > createSimpleBimap html > getProbeDataAffy html > getProbeData_1lq html > inpIDMapper html > makeOrgPackage html > makeProbePackage html > make_eg_to_go_map html > print.probetable html > sqlForge-makeCHIPDB html > sqlForge-popDB html > sqlForge-wrapDBPackages html > toSQLStringSet html > unlist2 html > ** building package indices > ** installing vignettes > ?AnnotationDbi.Rnw? > ?IntroToAnnotationPackages.Rnw? > ?NewSchema.Rnw? > ?SQLForge.Rnw? > ?makeProbePackage.Rnw? > ** testing if installed package can be loaded > > * DONE (AnnotationDbi) > > The downloaded source packages are in > ?/tmp/RtmpGs7sqo/downloaded_packages? > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 > LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 > [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C > LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tcltk stats graphics grDevices utils datasets methods base > > other attached packages: > [1] feature_1.2.8 ks_1.8.7 misc3d_0.8-2 rgl_0.92.880 mvtnorm_0.9-9992 > KernSmooth_2.23-7 > [7] limma_3.12.0 fields_6.6.3 spam_0.29-1 igraph_0.5.5-4 > BiocInstaller_1.4.4 > > loaded via a namespace (and not attached): > [1] tools_2.15.0 > > _______________________________________________ > 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
ADD REPLYlink written 7.2 years ago by nooshin290
On 05/29/2012 09:21 AM, omranian wrote: > > Hi, > > No I have again another problem: > > biocLite("AnnotationDbi") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.4. > Installing package(s) 'AnnotationDbi' > trying URL > 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotati onDbi_1.18.0.tar.gz' > > Error in download.file(url, destfile, method, mode = "wb", ...) : > cannot open URL > 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotati onDbi_1.18.0.tar.gz' > > In addition: Warning message: > In download.file(url, destfile, method, mode = "wb", ...) : > cannot open: HTTP status was '404 Not Found' > Warning in download.packages(pkgs, destdir = tmpd, available = available, : > download of package ?AnnotationDbi? failed try in a new R session; it looks like the list of available packages is old. Martin ] > > > Would you please help me? > > > > > > > > On 05/25/2012 06:36 PM, omranian wrote: >> On 05/25/2012 05:29 PM, Martin Morgan wrote: >>> On 05/25/2012 06:33 AM, omranian wrote: >>>> On 05/25/2012 03:20 PM, Martin Morgan wrote: >>>>> On 05/25/2012 06:13 AM, omranian wrote: >>>>>> On 05/25/2012 03:09 PM, Martin Morgan wrote: >>>>>>> On 05/25/2012 02:35 AM, omranian wrote: >>>>>>>> Hello, >>>>>>>> >>>>>>>> Can anybody help me to solve this error? I can not understand it :( >>>>>>>> >>>>>>>> library(org.Sc.sgd.db) >>>>>>>> frame <- toTable(org.Sc.sgdGO) >>>>>>>> goframeData <- data.frame(frame$go_id, frame$Evidence, >>>>>>>> frame$systematic_name) >>>>>>>> goFrame <- GOFrame(goframeData, organism = "Saccharomyces >>>>>>>> cerevisiae") >>>>>>>> Loading required package: GO.db >>>>>>>> >>>>>>>> Error in .testGOFrame(x, organism) : >>>>>>>> All of the Evidence codes in your data.frame object must be >>>>>>>> legitimate >>>>>>>> Evidence Codes. >>>>>>> >>>>>>> Hi Nooshin -- the AnnotationDbi package is slightly out of date with >>>>>>> respect to Evidence codes it selects; this is fixed in AnnotationDbi >>>>>>> 1.18.1, which will be available for download via biocLite in a >>>>>>> day or >>>>>>> so. A work-around is to drop the 13 'IRD' evidence codes, >>>>>>> >>>>>>> > idx = goframeData$frame.Evidence != "IRD" >>>>>>> > table(idx) >>>>>>> idx >>>>>>> FALSE TRUE >>>>>>> 13 73735 >>>>>>> > goframeData = goframeData[idx,] >>>>>>> >>>>>>> Martin >>>>>>> >>>>>>>> >>>>>>>> Thanks a lot. >>>>>>>> Nooshin >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> >>>>>>> >>>>>> Hi Martin, >>>>>> Thanks for the reply! >>>>>> I removed the package and reinstalled it many times, but doesn't >>>>>> help :( >>>>>> >>>>>> I used biocLite to install and hope it installed the latest version. >>>>>> Now, I really don't know what should I do?! >>>>> >>>>> wait two days and try again; the package had a bug, the bug has been >>>>> fixed (a few minutes ago); it takes a couple of days for the package >>>>> to be checked and made available to you. When it is ready, using >>>>> biocLite will download and install AnnotationDbi version 1.18.1. You >>>>> must be using R version 2.15.0. >>>>> >>>>> Martin >>>>> >>>>>> >>>>>> Best, >>>>>> Nooshin >>>>> >>>>> >>>> Thanks a lot. >>>> So, you believe if I wait it would work! >>>> I have R version 2.15.0 but the version of AnnotationDbi is 1.14.1 even >>>> when I uninstall and install it again. >>>> So I'll wait for two days and try it again. >>>> I hope it works by then. >>> >>> biocLite should not be installing AnnotationDbi 1.14.1 when using R >>> 2.15. If that is really the case, then please report (copy and paste) >>> the result of running the following commands in a new R session. >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("AnnotationDbi") >>> sessionInfo() >>> >>> Martin >>> >>>> >>>> Best, >>>> Nooshin >>> >>> >> >> I think I made a mistake by the version. But still is not working and >> I have to wait for another 2 days as you said! >> Nooshin >> >> > source("http://bioconductor.org/biocLite.R") >> > biocLite("AnnotationDbi") >> BioC_mirror: http://bioconductor.org >> Using R version 2.15, BiocInstaller version 1.4.4. >> Installing package(s) 'AnnotationDbi' >> trying URL >> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Annotat ionDbi_1.18.0.tar.gz' >> >> Content type 'application/x-gzip' length 4609048 bytes (4.4 Mb) >> opened URL >> ================================================== >> downloaded 4.4 Mb >> >> * installing *source* package ?AnnotationDbi? ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Creating a generic function for ?toString? from package ?base? in >> package ?AnnotationDbi? >> Creating a generic function for ?rev? from package ?base? in package >> ?AnnotationDbi? >> Creating a generic function for ?subset? from package ?base? in >> package ?AnnotationDbi? >> Creating a generic function for ?as.data.frame? from package ?base? in >> package ?AnnotationDbi? >> Creating a generic function for ?head? from package ?utils? in package >> ?AnnotationDbi? >> Creating a generic function for ?tail? from package ?utils? in package >> ?AnnotationDbi? >> Creating a generic function for ?as.list? from package ?base? in >> package ?AnnotationDbi? >> Creating a generic function for ?ls? from package ?base? in package >> ?AnnotationDbi? >> Creating a generic function for ?eapply? from package ?base? in >> package ?AnnotationDbi? >> Creating a generic function for ?exists? from package ?base? in >> package ?AnnotationDbi? >> Creating a generic function for ?sample? from package ?base? in >> package ?AnnotationDbi? >> ** help >> *** installing help indices >> converting help for package ?AnnotationDbi? >> finding HTML links ... done >> AnnDbBimap-envirAPI html >> AnnDbObj-class html >> AnnDbPkg-checker html >> AnnDbPkg-maker html >> AnnotationDb-class html >> AnnotationDbi-internals html >> Bimap-direction html >> Bimap-keys html >> Bimap-toTable html >> Bimap html >> BimapFiltering html >> BimapFormatting html >> GOFrame html >> GOTerms-class html >> KEGGFrame html >> NCBI_getters html >> available.db0pkgs html >> createSimpleBimap html >> getProbeDataAffy html >> getProbeData_1lq html >> inpIDMapper html >> makeOrgPackage html >> makeProbePackage html >> make_eg_to_go_map html >> print.probetable html >> sqlForge-makeCHIPDB html >> sqlForge-popDB html >> sqlForge-wrapDBPackages html >> toSQLStringSet html >> unlist2 html >> ** building package indices >> ** installing vignettes >> ?AnnotationDbi.Rnw? >> ?IntroToAnnotationPackages.Rnw? >> ?NewSchema.Rnw? >> ?SQLForge.Rnw? >> ?makeProbePackage.Rnw? >> ** testing if installed package can be loaded >> >> * DONE (AnnotationDbi) >> >> The downloaded source packages are in >> ?/tmp/RtmpGs7sqo/downloaded_packages? >> > sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 >> LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 >> [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] tcltk stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] feature_1.2.8 ks_1.8.7 misc3d_0.8-2 rgl_0.92.880 mvtnorm_0.9-9992 >> KernSmooth_2.23-7 >> [7] limma_3.12.0 fields_6.6.3 spam_0.29-1 igraph_0.5.5-4 >> BiocInstaller_1.4.4 >> >> loaded via a namespace (and not attached): >> [1] tools_2.15.0 >> >> _______________________________________________ >> 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 > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 7.2 years ago by Martin Morgan ♦♦ 23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 206 users visited in the last hour