search for: file_test

Duncan Murdoch writes: > On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote: > > I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. > > I don't know what is causing this bug. Perhaps a Linux user can > reproduce it and fix it. > > Here's what I see: > > file_test("-x") calls file.access(filename, 1L). T...

...r-project.org Subject: Re: [R] Missing dependencies in pkg installs Duncan Murdoch writes: > On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote: > > I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. > > I don't know what is causing this bug. Perhaps a Linux user can > reproduce it and fix it. > > Here's what I see: > > file_test("-x") calls file.access(filename, 1L). That...

On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote: > I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. I don't know what is causing this bug. Perhaps a Linux user can reproduce it and fix it. Here's what I see: file_test("-x") calls file.access(filename, 1L). That in turn calls the C library function...

I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. [1] "/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi" Browse[2]> dir(new) [1] "DESCRIPTION" "INSTALL" "LICENSE" "MD5" [5] "NAMESPACE" "NE...

...le -- see the 'R Installation and Administration Manual' *** I build my packages/tar balls on Windows. Is there are way to build it such that aroma.affymetrix/configure is executable? *** Looking at the code (http://svn.r-project.org/R/trunk/src/library/tools/R/install.R), there is if (file_test("-x", "configure")) { cmd <- paste(paste(configure_vars, collapse = " "), "./configure", paste(configure_args, collapse = " ")) if (debug) message("configure command: ", sQuote(cmd), domain = NA) res <- system(cmd) if (res) p...

*Summary: * During package loading the library function calls file.info to determine if a file is a directory. This uselessly invokes getpwuid and getgrgid which can be expensive if the user/group database are held on a network. Note that file_test ALSO uses file.info for the same purpose Suggest rebuilding file_test to use ‘stat’ based call for directory search, and using file_test in function library. Note that functions like R_unlink uses stat calls to determine if something is a directory. -Alex Brown *Detail:* While developing an ap...

Hi, I have just updated R from version 2.8.1 to version 2.9.1. I am running Windows XP Professional, Service Pack 3. With the update, I decided to update a set of packages that I maintain by compiling them for the new version. Everything worked fine except for one package. This package is unique (among the six I was working on) in that is stored on a UNIX-based file server that is

...not with writeBin, the writeBin command write from the beginning of the file and not from the current position and however in the doculentation it is written: ? If the connection is open it is read/written from its current position. Thank you Best regards Laurent Here is the tiny example: The file_test.txt before: 1234567890 1234567890 The file_test.txt after: ?AA AA7890 1234567890 The file should have been like that: 123456 AA AA1234567890 ## open the file in read/write mode + binary fname <- file.path(".","txt","file_test.txt") con_in <- file(fname,"...

...417 4545 | M +1 612 567 8287 -----Original Message----- From: Conklin, Mike (GfK) Sent: Friday, June 23, 2017 4:38 PM To: Don Cohen; Duncan Murdoch Cc: Martin Maechler; r-help at r-project.org Subject: Re: [R] Missing dependencies in pkg installs Checked all the permissions, and it appears that file_test returns a FALSE and system(ls -l) shows it is executable, so the problem seems to be in R and it's relationship to RHEL. I tried installing R3.3.3 to see if the older version would install stringi and had the same problem so it doesn't appear to be R3.4 related. I am now reaching out to s...

...all debug(do_install) after it has been created (typically just before it is called is a safe place to do this), and do the usual process. It's still very mysterious to me why configure is losing its executable bit. What I would do if I could reproduce this would be to run right up to the file_test("-x","configure") line, then print my working directory, and ctrl-Z out of R to look at the files there. That should confirm that configure is not executable. Then the hard part is figuring out why it isn't.... Duncan > > So, made a tempfunc that was a copy of to...

...fo <- post[common, file.info] changes <- preinfo != postinfo } else changes <- matrix(logical(0), nrow = length(common), ncol = 0, dimnames = list(common, character(0))) if (length(timestamp)) changes <- cbind(changes, Newer = file_test("-nt", common, timestamp)) if (md5sum) { premd5 <- pre[common, "md5sum"] postmd5 <- post[common, "md5sum"] changes <- cbind(changes, md5sum = premd5 != postmd5) } changes1 <- changes[rowSums(changes, na.rm = TRUE) >...

Not much progress..... I step through debug and it gets to the do.install() function which immediately errors with the same "configuration not executable" error. So, made a tempfunc that was a copy of tools:::.install_packages and edited the file_test("-x","configure") line to return a TRUE now I get a Permission Denied error (even if I run as root) > tempfunc("/home/meconk/stringi_1.1.5.tar.gz") * installing to library '/usr/lib64/R/library' * installing *source* package 'stringi' ... ** packag...

Good afternoon, As a clarification does it make sense to remove the second 'not' in the 'See Also' documentation for file_test ? Kind regards, Sean O'Riordain ----- Index: src/library/utils/man/filetest.Rd =================================================================== --- src/library/utils/man/filetest.Rd (revision 55639) +++ src/library/utils/man/filetest.Rd (working copy) @@ -35,7 +35,7 @@ } \seealso{...

...n package) { - paths <- character() - for(lib in lib.loc) { - dirs <- list.files(lib, - pattern = paste0("^", pkg, "$"), - full.names = TRUE) - ## Note that we cannot use tools::file_test() here, as - ## cyclic namespace dependencies are not supported. Argh. - paths <- c(paths, - dirs[dir.exists(dirs) & - file.exists(file.path(dirs, - "DESCRIPTION&quot...

...ure.output, checkCRAN , chooseCRANmirror, citation, citEntry, citHeader, citFooter, close.socket, combn, compareVersion, co ntrib.url, count.fields, data, data.entry, dataentry, de, de.ncols, de.restore, de.setup, debugger, d emo, download.file, download.packages, dump.frames, edit, emacs, example, file_test, file.edit, find, fix, fixInNamespace, flush.console, formatOL, formatUL, getAnywhere, getFromNamespace, getS3method, glob2rx, head, head.matrix, help, help.search, help.start, history, index.search, install.packages, i nstalled.packages, limitedLabels, loadhistory, localeToCharset, ls.str, lsf.st...

..."myTst_*") > > ## More building & installing packages > ## NB: tests were added here for 2.11.0. > ## NB^2: do not do this in the R sources! > ## and this testdir is not installed. > pkgSrcPath <- file.path(Sys.getenv("SRCDIR"), "Pkgs") > if(file_test("-d", pkgSrcPath)) { + ## could use file.copy(recursive = TRUE) + system(paste('cp -r', shQuote(pkgSrcPath), shQuote(tempdir()))) + pkgPath <- file.path(tempdir(), "Pkgs") + op <- options(warn=2) # There should be *NO* warnings here! + ## pkg...

...ow to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] > getwd() [1] "/home/meconk" > file_test("-x","stringi/configure") stringi/configure TRUE > install.packages("stringi") Installing package into '/usr/lib64/R/library' (as 'lib' is unspecified) trying URL 'https://cloud.r-pro...

...gt; > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > [Previously saved workspace restored] > >> getwd() > [1] "/home/meconk" >> file_test("-x","stringi/configure") > stringi/configure > TRUE >> install.packages("stringi") Installing package into '/usr/lib64/R/library' > (as 'lib' is unspecified) > trying URL...

Hi, Starting with the XML package installed: > "XML" %in% rownames(installed.packages()) [1] TRUE > I ran the following script: pkgs <- c("XML") for (i in 1:100) { install.packages(pkgs, repos="http://cran.fhcrc.org") if (!all(pkgs %in% rownames(installed.packages()))) { print("failed to install pkgs!")

...hs <- character() > - for(lib in lib.loc) { > - dirs <- list.files(lib, > - pattern = paste0("^", pkg, "$"), > - full.names = TRUE) > - ## Note that we cannot use tools::file_test() here, as > - ## cyclic namespace dependencies are not supported. Argh. > - paths <- c(paths, > - dirs[dir.exists(dirs) & > - file.exists(file.path(dirs, > -...