Hello, Indeed I've had a lot of dependencies issues, but I'm solving them one after the other. Thanks for your time!
CR On Thu, May 28, 2015 at 5:33 PM, Martin Morgan <mtmor...@fredhutch.org> wrote: > On 05/28/2015 08:21 AM, Duncan Murdoch wrote: > >> On 28/05/2015 6:10 AM, Claire Rioualen wrote: >> >>> Hello, >>> >>> I can't seem to install R packages, since it seemed there were some >>> permission problems I "chmoded" /usr/share/R/ and /usr/lib/R/. However, >>> there are still errors in the process. Here's my config: >>> >>> > sessionInfo() >>> R version 3.1.1 (2014-07-10) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] ggplot2_1.0.1 BiocInstaller_1.16.5 >>> >>> loaded via a namespace (and not attached): >>> [1] colorspace_1.2-6 digest_0.6.8 grid_3.1.1 gtable_0.1.2 >>> [5] magrittr_1.5 MASS_7.3-40 munsell_0.4.2 plyr_1.8.2 >>> [9] proto_0.3-10 Rcpp_0.11.6 reshape2_1.4.1 scales_0.2.4 >>> [13] stringi_0.4-1 stringr_1.0.0 tcltk_3.1.1 tools_3.1.1 >>> >>> And here are some packages I tried to install: >>> >>> *> install.packages("XML")* >>> Installing package into ���/packages/rsat/R-scripts/Rpackages��� >>> (as ���lib��� is unspecified) >>> trying URL ' >>> http://ftp.igh.cnrs.fr/pub/CRAN/src/contrib/XML_3.98-1.1.tar.gz' >>> Content type 'text/html' length 1582216 bytes (1.5 Mb) >>> opened URL >>> ================================================== >>> downloaded 1.5 Mb >>> >>> * installing *source* package ���XML��� ... >>> ** package ���XML��� successfully unpacked and MD5 sums checked >>> checking for gcc... gcc >>> checking for C compiler default output file name... rm: cannot remove >>> 'a.out.dSYM': Is a directory >>> 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 >>> 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 ���/packages/rsat/R-scripts/Rpackages/XML��� >>> >> > this is a missing system dependency, requiring the libxml2 'dev' headers. > On my linux this is > > sudo apt-get installl libxml2-dev > > likely you'll also end up needing curl via libcurl4-openssl-dev or similar > > >>> The downloaded source packages are in >>> ���/tmp/RtmphODjkn/downloaded_packages��� >>> Warning message: >>> In install.packages("XML") : >>> installation of package ���XML��� had non-zero exit status >>> >>> >>> *> install.packages("Biostrings")* >>> Installing package into ���/packages/rsat/R-scripts/Rpackages��� >>> (as ���lib��� is unspecified) >>> Warning message: >>> package ���Biostrings��� is not available (for R version 3.1.1) >>> >> > >>> *> biocLite("Biostrings")* >>> >> > > Yes,Bioconductor versions packages differently from CRAN (we have > twice-yearly releases and stable 'release' and 'devel' branches). Following > the instructions for package installation at > > http://bioconductor.org/packages/Biostrings > > but... > > > [...] >>> io_utils.c:16:18: fatal error: zlib.h: No such file or directory >>> #include <zlib.h> >>> ^ >>> >> > this seems like a relatively basic header to be missing, installable from > zlib1g-dev, but I wonder if you're taking a mis-step earlier, e.g., trying > to install on a cluster node that is configured for software use but not > installation? > > Also the instructions here to install R > > http://cran.r-project.org/bin/linux/ > > would likely include these basic dependencies 'out of the box'. > > Martin > > compilation terminated. >>> /usr/lib/R/etc/Makeconf:128: recipe for target 'io_utils.o' failed >>> make: *** [io_utils.o] Error 1 >>> ERROR: compilation failed for package ���Biostrings��� >>> * removing ���/packages/rsat/R-scripts/Rpackages/Biostrings��� >>> >>> The downloaded source packages are in >>> ���/tmp/RtmphODjkn/downloaded_packages��� >>> Warning message: >>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>> installation of package ���Biostrings��� had non-zero exit status >>> >>> >>> I've used R on several machines before and never had such problems. >>> Thanks for any clue! >>> >>> It's hard to read your message (I think it was posted in HTML), but I >> think >> those are all valid errors in building those packages. You appear to be >> missing >> some of their dependencies. This is not likely related to permissions. >> >> Duncan Murdoch >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > -- Claire Rioualen -- Lab. Technological Advances for Genomics and Clinics (TAGC) INSERM Unit U1090, Aix-Marseille Université (AMU). 163, Avenue de Luminy, 13288 MARSEILLE cedex 09. France [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.