On 01/16/2012 01:26 PM, Weiner, Michael wrote: > From: Martin Morgan [mailto:mtmorgan at fhcrc.org] >> Hi Michael >> >> Some of your packages are out of date, and some additional > dependencies >> need to be installed. You should >> >> source("http://bioconductor.org/biocLite.R") >> biocLite(character()) ## to update old packages >> biocLite('ggbio") ## to install new pkg and dependencies >> >> It looks like perhaps other packages have not been installed > correctly; >> I'd guess at biocLite('GenomicFeatures') as another step to iterate if > >> ggbio continues to fail to install. >> >> Martin > > Nope, unfortunately the biocLite(character()) downloads a bunch of packages and installs some, but then fails with a bunch as in the following: > > There were 50 or more warnings (use warnings() to see the first 50) >> warnings() > Warning messages: > 1: In install.packages(update[instlib == l, "Package"], l, ... : > installation of package ?abc? had non-zero exit status > 2: In install.packages(update[instlib == l, "Package"], l, ... : > installation of package ?adabag? had non-zero exit status > 3: In install.packages(update[instlib == l, "Package"], l, ... : > installation of package ?adehabitatLT? had non-zero exit status > 4: In install.packages(update[instlib == l, "Package"], l, ... : > installation of package ?alphahull? had non-zero exit status > > and loads of others :( Any other suggestions perhaps? Each of these packages would have failed more explicitly earlier in the installation process; you could biocLite('abc') to see what the details are, and repeat... The errors could be any number of things. These look like they are alphabetical, and that there are a lot of them. I guess you have something like 'all of CRAN' installed, which means that you've tasked yourself with managing a very large number of packages and their system dependencies. Yikes. In some ways I feel like you've got yourself in a mess, e.g., incompatible versions of many packages, perhaps installed for unintended versions of R. The way forward might be to figure out, e.g., on a clean system, how you should have proceeded, and then work back to cleaning up your full system. A basic starting point is to make sure that packages are installed in R version-specific directories. If you wanted to back-track to the initial problem, then ** preparing package for lazy loading Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : package ?bitops? does not have a NAMESPACE and should be re- installed here you could biocLite('bitops') which will re-install bitops, presumably with a NAMESPACE. ERROR: lazy loading failed for package ?rtracklayer? * removing ?/usr/lib64/R/library/rtracklayer? and here biocLite('rtracklayer'). If this fails then track down what the problems are, because without rtracklayer you can't proceed ERROR: dependency ?rtracklayer? is not available for package ?GenomicFeatures? * removing ?/usr/lib64/R/library/GenomicFeatures? ... and so on. For what it's worth, the troubles you are having are NOT normal but reflect some earlier inappropriate installation. Normally, (e.g., on a clean R system) source('http://bioconductor.org/biocLite.R'); biocLite('ggbio') would just work. Martin > > Thanks > Michael Weiner > > =================================== > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News& World Report (2010). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: This message is intended for use\...{{dropped:13}} > > _______________________________________________ > 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

I don't believe I've seen a sessionInfo() result from your system. I just installed ggbio in R 2.14 with the following sessionInfo: > sessionInfo() R version 2.14.0 Patched (2011-11-09 r57622) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices datasets tools utils [8] methods base other attached packages: [1] ggbio_1.0.1 ggplot2_0.8.9 proto_0.3-9.2 [4] reshape_0.8.4 plyr_1.7.1 biovizBase_1.0.0 [7] weaver_1.20.0 codetools_0.2-8 digest_0.5.1 [10] BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.16.2 Biobase_2.14.0 biomaRt_2.10.0 [4] Biostrings_2.22.0 bitops_1.0-4.1 BSgenome_1.22.0 [7] colorspace_1.1-0 DBI_0.2-5 dichromat_1.2-4 [10] GenomicFeatures_1.7.1 GenomicRanges_1.6.2 gridExtra_0.9 [13] IRanges_1.12.1 munsell_0.3 RColorBrewer_1.0-5 [16] RCurl_1.7-0 Rsamtools_1.7.1 RSQLite_0.10.0 [19] rtracklayer_1.14.2 scales_0.1.0 stringr_0.6 [22] XML_3.4-3 zlibbioc_1.0.0 I suggest you manually push your system as close to this configuration as you can. As individual packages fail, you need to figure out why. Detailed error messages can be reported back to the list if necessary. On Mon, Jan 16, 2012 at 4:26 PM, Weiner, Michael <weinerm at="" ccf.org=""> wrote: > From: Martin Morgan [mailto:mtmorgan at fhcrc.org] >> Hi Michael >> >> Some of your packages are out of date, and some additional > dependencies >> need to be installed. You should >> >> ? ?source("http://bioconductor.org/biocLite.R") >> ? ?biocLite(character()) ## to update old packages >> ? ?biocLite('ggbio") ? ? ## to install new pkg and dependencies >> >> It looks like perhaps other packages have not been installed > correctly; >> I'd guess at biocLite('GenomicFeatures') as another step to iterate if > >> ggbio continues to fail to install. >> >> Martin > > Nope, unfortunately the biocLite(character()) downloads a bunch of packages and installs some, but then fails with a bunch as in the following: > > There were 50 or more warnings (use warnings() to see the first 50) >> warnings() > Warning messages: > 1: In install.packages(update[instlib == l, "Package"], l, ?... : > ?installation of package ?abc? had non-zero exit status > 2: In install.packages(update[instlib == l, "Package"], l, ?... : > ?installation of package ?adabag? had non-zero exit status > 3: In install.packages(update[instlib == l, "Package"], l, ?... : > ?installation of package ?adehabitatLT? had non-zero exit status > 4: In install.packages(update[instlib == l, "Package"], l, ?... : > ?installation of package ?alphahull? had non-zero exit status > > and loads of others :( Any other suggestions perhaps? > > Thanks > Michael Weiner > > =================================== > > ?Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked one of the top hospitals > in America by U.S.News & World Report (2010). > Visit us online at http://www.clevelandclinic.org for > a complete listing of our services, staff and > locations. > > > Confidentiality Note: ?This message is intended for use\...{{dropped:13}} > > _______________________________________________ > 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