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@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'

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’
* 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? 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

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