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Joelgranados / EcoIP

Scripts to Analyze Color Data
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EcoIP tar.gz file does not download properly on windows. #49

Closed joelissues closed 10 years ago

joelissues commented 11 years ago

I have tried installing the ecoip framework using an r shell, but have been unsuccessful. I am running a windows 7 ultimate x64 pc onto which I have installed the required imagemagick and gtk2.0, as well as R versions 2.15.0,2.15.2, and 3.01.2. In all these versions, I run the commands

source("http://sourceforge.net/projects/ecoip/files/ecoip_install.R/download")

eip.install()

After doing so, I get the following output

[1] "http://sourceforge.net/projects/ecoip/files/20130531/EcoIP_0.1-20130531.tar.gz/download" [1] "~/EcoIP_0.1-20130531.tar.gz" cygwin warning: MS-DOS style path detected: C:\Users\Documents/EcoIP_0.1-20130531.tar.gz Preferred POSIX equivalent is: /cygdrive/c/Users//Documents/EcoIP_0.1-20130531.tar.gz CYGWIN environment variable option "nodosfilewarning" turns off this warning. Consult the user's guide for more details about POSIX paths: http://cygwin.com/cygwin-ug-net/using.html#using-pathnames --2013-07-01 13:10:44-- http://sourceforge.net/projects/ecoip/files/20130531/EcoIP_0.1-20130531.tar.gz/download Resolving sourceforge.net (sourceforge.net)... 216.34.181.60 Connecting to sourceforge.net (sourceforge.net)|216.34.181.60|:80... connected. HTTP request sent, awaiting response... 302 Found Location: http://downloads.sourceforge.net/project/ecoip/20130531/EcoIP_0.1-20130531.tar.gz?r=&ts=1372698647&use_mirror=iweb [following] --2013-07-01 13:10:45-- http://downloads.sourceforge.net/project/ecoip/20130531/EcoIP_0.1-20130531.tar.gz?r=&ts=1372698647&use_mirror=iweb Resolving downloads.sourceforge.net (downloads.sourceforge.net)... 216.34.181.59 Connecting to downloads.sourceforge.net (downloads.sourceforge.net)|216.34.181.59|:80... connected. HTTP request sent, awaiting response... 302 Found Location: http://iweb.dl.sourceforge.net/project/ecoip/20130531/EcoIP_0.1-20130531.tar.gz [following] --2013-07-01 13:10:45-- http://iweb.dl.sourceforge.net/project/ecoip/20130531/EcoIP_0.1-20130531.tar.gz Resolving iweb.dl.sourceforge.net (iweb.dl.sourceforge.net)... 70.38.0.134, 2607:f748:10:12::5f:2 Connecting to iweb.dl.sourceforge.net (iweb.dl.sourceforge.net)|70.38.0.134|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 6427656 (6.1M) [application/x-gzip] Saving to: C:\\Users\\<USER>\\Documents/EcoIP_0.1-20130531.tar.gz' ' 0K .......... .......... .......... .......... .......... 0% 596K 10s 50K .......... .......... .......... .......... .......... 1% 1.17M 8s 100K .......... .......... .......... .......... .......... 2% 938K 7s 150K .......... .......... .......... .......... .......... 3% 1.26M 7s 200K .......... .......... .......... .......... .......... 3% 1.25M 6s 250K .......... .......... .......... .......... .......... 4% 1.31M 6s 300K .......... .......... .......... .......... .......... 5% 869K 6s 350K .......... .......... .......... .......... .......... 6% 989K 6s 400K .......... .......... .......... .......... .......... 7% 890K 6s 450K .......... .......... .......... .......... .......... 7% 1.26M 6s 500K .......... .......... .......... .......... .......... 8% 945K 6s 550K .......... .......... .......... .......... 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Installing package(s) into ‘C:/Users/Dmitri/Documents/R/win-library/2.15’ (as ‘lib’ is unspecified) --- Please select a CRAN mirror for use in this session --- Warning message: package ‘~/EcoIP_0.1-20130531.tar.gz’ is not available (for R version 2.15.2)

Any idea as to how to resolve this?

Joelgranados commented 11 years ago

I noticed that you are running R in a cygwin environment. Can you try to install EcoIP by using the R console that is provided by the R windows installation (instead of running it on cygwin)? Be sure to execute RGui.exe (http://data.princeton.edu/R/gettingStarted.html)

joelissues commented 11 years ago

I also noticed that cygwin saw the filepaths and did some regex parsing. The thing is, I was running these commands through the R console as opposed to through cygwin or command prompt. I'm not sure of how to separate cygwin from the R console.

Joelgranados commented 11 years ago

Hrm.

From where did you install R? Where did you download it from? I'm going to test on a windows box that I have and I want to replicate your setup.

Regards

On Tue, Jul 2, 2013 at 7:27 PM, joelissues notifications@github.com wrote:

I also noticed that cygwin saw the filepaths and did some regex parsing. The thing is, I was running these commands through the R console as opposed to through cygwin or command prompt. I'm not sure of how to separate cygwin from the R console.

— Reply to this email directly or view it on GitHubhttps://github.com/Joelgranados/EcoIP/issues/49#issuecomment-20361398 .

Joel Andrés Granados IT University of Copenhagen Copenhagen, Denmark.

Joelgranados commented 11 years ago

I've manged to Recreate the bug. To start I have created a new version of EcoIP that is released with R 3.0.0 so we should stop having the error message that warned about the wrong R version. To install this new version just follow the same instructions as before (https://github.com/Joelgranados/EcoIP/wiki/How-to-Install).

I'm going to test this new version on my test box back at home. I'll update the bug report once I have more information. I encourage you to test in your environment to see if the new EcoIP actually fixes stuff :)

Joelgranados commented 11 years ago

I think I found the culprit of the issue. I was using "wget" to download the source (this does not work with windows). I was also using "~" to refer to the home directory (this does not work on windows). I have made a new release of EcoIP in the hope to address this issue. Please test and get back to me if it's still is a problem.

Joelgranados commented 11 years ago

Hey Dmitri

I tested again with the new build and it apparently keeps on failing. It seems that the automatic download is failing to correctly download the file (only on windows). A work around is to download the file from  http://sourceforge.net/projects/ecoip/ and use it for installation. Execute 'R CMD INSTALL ecoipfile.tar.gz'. If you have all the dependencies installed it should work.

If you don't have all the dependencies installed, you need to install them all. R will tell you which packages you need to install to get EcoIP going. Notice that you might have to compile some packages (SVG package) in order to install it; this is possible with the Rtools package for windows (so you might have to install Rtools as well).

I'm going to leave this issue open until I figure out why the download method does not download properly on windows

Joelgranados commented 11 years ago

This issue could be related to https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=7991 and to http://tolstoy.newcastle.edu.au/R/devel/06/06/5792.html#5796qlink1

Joelgranados commented 10 years ago

I tested the download feature in R and there seems to be something fishy.... I downloaded with "auto" and "internal" and in both cases the download detects a file of 6430711 bytes but downloads (I don't know from where) 6453589 bytes. When I download with Firefox I get the correct size of 6430711.

The R log: """

eip.trz = "EcoIP_0.1-20130717.tar.gz" eip.from = paste("http://sourceforge.net/projects/ecoip/files/20130717/", eip.trz, "/download", sep="") download.file(eip.from, eip.trz, method="auto") essai de l'URL 'http://sourceforge.net/projects/ecoip/files/20130717/EcoIP_0.1-20130717.tar.gz/download' Content type 'application/x-gzip' length 6430711 bytes (6.1 Mb) URL ouverte downloaded 6.1 Mb

file.info("EcoIP_0.1-20130717.tar.gz")[1] size EcoIP_0.1-20130717.tar.gz 6453589 unlink("EcoIP_0.1-20130717.tar.gz")

download.file(eip.from, eip.trz, method="internal") essai de l'URL 'http://sourceforge.net/projects/ecoip/files/20130717/EcoIP_0.1-20130717.tar.gz/download' Content type 'application/x-gzip' length 6430711 bytes (6.1 Mb) URL ouverte downloaded 6.1 Mb

file.info("EcoIP_0.1-20130717.tar.gz")[1] size EcoIP_0.1-20130717.tar.gz 6453589 unlink("EcoIP_0.1-20130717.tar.gz")

file.info("EcoIP_0.1-20130717.tar.gz")[1] size EcoIP_0.1-20130717.tar.gz 6430711 """

Joelgranados commented 10 years ago

I just created a new bug-report in the R bug tracking system. https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15398

Joelgranados commented 10 years ago

This issue should be solved with the latest version. EcoIP_0.1-20130722