[BioC] biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") fails

[Dan Tenenbaum]

On Wed, Mar 13, 2013 at 1:46 PM, Wim Kreinen <wkreinen at gmail.com> wrote:
> Hello,
>
> I am not able to install TxDb.Hsapiens... and other packages and I don't
> understand why.
>
> With
> biocLite()
>
> for instance I installed
>
> wkreinen at nord:~/R/x86_64-pc-linux-gnu-library/2.15$ ls
> ALL            bitops      evaluate         hexbin     labeling
> munsell       reshape2   SparseM
> AnnotationDbi  BSgenome    genomeIntervals  HiTC       latticeExtra
> mvtnorm       Rsamtools  stringr
> Biobase        colorspace  GenomicRanges    Hmisc      mapproj
> plyr          RSQLite    testthat
> BiocGenerics   DBI         ggplot2          hwriter    maps
> proto         scales     zlibbioc
> BiocInstaller  dichromat   girafe           intervals  maptools
> quantreg      ShortRead
> Biostrings     digest      gtable           IRanges    multcomp
> RColorBrewer  sp
>
> ...but got the error message
>
> Warnmeldung:
> installed directory not writable, cannot update packages 'KernSmooth',
>   'spatial', 'survival'
>

This is not actually a failure, just a warning, saying that these
built-in packages could not be updated because the directory they are
in (not the same directory you are listing above) is not writable by
you. That's OK, it means that R was installed at the system level by a
system administrator.


> Further I was - as already mentioned - not able to install TxDb...
>
>
>
>> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'TxDb.Hsapiens.UCSC.hg19.knownGene'
> also installing the dependencies ‘XML’, ‘rtracklayer’, ‘biomaRt’, ‘RCurl’,
> ‘GenomicFeatures’
>
> versuche URL '
> http://mirrors.softliste.de/cran/src/contrib/XML_3.95-0.2.tar.gz'
> Content type 'application/x-gzip' length 1688802 bytes (1.6 Mb)
> URL geöffnet
> ==================================================
> downloaded 1.6 Mb
>
> versuche URL '
> http://bioconductor.org/packages/2.11/bioc/src/contrib/rtracklayer_1.18.2.tar.gz
> '
> Content type 'application/x-gzip' length 1308890 bytes (1.2 Mb)
> URL geöffnet
> ==================================================
> downloaded 1.2 Mb
>
> versuche URL '
> http://bioconductor.org/packages/2.11/bioc/src/contrib/biomaRt_2.14.0.tar.gz
> '
> Content type 'application/x-gzip' length 276758 bytes (270 Kb)
> URL geöffnet
> ==================================================
> downloaded 270 Kb
>
> versuche URL '
> http://mirrors.softliste.de/cran/src/contrib/RCurl_1.95-4.1.tar.gz'
> Content type 'application/x-gzip' length 870915 bytes (850 Kb)
> URL geöffnet
> ==================================================
> downloaded 850 Kb
>
> versuche URL '
> http://bioconductor.org/packages/2.11/bioc/src/contrib/GenomicFeatures_1.10.2.tar.gz
> '
> Content type 'application/x-gzip' length 742787 bytes (725 Kb)
> URL geöffnet
> ==================================================
> downloaded 725 Kb
>
> versuche URL '
> http://bioconductor.org/packages/2.11/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0.tar.gz
> '
> Content type 'application/x-gzip' length 17187854 bytes (16.4 Mb)
> URL geöffnet
> ==================================================
> downloaded 16.4 Mb
>
> * installing *source* package ‘XML’ ...
> ** Paket ‘XML’ erfolgreich entpackt und MD5 Summen überprüft
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> No ability to remove finalizers on externalptr objects in this verison of R
> checking for sed... /bin/sed
> checking for pkg-config... /usr/bin/pkg-config
> checking for xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package ‘XML’
> * removing ‘/home/wkreinen/R/x86_64-pc-linux-gnu-library/2.15/XML’
> * installing *source* package ‘RCurl’ ...
> ** Paket ‘RCurl’ erfolgreich entpackt und MD5 Summen überprüft
> checking for curl-config... no
> Cannot find curl-config
> ERROR: configuration failed for package ‘RCurl’


This means you need libcurl on your system. I'm not sure which linux
distribution you are running but on Ubuntu the command to install this
is:

sudo apt-get insgtall libxml2-dev libcurl-dev


> * removing ‘/home/wkreinen/R/x86_64-pc-linux-gnu-library/2.15/RCurl’
> ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package
> ‘rtracklayer’
> * removing ‘/home/wkreinen/R/x86_64-pc-linux-gnu-library/2.15/rtracklayer’
> ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’
> * removing ‘/home/wkreinen/R/x86_64-pc-linux-gnu-library/2.15/biomaRt’
> ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for
> package ‘GenomicFeatures’
> * removing
> ‘/home/wkreinen/R/x86_64-pc-linux-gnu-library/2.15/GenomicFeatures’
> ERROR: dependency ‘GenomicFeatures’ is not available for package
> ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
>> biocLite ("BiocUpgrade")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Warnmeldungen:
> 1: Bioconductor version 2.11 is the latest available for R version 2.15
> 2: installed directory not writable, cannot update packages 'KernSmooth',
>   'spatial', 'survival'
>> * removing
> ‘/home/wkreinen/R/x86_64-pc-linux-gnu-library/2.15/TxDb.Hsapiens.UCSC.hg19.knownGene’
>
>> sessionInfo ()
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
>  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
> [1] tcltk_2.15.3 tools_2.15.3
>
>
> Please give me a hint.
> "installed directory not writeable" - which directory is addressed?



You can find out with this R command:
system.file(package="KernSmooth")

Again, this is just a warning that some packages could no tbe updated.

Dan



>  I
> thought that /R/x86_64-pc-linux-gnu-library/2.15$ is target directory and
> this is writeable. So please instruct me to choose the correct path. Thanks.
>
> Wim
>
>         [[alternative HTML version deleted]]
>
>
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