search for: packages2

...ix solves the issue I mentioned but now I have more issues. I can install clang, but when running I cannot compile and link files. If I compile with -c flag it works but compiling the following x.c file gives an error: x.c: int main(void) { return 0; } > ./clang x.c /project/helder/scratch/packages2/bin/ld: unrecognized option '-C' /project/helder/scratch/packages2/bin/ld: use the --help option for usage information clang: error: linker command failed with exit code 1 (use -v to see invocation) > ./clang -v x.c clang version 3.3 (tags/RELEASE_33/final) Target: i386-pc-solaris2.10...

I run configure in a build folder using CC=gcc CXX=g++ ../configure --prefix=/project/scratch/packages2/clang \ --enable-targets=host --enable-shared The configure runs fine but when I type make I get the error: make[1]: Entering directory `/project/scratch/tmp/llvm-3.3/build/lib/Support' llvm[1]: Compiling APFloat.cpp for Release+Asserts build In file included from /project/scratch/tmp/llvm...

Hi there, I am a bioinformatician working in DFCI. I am new to R. Yesterday I installed the R-1.7.1 to my Linux (since I am not able to find R-1.8 on the webpage). But I have some package installation problems ... 1. install.packages2() function isn't available. If I type at R prompt: >install.packages2("Biobase") Error: couldn't find function "install.packages2" ***************************************************** 2. If I try this: >install.packages("Biobase") trying URL `http://cr...

...translated and our user base is international, it is difficult to catch and process by the biocLite() script. Is there a revised wording that could be employed to more accurately convey the reason for the failure, or is this an opportunity to use the condition system? Index: src/library/utils/R/packages2.R =================================================================== --- src/library/utils/R/packages2.R (revision 66562) +++ src/library/utils/R/packages2.R (working copy) @@ -46,12 +46,12 @@ p0 <- unique(pkgs) miss <- !p0 %in% row.names(available) if(sum(miss)) { - warni...

...the help. Applying the fix solves the issue I mentioned but now I > have more issues. > > I can install clang, but when running I cannot compile and link files. > If I compile with -c flag it works but compiling the following x.c file > gives an error: > /project/helder/scratch/packages2/bin/ld: unrecognized option '-C' > /project/helder/scratch/packages2/bin/ld: use the --help option for usage > information > clang: error: linker command failed with exit code 1 (use -v to see > invocation) -C is a flag for the Solaris linker only (/usr/bin/ld). It looks like /...

...'foo' are not availabledependencies 'bar' are not available ^^^^^^^^^^^^^^^^^^^^ With the following change (see below) I get what I suspect is the intended warning message: dependencies 'foo', 'bar' are not available + seth Index: packages2.R =================================================================== --- packages2.R (revision 33678) +++ packages2.R (working copy) @@ -125,7 +125,7 @@ cat(sprintf(ngettext(sum(miss), "dependency %s is not available",...

...issue I mentioned but > now I > > have more issues. > > > > I can install clang, but when running I cannot compile and link files. > > If I compile with -c flag it works but compiling the following x.c file > > gives an error: > > > /project/helder/scratch/packages2/bin/ld: unrecognized option '-C' > > /project/helder/scratch/packages2/bin/ld: use the --help option for usage > > information > > clang: error: linker command failed with exit code 1 (use -v to see > > invocation) > > -C is a flag for the Solaris linker only (...

...fer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Hi, I get exactly the same error message as in report no 6920. Furthermore, starting "update Bioconducter" the following message appears (running Mac OS X 10.3.4 (7H63)) : > {library(reposTools);update.packages2(getAllDeps=TRUE)} Synching your local package management information ... Packages which have been added/updated: sm sma wavethresh Note: reposTools can not access /Library/Frameworks/R.framework/Resources/library. This will not affect your R session unless you wish to install/update/rem...

...re may be another reason). This has been spotted in the wild [*]. When %USERPROFILE% contains spaces, this results in tempdir() also containing spaces and prevents the user from being able to install source packages. As of <https://svn.r-project.org/R/trunk at 77563>, - src/library/utils/R/packages2.R line 839 contains an unquoted temporary file path (fil) passed to system2(), which results in it being split and R CMD INSTALL not being able to find the package file. In other invocations of R CMD INSTALL in the same file, the path is properly quoted. - src/library/tools/R/check.R...

...hVers = installWithVers, type) + installWithVers = installWithVers, type = type) } } For the second, problem, I don't know what to do. grepping R-patched_2005-05-03.tar.gz source found only one instance of .install.macbinary(): the failed call in R-patched/src/library/utils/R/packages2.R. I couldn't find the definition of the function. Do I really have to use GUI? Uh. cheers, jari oksanen

I have copied the R FAQ pertaining to available packages into an EXCEL file. They take the following form - Design Regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. Design is a etc. Devore5 Data sets and sample analyses from "Probability and Statistics for Engineering and the Sciences (5th

...once subscribed to this list, but then my subscription was not accepted. Now to the business: The final failure came from missing .install.macbinary() function. I grepped R-patched sourcesand the only instance of .install.macbinary() was the call to the function in R- patched/src/library/utils/R/packages2.R (stupid automatic linefeed in mail composer: just parse it). There was no definition of the function, so I don't know from where should that function be loaded. I looked at the R-patched/src/library/utils/R/aqua/GUI.R today (it was the only file in that directory), and it had a function inst...

...type = type) > > } > > } > > > > > > For the second, problem, I don't know what to do. grepping > > R-patched_2005-05-03.tar.gz source found only one instance of > > .install.macbinary(): the failed call in > > R-patched/src/library/utils/R/packages2.R. I couldn't find the definition of the > > function. > > > > Do I really have to use GUI? Uh. > > > > cheers, jari oksanen > > > > ______________________________________________ > > R-devel@stat.math.ethz.ch mailing list > > https://stat.e...

...RUE fails, while it works with the default quiet = FALSE. The problem seems to be caused by the fact that when quiet = TRUE, stdout and stderr are set to FALSE when calling "R CMD INSTALL" with base::system2() here: https://github.com/wch/r-source/blob/tags/R-3-4-3/src/library/utils/R/packages2.R#L660-L661. > trace(base::system2, quote(print(ls.str()))) Tracing function "system2" in package "base" [1] "system2" > utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, lib = tempdir(), quiet = TRUE) Tracing system2(cmd0, args, env...

...charset=US-ASCII; > format=flowed > > Hi, > > I get exactly the same error message as in report no 6920. Furthermore, > starting "update Bioconducter" the following message appears (running > Mac OS X 10.3.4 (7H63)) : > > > {library(reposTools);update.packages2(getAllDeps=TRUE)} > > Synching your local package management information ... > Packages which have been added/updated: > sm > sma > wavethresh > > > > Note: reposTools can not access > /Library/Frameworks/R.framework/Resources/library. > This will not...

...es/R/x86_64-unknown-linux-gnu-library/2.12" [2] "/home/hpages/R-2.12/library" > install.packages("car") Error in sprintf(gettext(fmt, domain = domain), ...) : too few arguments Looks like the problem is in these lines (lines 194-197 in file src/library/utils/R/packages2.R): lib <- .libPaths()[1L] if (length(.libPaths()) > 1L) message(gettextf("Installing package(s) into %s\n(as %s is unspecified)", sQuote(lib)), domain = NA) Cheers, H. > sessionInfo() R version 2.12.0 Under development (unstable) (2010-07-19 r52...

...et=TRUE fails, while it works with the default quiet = FALSE. The problem seems to be caused by the fact that when quiet = TRUE, stdout and stderr are set to FALSE when calling "R CMD INSTALL" with base::system2() here: https://github.com/wch/r-source/blob/tags/R-3-4-3/src/library/utils/R/packages2.R#L660-L661. >>> trace(base::system2, quote(print(ls.str()))) >> Tracing function "system2" in package "base" >> [1] "system2" >>> utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, lib >> = tempdir(), quie...

Hi everyone, My purpose is to read a .CEL file into R. The .CEL file was created from a .CAB by using DTT software found on Affymetrix website I read the .CEL file in R using ReadAffy as follows: > d2=ReadAffy(widget=T) and I complete the fields as required. It does not complain. For example I could find the description: > description(d2) Experimenter name: BB Laboratory: FFL Contact

I've noticed that install.packages() [https://svn.r-project.org/R/trunk/src/library/utils/R/packages.R] and update.packages() [https://svn.r-project.org/R/trunk/src/library/utils/R/packages2.R] sometimes output to stdout and sometimes to stderr. It looks like stderr is used (e.g. via cat()) when the message is part of querying the user, e.g. update.packages <- function(lib.loc = NULL, repos = getOption("repos"), [...] cat(old[k, "Package"], ":\...

...works with the default quiet = FALSE. > The problem seems to be caused by the fact that when quiet = TRUE, > stdout and stderr are set to FALSE when calling "R CMD INSTALL" with > base::system2() here: > https://github.com/wch/r-source/blob/tags/R-3-4-3/src/library/utils/R/packages2.R#L660-L661. > > >> trace(base::system2, quote(print(ls.str()))) > Tracing function "system2" in package "base" > [1] "system2" > > >> utils::install.packages("partDF_1.0.0.9001.tar.gz", repos = NULL, lib > = tempdir(),...