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
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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
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