Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • DESeq: problem updating to new version

    Hi All,

    I attempted to upgrade DESeq to the new version and received an error that I was missing library 'xtable'.

    I checked cran and the link to xtable is dead.
    This is on a Mac 10.6.8
    Suggestions?




    installing *source* package ‘DESeq’ ...
    ** libs
    *** arch - i386
    gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c pval.c -o pval.o
    gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DESeq.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/DESeq/libs/i386
    *** arch - x86_64
    gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -c pval.c -o pval.o
    gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DESeq.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/DESeq/libs/x86_64
    ** R
    ** inst
    ** preparing package for lazy loading
    locfit 1.5-6 2010-01-20
    Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
    there is no package called ‘xtable’
    ERROR: lazy loading failed for package ‘DESeq’
    * removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/DESeq’
    * restoring previous ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/DESeq’

    The downloaded packages are in
    ‘/private/var/folders/eM/eMuaz8lA2RayeU+BYvAbo++++TI/-Tmp-/RtmpsnWPGf/downloaded_packages’
    > library("DESeq")
    Loading required package: Biobase

    Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")' and for packages 'citation("pkgname")'.

    Loading required package: locfit
    Loading required package: akima
    Loading required package: lattice
    locfit 1.5-6 2010-01-20
    Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
    there is no package called ‘xtable’
    In addition: Warning message:
    In install.packages(c("DESeq"), lib = "/Library/Frameworks/R.framework/Resources/library/", :
    installation of package ‘DESeq’ had non-zero exit status
    Error: package/namespace load failed for ‘DESeq’
    > sessionInfo()
    R version 2.14.0 (2011-10-31)
    Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

    locale:
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

    other attached packages:
    [1] locfit_1.5-6 lattice_0.20-0 akima_0.5-4 Biobase_2.14.0

    loaded via a namespace (and not attached):
    [1] grid_2.14.0 tools_2.14.0

  • #2
    First: Well, have you tried installing the xtable package?

    Second: If you use the proper Bioconductor install script, as described here, such dependencies will be resolved automatically for you.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-27-2024, 06:37 PM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Working...
    X