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_1.1 8.2.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 [[alternative HTML version deleted]]

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 ge?ffnet > ================================================== > 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 ge?ffnet > ================================================== > 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 ge?ffnet > ================================================== > 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 ge?ffnet > ================================================== > downloaded 850 Kb > > versuche URL ' > http://bioconductor.org/packages/2.11/bioc/src/contrib/GenomicFeatur es_1.10.2.tar.gz > ' > Content type 'application/x-gzip' length 742787 bytes (725 Kb) > URL ge?ffnet > ================================================== > downloaded 725 Kb > > versuche URL ' > http://bioconductor.org/packages/2.11/data/annotation/src/contrib/Tx Db.Hsapiens.UCSC.hg19.knownGene_2.8.0.tar.gz > ' > Content type 'application/x-gzip' length 17187854 bytes (16.4 Mb) > URL ge?ffnet > ================================================== > downloaded 16.4 Mb > > * installing *source* package ?XML? ... > ** Paket ?XML? erfolgreich entpackt und MD5 Summen ?berpr?ft > 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 ?berpr?ft > 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]] > > > _______________________________________________ > 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