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  • #16
    Same issue

    I am glad I'm not the only one pulling my hair out over this issue. I've tried updating to the latest version of R and CummeRbund in both Windows 7 and Ubuntu 12.04. Reinstalled RSQLite a couple times along with it's dependencies. Am I missing something?

    > library(cummeRbund)
    Loading required package: BiocGenerics
    Loading required package: parallel

    Attaching package: ‘BiocGenerics’

    The following objects are masked from ‘packagearallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
    parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

    The following object is masked from ‘package:stats’:

    xtabs

    The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq,
    Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unlist, unsplit

    Loading required package: RSQLite
    Loading required package: DBI
    Loading required package: ggplot2
    Loading required package: reshape2
    Loading required package: fastcluster

    Attaching package: ‘fastcluster’

    The following object is masked from ‘package:stats’:

    hclust

    Loading required package: rtracklayer
    Loading required package: GenomicRanges
    Loading required package: S4Vectors
    Loading required package: stats4
    Loading required package: IRanges
    Loading required package: GenomeInfoDb
    Loading required package: Gviz
    Loading required package: grid

    Attaching package: ‘cummeRbund’

    The following object is masked from ‘package:GenomicRanges’:

    promoters

    The following object is masked from ‘package:IRanges’:

    promoters

    The following object is masked from ‘package:BiocGenerics’:

    conditions

    > wd <- "/home/brian/diff_out/"
    > setwd(wd)

    > gtfFile <- "mm10_genes.gtf"
    > cuff <- readCufflinks(dir=getwd(), gtfFile=gtfFile, genome="mm10", rebuild=TRUE)
    Creating database /home/brian/diff_out/cuffData.db
    Error in FUN(c("\n-- Creator: MySQL Workbench 5.2.33/ExportSQLite plugin 2009.12.02\n-- Author: Loyal Goff\n-- Caption: New Model\n-- Project: Name of the project\n-- Changed: 2012-04-30 22:21\n-- Created: 2011-05-02 12:52\nPRAGMA foreign_keys = OFF", :
    could not find function "sqliteQuickSQL"

    I get no errors loading CummeRbund, only when I try to create an SQLite database using readCufflinks().

    > sessionInfo()
    R version 3.1.1 (2014-07-10)
    Platform: x86_64-unknown-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
    [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
    [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

    attached base packages:
    [1] grid stats4 parallel stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] cummeRbund_2.8.0 Gviz_1.10.1 rtracklayer_1.26.1 GenomicRanges_1.18.1 GenomeInfoDb_1.2.2
    [6] IRanges_2.0.0 S4Vectors_0.4.0 fastcluster_1.1.13 reshape2_1.4 ggplot2_1.0.0
    [11] RSQLite_1.0.0 DBI_0.3.1 BiocGenerics_0.12.0

    loaded via a namespace (and not attached):
    [1] acepack_1.3-3.3 AnnotationDbi_1.28.1 base64enc_0.1-2 BatchJobs_1.4
    [5] BBmisc_1.7 Biobase_2.26.0 BiocParallel_1.0.0 biomaRt_2.22.0
    [9] Biostrings_2.34.0 biovizBase_1.14.0 bitops_1.0-6 brew_1.0-6
    [13] BSgenome_1.34.0 checkmate_1.5.0 cluster_1.15.3 codetools_0.2-9
    [17] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 fail_1.2
    [21] foreach_1.4.2 foreign_0.8-61 Formula_1.1-2 GenomicAlignments_1.2.0
    [25] GenomicFeatures_1.18.2 gtable_0.1.2 Hmisc_3.14-5 iterators_1.0.7
    [29] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-35 matrixStats_0.10.3
    [33] munsell_0.4.2 nnet_7.3-8 plyr_1.8.1 proto_0.3-10
    [37] RColorBrewer_1.0-5 Rcpp_0.11.3 RCurl_1.95-4.3 R.methodsS3_1.6.1
    [41] rpart_4.1-8 Rsamtools_1.18.1 scales_0.2.4 sendmailR_1.2-1
    [45] splines_3.1.1 stringr_0.6.2 survival_2.37-7 tools_3.1.1
    [49] VariantAnnotation_1.12.2 XML_3.98-1.1 XVector_0.6.0 zlibbioc_1.12.0

    Comment


    • #17
      Hey guys,

      I have test it in Ubuntu (14.04LTS), Mac, Windows, none of them worked. My R is 3.1.1

      For ubuntu OS:

      Of course I have installed libxml2-dev and libcurl4-openssl-dev. And I can launched cummeRbund but can not let it works in cuff <-readCufflinks("diff_out") which just gave 0 bytes cuffData.db.

      I have tried to install all the dependent packages (including changing the order of the installing for these packages), BiocGenerics, DBI, RSQLite, digest, ggplot2, reshape2, fastcluster, rtracklayer, GenomicFeatures, Gviz.

      It seems I was stuck by GenomicFeatures when I wanted to reinstall cummeRbund:

      Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
      ERROR: lazy loading failed for package ‘GenomicFeatures’
      * removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
      ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
      * removing ‘/usr/local/lib/R/site-library/biovizBase’
      ERROR: dependencies ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’
      * removing ‘/usr/local/lib/R/site-library/Gviz’
      ERROR: dependency ‘Gviz’ is not available for package ‘cummeRbund’
      * removing ‘/usr/local/lib/R/site-library/cummeRbund’

      And I can't install GenomicFeatures due to the same problem "Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'"

      So, I guess, for me, the problem is sqliteQuickSQL.

      How do you think?

      Thanks!

      Comment


      • #18
        Hi, have you found the solution? I also meet the same problem.

        Originally posted by spzhangmit View Post
        Hey guys,

        I have test it in Ubuntu (14.04LTS), Mac, Windows, none of them worked. My R is 3.1.1

        For ubuntu OS:

        Of course I have installed libxml2-dev and libcurl4-openssl-dev. And I can launched cummeRbund but can not let it works in cuff <-readCufflinks("diff_out") which just gave 0 bytes cuffData.db.

        I have tried to install all the dependent packages (including changing the order of the installing for these packages), BiocGenerics, DBI, RSQLite, digest, ggplot2, reshape2, fastcluster, rtracklayer, GenomicFeatures, Gviz.

        It seems I was stuck by GenomicFeatures when I wanted to reinstall cummeRbund:

        Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
        ERROR: lazy loading failed for package ‘GenomicFeatures’
        * removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
        ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
        * removing ‘/usr/local/lib/R/site-library/biovizBase’
        ERROR: dependencies ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’
        * removing ‘/usr/local/lib/R/site-library/Gviz’
        ERROR: dependency ‘Gviz’ is not available for package ‘cummeRbund’
        * removing ‘/usr/local/lib/R/site-library/cummeRbund’

        And I can't install GenomicFeatures due to the same problem "Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'"

        So, I guess, for me, the problem is sqliteQuickSQL.

        How do you think?

        Thanks!

        Comment


        • #19
          I think I may have solved problem. And you can try my steps。
          First, upgrade biocLite:
          >source("http://www.bioconductor.org/biocLite.R")
          >biocLite("BiocUpgrade")

          Then, install "cummeRbund"
          >biocLite("cummeRbund")

          Last, install or reinstall "RSQLite"
          >biocLite("RSQLite")

          I hope it works for you.

          Comment


          • #20
            I have finally completely uninstalled and re-installed RSQLite as suggested, and it solved the problem!
            Although it was loaded in the session previously and it is the same version of the package, now reading in data with "readCufflinks" works...

            When I first tried to re-install it, I faced that error message:
            "
            ERROR: failed to lock directory ‘/nfs/users/test/R/x86_64-redhat-linux-gnu-library/3.1’ for modifying
            Try removing ‘/nfs/users/test/R/x86_64-redhat-linux-gnu-library/3.1/00LOCK-RSQLite’

            The downloaded source packages are in
            ‘/tmp/Rtmp7rm8UF/downloaded_packages’
            Warning message:
            In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
            installation of package ‘RSQLite’ had non-zero exit status
            "

            which is simply solved by removing the "locked" folder, in case you face the same issue:
            rm -r /nfs/users/test/R/x86_64-redhat-linux-gnu-library/3.1/00LOCK-RSQLite/

            I opened a fresh R session and simply re-installed RSQLite using biocLite:
            source("http://www.bioconductor.org/biocLite.R")
            biocLite("RSQLite")

            Still don't really understand the issue, but well, it works :-)

            Comment


            • #21
              Originally posted by RomaChicken View Post
              I think I may have solved problem. And you can try my steps。
              First, upgrade biocLite:
              >source("http://www.bioconductor.org/biocLite.R")
              >biocLite("BiocUpgrade")

              Then, install "cummeRbund"
              >biocLite("cummeRbund")

              Last, install or reinstall "RSQLite"
              >biocLite("RSQLite")

              I hope it works for you.
              I tried your solution of uninstalling both and reinstalling, but it didn't work for me. The only thing that I noticed was odd was trying to upgrade bioconductor...

              R version 3.1.1 (2014-07-10) -- "Sock it to Me"
              Copyright (C) 2014 The R Foundation for Statistical Computing
              Platform: x86_64-unknown-linux-gnu (64-bit)

              R is free software and comes with ABSOLUTELY NO WARRANTY.
              You are welcome to redistribute it under certain conditions.
              Type 'license()' or 'licence()' for distribution details.

              Natural language support but running in an English locale

              R is a collaborative project with many contributors.
              Type 'contributors()' for more information and
              'citation()' on how to cite R or R packages in publications.

              Type 'demo()' for some demos, 'help()' for on-line help, or
              'help.start()' for an HTML browser interface to help.
              Type 'q()' to quit R.

              > source("http://www.bioconductor.org/biocLite.R")
              Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
              > biocLite("BiocUpgrade")
              Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0
              > biocLite("cummeRbund")
              BioC_mirror: http://bioconductor.org
              Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1.
              Installing package(s) 'cummeRbund'
              also installing the dependency ‘RSQLite’

              Comment


              • #22
                In fact, I am also stop at the problem below:
                > readCufflinks()
                Creating database ./diff_out/cuffData.db
                Error in FUN(c("\n-- Creator: MySQL Workbench 5.2.33/ExportSQLite plugin 2009.12.02\n-- Author: Loyal Goff\n-- Caption: CuffData.db Model\n-- Project: cummeRbund\n-- Changed: 2011-08-02 14:03\n-- Created: 2011-05-02 12:52\nPRAGMA foreign_keys = OFF", :
                could not find function "sqliteQuickSQL"


                I don't know how I can resolve the "sqliteQuickSQL" function problem.


                Originally posted by BrianU View Post
                I tried your solution of uninstalling both and reinstalling, but it didn't work for me. The only thing that I noticed was odd was trying to upgrade bioconductor...

                Comment


                • #23
                  In fact, I haven't met your problem before. Maybe you can check with the weblink here:http://www.bioconductor.org/install
                  Originally posted by BrianU View Post
                  I tried your solution of uninstalling both and reinstalling, but it didn't work for me. The only thing that I noticed was odd was trying to upgrade bioconductor...

                  Comment


                  • #24
                    Downloading a previous version of the RSQLite package worked for me, as it actually contains the necessary function. I chose the 0.11.4 version from this archive:
                    http://cran.r-project.org/src/contrib/Archive/RSQLite/
                    Last edited by gopher; 10-30-2014, 08:42 AM. Reason: bad link

                    Comment


                    • #25
                      So basically what you're saying is that cummeRbund does not work with the updated RSQLite package.

                      Probably because (whether by mistake or not) RSQLite 1.0.0 does not have the sqliteQuickSQL function anymore.

                      So this solution may work but also only for Linux. Does anyone know where to find archived R packages of Windows binaries?

                      Comment


                      • #26
                        Originally posted by axa9070 View Post
                        So basically what you're saying is that cummeRbund does not work with the updated RSQLite package.

                        Probably because (whether by mistake or not) RSQLite 1.0.0 does not have the sqliteQuickSQL function anymore.

                        So this solution may work but also only for Linux. Does anyone know where to find archived R packages of Windows binaries?
                        Nevermind. This way of finding it was totally janky! (If you look at the packages off of these links you'll know what I mean http://cran.fhcrc.org/bin/windows/contrib/)
                        But the old windows binaries of RSQLite can be found here.

                        I do hope cummeRbund is updated soon -___- I'm growing tired of all this R garbage in Bioinformatics as it is.
                        Last edited by axa9070; 10-30-2014, 09:53 AM. Reason: Doesn't actually work with latest R =-/

                        Comment


                        • #27
                          Originally posted by gopher View Post
                          Downloading a previous version of the RSQLite package worked for me, as it actually contains the necessary function. I chose the 0.11.4 version from this archive:
                          http://cran.r-project.org/src/contrib/Archive/RSQLite/
                          Thanks gopher, this worked for me. Just incase anyone was confused..

                          In Linux, I cd into my R directory
                          > cd /home/<me>/R/.../3.1/
                          removed the RSQLite folder to delete the package.
                          > rm -rf RSQLite/ (there is probably a more elegant way to delete libraries, but it worked.)

                          Downladed the older version of RSQLite from the link gopher posted. Then installed the package through RStudio's Package manager. Reload CummeRbund. Done.

                          Comment


                          • #28
                            Yeah the most recent package must no longer have that function. Hope that helped, and thank y'all for further clarifying the download process.

                            Also Brian, the Bioconductor 3.0 version is the current one, no? It at least appears so on the website. So I think your inability to update just means you have the latest version available, the R output just phrases it like an error.
                            Last edited by gopher; 10-30-2014, 10:40 AM.

                            Comment


                            • #29
                              Yes, you are right.
                              I apologize for my previously misleading posts.

                              I keep forgetting that I need to delete the Cuffdiff database to generate a new one.
                              Otherwise, the function readCufflinks() works, but that is simply because it is not generating a new database. As soon as I deleted the old database, I got the same error message as everyone else.

                              Comment


                              • #30
                                Fix is in the works...

                                Hi Guys,
                                Apologies for not catching this sooner, but it's been brought to my attention that there was a major overhaul of RSQLite with the release of version 1.0.0. This broke a good deal of functionality in cummeRbund. I'm working on brining the code up to spec so that it's compatible with RSQLite 1.0.0 but I'm not sure when this will be available. In the meantime, if you need to use cummeRbund, you should be able to downgrate to an earlier version of RSQLite (<1.0.0) and preserve compatibility. I'll try to remember to post here, and on the cummeRbund website, when the fix is pushed to BioC. Thanks to a few of you guys for contacting me directly to let me know about this issue.

                                Cheers,
                                Loyal

                                Comment

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