Frede... Windows uses zip files (binary, aka pre-compiled format) for packages by default, because most installations don't have the development tools installed. You need to setup RTools and use the "source" option to install_package in order to handle the tar.gz package file, or download and install the zip file instead. --------------------------------------------------------------------------- Jeff Newmiller The ..... ..... Go Live... DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --------------------------------------------------------------------------- Sent from my phone. Please excuse my brevity.
On April 20, 2014 11:01:17 PM PDT, "Frede Aakmann Tøgersen" <fr...@vestas.com> wrote: >Well now, I think I have seen something similar to Alpesh. > >Recently I needed the climatol package that I have used some time ago. >It is not maintained anymore but I downloaded the latest version, >climatol_2.2.tar.gz, from archives >(http://cran.r-project.org/src/contrib/Archive/climatol/climatol_2.2.tar.gz >) . Trying to install that package from local file using R-3.1.0 on >Windows 8 resulted in this: > >## From R Console >> utils:::menuInstallLocal() >Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", >"Type")) : > cannot open the connection >In addition: Warning messages: >1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip >file >2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) >: >cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable >reason 'No such file or directory' >> > >And yes I know where the file is located, since choose.files() is used. > >However I tried the same on our linux (R-3.0.2) cluster and it >succeeded: > >[frtog@dkrdsfshn2 ~]$ R CMD INSTALL climatol_2.2.tar.gz >* installing to library >?/gpfs02/gcdistro/app/R/3.0.2-gcc4.8.2/lib64/R/library? >* installing *source* package ?climatol? ... >** R >** data >** inst >** preparing package for lazy loading >** help >*** installing help indices >** building package indices >** installing vignettes >** testing if installed package can be loaded >* DONE (climatol) >[frtog@dkrdsfshn2 ~]$ R > >R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" >Copyright (C) 2013 The R Foundation for Statistical Computing >Platform: x86_64-unknown-linux-gnu (64-bit) > >R is free software and comes with ABSOLUTELY NO WARRANTY. >You are welcome to redistribute it under certain conditions. >Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > >R is a collaborative project with many contributors. >Type 'contributors()' for more information and >'citation()' on how 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. > >> library("climatol") >> ?rosavent >> q() >Save workspace image? [y/n/c]: n >[frtog@dkrdsfshn2 ~]$ > > >Now unzipping and untaring climatol_2.2.tar.gz I thought to examine >whether I could build the package on my Windows box. Only R stuff and >no foreign language as C, FORTRAN, etc. so it should be easy. > >## Command shell in Windows >Microsoft Windows [Version 6.2.9200] >(c) 2012 Microsoft Corporation. All rights reserved. > >C:\Users\frtog>cd Desktop > >C:\Users\frtog\Desktop>c:\Programmer\R\R-3.1.0\bin\x64\R CMD build >climatol >* checking for file 'climatol/DESCRIPTION' ... OK >* preparing 'climatol': >* checking DESCRIPTION meta-information ... OK >* checking for LF line-endings in source and make files >* checking for empty or unneeded directories >* looking to see if a 'data/datalist' file should be added >* building 'climatol_2.2.tar.gz' > >Now trying to install from that local file I Still got the same error >as above. > > > >Trying to do some debugging on read.dcf() (Emacs/ESS) > > >R version 3.1.0 (2014-04-10) -- "Spring Dance" >Copyright (C) 2014 The R Foundation for Statistical Computing >Platform: x86_64-w64-mingw32/x64 (64-bit) > >R is free software and comes with ABSOLUTELY NO WARRANTY. >You are welcome to redistribute it under certain conditions. >Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > >R is a collaborative project with many contributors. >Type 'contributors()' for more information and >'citation()' on how 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. > >> > options(chmhelp=FALSE, help_type="text") >> options(STERM='iESS', str.dendrogram.last="'", >editor='emacsclient.exe', show.error.locations=TRUE) >> debug(read.dcf) >> install.packages("~/Desktop/climatol_2.2.tar.gz", repos = NULL) >debugging in: read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", >"Type")) >debug: { > if (is.character(file)) { > file <- gzfile(file) > on.exit(close(file)) > } > if (!inherits(file, "connection")) > stop("'file' must be a character string or connection") > if (!all) > return(.Internal(readDCF(file, fields, keep.white))) > .assemble_things_into_a_data_frame <- function(tags, vals, > nums) { > tf <- factor(tags, levels = unique(tags)) > cnts <- table(nums, tf) > out <- array(NA_character_, dim = dim(cnts), dimnames = list(NULL, > levels(tf))) > if (all(cnts <= 1L)) { > out[cbind(nums, tf)] <- vals > out <- as.data.frame(out, stringsAsFactors = FALSE) > } > else { > levs <- colSums(cnts > 1L) == 0L > if (any(levs)) { > inds <- tf %in% levels(tf)[levs] > out[cbind(nums[inds], tf[inds])] <- vals[inds] > } > out <- as.data.frame(out, stringsAsFactors = FALSE) > for (l in levels(tf)[!levs]) { > out[[l]] <- rep.int(list(NA_character_), nrow(cnts)) > i <- tf == l > out[[l]][unique(nums[i])] <- split(vals[i], nums[i]) > } > } > out > } > on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")), > add = TRUE) > Sys.setlocale("LC_CTYPE", "C") > lines <- readLines(file) > ind <- grep("^[^[:blank:]][^:]*$", lines) > if (length(ind)) { > lines <- strtrim(lines[ind], 0.7 * getOption("width")) >stop(gettextf("Invalid DCF format.\nRegular lines must have a >tag.\nOffending lines start with:\n%s", > paste0(" ", lines, collapse = "\n")), domain = NA) > } > line_is_not_empty <- !grepl("^[[:space:]]*$", lines) > nums <- cumsum(diff(c(FALSE, line_is_not_empty) > 0L) > 0L) > nums <- nums[line_is_not_empty] > lines <- lines[line_is_not_empty] > line_is_escaped_blank <- grepl("^[[:space:]]+\\.[[:space:]]*$", > lines) > if (any(line_is_escaped_blank)) > lines[line_is_escaped_blank] <- "" > line_has_tag <- grepl("^[^[:blank:]][^:]*:", lines) > ind <- which(!line_has_tag[which(diff(nums) > 0L) + 1L]) > if (length(ind)) { > lines <- strtrim(lines[ind], 0.7 * getOption("width")) >stop(gettextf("Invalid DCF format.\nContinuation lines must not start a >record.\nOffending lines start with:\n%s", > paste0(" ", lines, collapse = "\n")), domain = NA) > } > lengths <- rle(cumsum(line_has_tag))$lengths > pos <- cumsum(lengths) > tags <- sub(":.*", "", lines[line_has_tag]) >lines[line_has_tag] <- sub("[^:]*:[[:space:]]*", "", >lines[line_has_tag]) > foldable <- rep.int(is.na(match(tags, keep.white)), lengths) > lines[foldable] <- sub("^[[:space:]]*", "", lines[foldable]) > lines[foldable] <- sub("[[:space:]]*$", "", lines[foldable]) >vals <- mapply(function(from, to) paste(lines[from:to], collapse = >"\n"), > c(1L, pos[-length(pos)] + 1L), pos) > out <- .assemble_things_into_a_data_frame(tags, vals, nums[pos]) > if (!is.null(fields)) > out <- out[fields] > out >} >Browse[2]> str(file) > chr "climatol_2.2.tar.gz/DESCRIPTION" >Browse[2]> head(file) >[1] "climatol_2.2.tar.gz/DESCRIPTION" >Browse[2]> >debug: if (is.character(file)) { > file <- gzfile(file) > on.exit(close(file)) >} >Browse[2]> >debug: file <- gzfile(file) >Browse[2]> >debug: on.exit(close(file)) >Browse[2]> >debug: if (!inherits(file, "connection")) stop("'file' must be a >character string or connection") >Browse[2]> >debug: if (!all) return(.Internal(readDCF(file, fields, keep.white))) >Browse[2]> str(file) >Classes 'gzfile', 'connection' atomic [1:1] 3 > ..- attr(*, "conn_id")=<externalptr> >Browse[2]> file > description class >"climatol_2.2.tar.gz/DESCRIPTION" "gzfile" > mode text > "rb" "text" > opened can read > "closed" "yes" > can write > "yes" >Browse[2]> >debug: return(.Internal(readDCF(file, fields, keep.white))) >Browse[2]> >Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", >"Type")) : > cannot open the connection >In addition: Warning message: >In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : >cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable >reason 'No such file or directory' >> > >Well coming to debug: if (!all) return(.Internal(readDCF(file, fields, >keep.white))) I loose control and R returns to prompt with an error. > >Hopefully one of you can replicate this. If not then it must have >something with Windows OS to do. But what? > > > >Yours sincerely / Med venlig hilsen > > >Frede Aakmann Tøgersen >Specialist, M.Sc., Ph.D. >Plant Performance & Modeling > >Technology & Service Solutions >T +45 9730 5135 >M +45 2547 6050 >fr...@vestas.com >http://www.vestas.com > >Company reg. name: Vestas Wind Systems A/S >This e-mail is subject to our e-mail disclaimer statement. >Please refer to www.vestas.com/legal/notice >If you have received this e-mail in error please contact the sender. > >> -----Original Message----- >> From: r-help-boun...@r-project.org >[mailto:r-help-boun...@r-project.org] >> On Behalf Of Jeff Newmiller >> Sent: 20. april 2014 23:33 >> To: Alpesh Pandya; Rui Barradas >> Cc: r-help@r-project.org; Uwe Ligges >> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package >> >> Hard to help you when the problem simply does not happen for others. >> >> As for Windows being not a focus, that is not at all true. I use it >regularly on >> Windows at work. That being said, there are thousands of packages and >> those each involve their own subset of R users. There are also many >> operating system configurations that may not all be fully tested. >Blaming "R" >> or "Windows", or blaming us for "preventing" you from getting your >> education (isn't that something between you and your educational >> institution?) are not going to be effective strategies for problem >solving. >> >> Are you able to use other aspects of R beyond the XML package? Have >you >> tried communicating with the maintainers of that package? >> >--------------------------------------------------------------------------- >> Jeff Newmiller The ..... ..... Go >Live... >> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live >Go... >> Live: OO#.. Dead: OO#.. >Playing >> Research Engineer (Solar/Batteries O.O#. #.O#. with >> /Software/Embedded Controllers) .OO#. .OO#. >rocks...1k >> >--------------------------------------------------------------------------- >> Sent from my phone. Please excuse my brevity. >> >> On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya >> <alpeshpan...@gmail.com> wrote: >> >I keep on trying from various networks but I still get the same >error. >> >I >> >don't this this has anything to do with network or ability to >download >> >the >> >package (as I can install other packages fine). This must be >something >> >in >> >base R or dependencies issues (that R is not spelling out). >> > >> >I know R is geared for Mac and Windows is kind of looked down upon >but >> >I >> >have no option but use windows and need this XML package running to >> >complete my education. Any help on this would be appreciated. >> > >> > >> >On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya >> ><alpeshpan...@gmail.com>wrote: >> > >> >> Thank you for response Rui. >> >> >> >> I still get the same error with this repository. >> >> >> >> Installing package into >> >���C:/Users/APandya/Documents/R/win-library/3.0��� >> >> (as ���lib��� is unspecified) >> >> trying URL ' >> >> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip' >> >> Content type 'application/zip' length 4288136 bytes (4.1 Mb) >> >> opened URL >> >> downloaded 4.1 Mb >> >> >> >> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", >> >"Type")) >> >> : >> >> cannot open the connection >> >> In addition: Warning messages: >> >> 1: In download.file(url, destfile, method, mode = "wb", ...) : >> >> downloaded length 4276224 != reported length 4288136 >> >> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from >zip >> >file >> >> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", >> >"Type")) : >> >> cannot open compressed file 'XML/DESCRIPTION', probable reason >'No >> >such >> >> file or directory' >> >> >> >> >> >> >> >> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas >> ><ruipbarra...@sapo.pt>wrote: >> >> >> >>> Hello, >> >>> I have package XML installed on Windows 7, R 3.0.3 and I had no >> >problem >> >>> at all. Can't you try (it worked with me) >> >>> >> >>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt") >> >>> >> >>> Hope this helps, >> >>> >> >>> Rui Barradas >> >>> >> >>> Em 14-04-2014 16:24, Alpesh Pandya escreveu: >> >>> >> >>> I have tried these sources (almost all US mirrors): >> >>>> >> >>>> >> >>http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip >> >>>> >http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip >> >>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/ >> >>>> 3.0/XML_3.98-1.1.zip >> >>>> >> >http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip >> >>>> >> >>http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip >> >>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/ >> >>>> contrib/3.0/XML_3.98-1.1.zip >> >>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip >> >>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip >> >>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip >> >>>> >> >>http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip >> >>>> >> >http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98- >> 1.1.zip >> >>>> >> >>>> I have confirmed with IT that there is no restriction on >> >downloading this >> >>>> zip file from any of these sources. Also I am getting same error >> >when I >> >>>> try >> >>>> from my home network as well. >> >>>> >> >>>> >> >>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges < >> >>>> lig...@statistik.tu-dortmund.de >> >>>> >> >>>>> wrote: >> >>>>> >> >>>> >> >>>> >> >>>>> >> >>>>> On 13.04.2014 01:30, Alpesh Pandya wrote: >> >>>>> >> >>>>> @Uwe I tried the same steps from office as well as home >network >> >with >> >>>>>> same >> >>>>>> results. Are you using windows 7 with R 3.0.3? >> >>>>>> >> >>>>>> I have seen same question being asked by others without any >> >>>>>> resolution. Is >> >>>>>> anything special about XML package? I am OK use older version >of >> >>>>>> package >> >>>>>> but in archives there are no zip files (only gz files). Is >> >windows >> >>>>>> platform >> >>>>>> not recommended for R? >> >>>>>> >> >>>>>> >> >>>>> Right, and you can try to install these from sources. >> >>>>> But I doubt you need it. You still have not told us if you >tried >> >another >> >>>>> mirror to download the XML file from and what you local IT >support >> >tells >> >>>>> you while your downloads are incomplete. >> >>>>> >> >>>>> Best, >> >>>>> Uwe Ligges >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges < >> >>>>>> lig...@statistik.tu-dortmund.de >> >>>>>> >> >>>>>> wrote: >> >>>>>>> >> >>>>>>> >> >>>>>> >> >>>>>> >> >>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote: >> >>>>>>> >> >>>>>>> Thank you for response Uwe. I tried multiple times by >> >downloading >> >>>>>>> the >> >>>>>>> >> >>>>>>>> zip >> >>>>>>>> file from many sources but still the same error. This is a >> >major road >> >>>>>>>> block >> >>>>>>>> for me in using R. Appreciate any help on this. >> >>>>>>>> >> >>>>>>>> >> >>>>>>>> Please ask your local IT staff. >> >>>>>>> >> >>>>>>> I get, using the same mirror: >> >>>>>>> >> >>>>>>> >> >options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror")) >> >>>>>>> >> >>>>>>>> install.packages("XML", lib="d:/temp") >> >>>>>>>> >> >>>>>>>> >> >>>>>>> trying URL >'http://watson.nci.nih.gov/cran_mirror/bin/windows/ >> >>>>>>> >> >>>>>>> contrib/3.0/XML_3.98-1.1.zip' >> >>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb) >> >>>>>>> opened URL >> >>>>>>> downloaded 4.1 Mb >> >>>>>>> >> >>>>>>> package 'XML' successfully unpacked and MD5 sums checked >> >>>>>>> >> >>>>>>> The downloaded binary packages are in >> >>>>>>> d:\temp\RtmpqMqL8L\downloaded_packages >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> Best, >> >>>>>>> Uwe Ligges >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges < >> >>>>>>>> lig...@statistik.tu-dortmund.de >> >>>>>>>> >> >>>>>>>> wrote: >> >>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> Works for me. >> >>>>>>>> >> >>>>>>>> >> >>>>>>>>> Best, >> >>>>>>>>> Uwe Ligges >> >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote: >> >>>>>>>>> >> >>>>>>>>> Using install.package('XML') command produces this >error: >> >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>>> trying URL >> >>>>>>>>>> ' >> >>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/ >> >>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip >> >>>>>>>>>> ' >> >>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 >Mb) >> >>>>>>>>>> opened URL >> >>>>>>>>>> downloaded 4.1 Mb >> >>>>>>>>>> >> >>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), >> >c("Package", >> >>>>>>>>>> "Type")) : >> >>>>>>>>>> cannot open the connection >> >>>>>>>>>> In addition: Warning messages: >> >>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb", >...) >> >: >> >>>>>>>>>> downloaded length 4276224 != reported length 4288136 >> >>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting >> >from zip >> >>>>>>>>>> file >> >>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), >> >c("Package", >> >>>>>>>>>> "Type")) >> >>>>>>>>>> : >> >>>>>>>>>> cannot open compressed file 'XML/DESCRIPTION', >probable >> >>>>>>>>>> reason >> >>>>>>>>>> 'No >> >>>>>>>>>> such >> >>>>>>>>>> file or directory' >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip >> >directly >> >>>>>>>>>> from >> >>>>>>>>>> cran >> >>>>>>>>>> site. But this zip file is not a valid archive (cannot >open >> >using >> >>>>>>>>>> winzip). >> >>>>>>>>>> Also trying to install using this downloaded file produces >> >the >> >>>>>>>>>> following >> >>>>>>>>>> error: >> >>>>>>>>>> >> >>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/ >> >>>>>>>>>> win-library/3.0' >> >>>>>>>>>> (as 'lib' is unspecified) >> >>>>>>>>>> Warning in install.packages : >> >>>>>>>>>> error 1 in extracting from zip file >> >>>>>>>>>> Warning in install.packages : >> >>>>>>>>>> cannot open compressed file 'XML/DESCRIPTION', >probable >> >>>>>>>>>> reason >> >>>>>>>>>> 'No >> >>>>>>>>>> such >> >>>>>>>>>> file or directory' >> >>>>>>>>>> Error in install.packages : cannot open the connection >> >>>>>>>>>> >> >>>>>>>>>> I downloaded this zip file from multiple sources and >tried >> >to >> >>>>>>>>>> install >> >>>>>>>>>> with >> >>>>>>>>>> same result. >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>> >> >>>>>>>> >> >>>>>> >> >>>>>> >> >>>> >> >>>> >> >> >> >> >> >> -- >> >> Thanks and Regards >> >> Alpesh >> >> >> >> ______________________________________________ >> R-help@r-project.org mailing list >> 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. ______________________________________________ R-help@r-project.org mailing list 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.