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dcomtois / summarytools

R Package to Quickly and Neatly Summarize Data
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error in downloading summarytools package #67

Open rrodirodi opened 5 years ago

rrodirodi commented 5 years ago

Hi, I am trying to download the summarytools package in R using the install.packages command, and I get the output below. I would appreciate your help in getting this package installed.

There is a binary version available but the source version is later: binary source needs_compilation summarytools 0.9.2 0.9.3 FALSE

installing the source package ‘summarytools’

trying URL 'https://cran.rstudio.com/src/contrib/summarytools_0.9.3.tar.gz' Content type 'application/x-gzip' length 566250 bytes (552 KB)

downloaded 552 KB

The downloaded source packages are in ‘/private/var/folders/v5/f1sp8lnd7_d3hvtl6f222hcw0000gn/T/RtmpVUyALx/downloaded_packages’

dcomtois commented 5 years ago

Hi,

Have you tried installing XQuartz? Also, could you paste the results from capabilities() pls? Hopefully we quickly find what's going on, since you're not the only one reporting the issue with the latest release.

Thanks

scisus commented 5 years ago

Perhaps related - I successfully installed summarytools (from github). But when I try to load it, it warns me that 

library(summarytools)
system has no X11 capabilities, therefore only ascii graphs will be produced by dfSummary()

And so I don't get any little graphs, just percentages when using view(dfSummary(foo))

Results from capabilities() are

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua    http/ftp 
       TRUE        TRUE        TRUE        TRUE        TRUE       FALSE        TRUE 
    sockets      libxml        fifo      cledit       iconv         NLS     profmem 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
      cairo         ICU long.double     libcurl 
       TRUE       FALSE        TRUE        TRUE
dcomtois commented 5 years ago

@scisus This is a separate issue. The issue raised by @rrodirodi was resolved after the installation of XQuartz.

Not sure what is happening in your case. The condition for displaying that startup message is as follows:

if (Sys.info()[["sysname"]] != "Windows" && !isTRUE(capabilities("X11"))) {
    packageStartupMessage("system has no X11 capabilities, therefore only ",
                          "ascii graphs will be produced by dfSummary()")
  }

Clearly X11 is not the issue... So what does Sys.info()[["sysname"]] show in your case?

Thanks

dcomtois commented 5 years ago

@scisus If you can find a few moments, I'd like to go to the bottom of this... I'm thinking of making some changes for next CRAN release, but I'm lacking information at this point. Thx :)

scisus commented 5 years ago

Here you go - 

> Sys.info()[["sysname"]]
[1] "Linux"

Let me know if there's anything else you'd like me to try!

dcomtois commented 5 years ago

Thanks for the info. I'm working on something which should get rid of the problem. Meanwhile, you can use this patched version which skips the problematic check:

devtools::intall_github("dcomtois/summarytools", ref = "no-x11-check")

EDIT

Rather than ref = "no-x11-check", using ref = "dev-current" is now recommended; it should take care of this issue. See the NEWS file for more details.

Thx

benjaminwnelson commented 5 years ago

I'm also having issues with the download. When I try to load the package I get this error

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Warning message: In system2("/usr/bin/otool", c("-L", shQuote(DSO)), stdout = TRUE) : running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1

dcomtois commented 5 years ago

@benjaminwnelson Could you give a try to the solution posted here regarding this issue? Thx.

benjaminwnelson commented 5 years ago

@dcomtois, thanks for the reply. I tried the solution that you posted before my first message, but the issue wasn't fixed. It looks like if I load the package, rather than using summaryTools:: it works just fine.

dcomtois commented 5 years ago

@scisus Is this still an issue or were you able to install the package successfully?

elizabeth-upton commented 5 years ago

I am also having issues downloading this package. I tried: library(summarytools) and receive the message:

Error: package or namespace load failed for ‘summarytools’: .onLoad failed in loadNamespace() for 'tcltk', details: call: fun(libname, pkgname) error: X11 library is missing: install XQuartz from xquartz.macosforge.org

I tried downloading XQuartz but it is not available for my version of R (3.6.1: Action of the Toes)

On an older version of R I was able to use summarytools without a problem. Suggestions?

Also, I tried devtools::install_github("dcomtois/summarytools", ref = "no-x11-check") with no luck

dcomtois commented 5 years ago

@elizabeth-upton Hi, I'm not sure I'm following re: XQuartz not available for your version of R... Were you able to install "https://dl.bintray.com/xquartz/downloads/XQuartz-2.7.11.dmg"?

A (temporary, hopefully) solution would be to install an older version of summarytools, like so:

devtools::install_github('dcomtois/summarytools', ref='0-8-9')

caislin commented 4 years ago

Hi I am having a similiar issue with installing summary tools. I initially installed summary tools and received the error message "X11 library is missing: install XQuartz from xquartz.macosforge.org"

After installing XQuartz-2.7.11 I installed summarytools and received the error: "system has no X11 capabilities, therefore only ascii graphs will be produced by dfSummary() Warning message: In fun(libname, pkgname) : couldn't connect to display ":0""

When I ran the suggestion above: devtools::install_github("dcomtois/summarytools", ref = "no-x11-check") if received this error: Downloading GitHub repo dcomtois/summarytools@no-x11-check Error in utils::download.file(url, path, method = method, quiet = quiet, : cannot open URL 'https://api.github.com/repos/dcomtois/summarytools/tarball/no-x11-check'

When I installed an older version of summarytools from devtools::install_github('dcomtois/summarytools', ref='0-8-9') The output is unformatted

Any suggestions? Thank you!

dcomtois commented 4 years ago

Hello,

Have you tried the "dev-current" github version (instead of no-x11-check)?

On Sat., Nov. 9, 2019, 12:37 caislin, notifications@github.com wrote:

Hi I am having a similiar issue with installing summary tools. I initially installed summary tools and received the error message "X11 library is missing: install XQuartz from xquartz.macosforge.org"

After installing XQuartz-2.7.11 I installed summarytools and received the error: "system has no X11 capabilities, therefore only ascii graphs will be produced by dfSummary() Warning message: In fun(libname, pkgname) : couldn't connect to display ":0""

When I ran the suggestion above: devtools::install_github("dcomtois/summarytools", ref = "no-x11-check") if received this error: Downloading GitHub repo dcomtois/summarytools@no-x11-check Error in utils::download.file(url, path, method = method, quiet = quiet, : cannot open URL ' https://api.github.com/repos/dcomtois/summarytools/tarball/no-x11-check'

When I installed an older version of summarytools from devtools::install_github('dcomtois/summarytools', ref='0-8-9') The output is unformatted

Any suggestions? Thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dcomtois/summarytools/issues/67?email_source=notifications&email_token=ABNVLA2LLV4XMARCKRVYMMDQS3YLZA5CNFSM4HFSHII2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDULFOI#issuecomment-552121017, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNVLA5NVB4JOOW2NPQQ3TTQS3YLZANCNFSM4HFSHIIQ .

unomics20 commented 4 years ago

Hi I use MacOS Mojave. I am trying to use the summary tools package.

install.packages("summarytools")`
Installing package into ‘/Users/I REMOVED MY PERSONAL INFO HRE/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/summarytools_0.9.4.tgz'
Content type 'application/x-gzip' length 874679 bytes (854 KB)
==================================================
downloaded 854 KB

When I call the library it runs for hours without stopping unless forced to stop.

I have downloaded XQuartz -2.7.1 (though when I click on the app it doesn't open or fo anything.

dcomtois commented 4 years ago

@unomics20 The XQuartz installation might be the cause for this, so I would try reinstalling it after a system reboot. If it still fails, I'd try to get help by posting the issue on a forum, maybe StackOverflow or SuperUser.

After that is settled, I recommend doing the following:

install.packages("remotes")
remotes::install_github("dcomtois/summarytools")

Hope this helps!

unomics20 commented 4 years ago

HI @dcomtois,

Thank you so much for your help. The issue was that I was using an older version of Rstudio. I uninstalled and reinstalled a newer verison and the code works fine.

Although, it initially worked with what you listed above it stopped working randomly.

Quick question though, regarding the dfsummary

print(dfSummary(data ,graph.magnif = .75), method = 'render')

The resulting summary stat does not include graphs, do you know why this maybe? Is there a work around? Is there a data sz limit to the graphs being included in the summary table.

Thanks so much for writing this package! It is the most comprehensive for mixed data types (quantitative and qualitative data)

dcomtois commented 4 years ago

@unomics20 Is this happening with the GitHub version? There is an issue with the 0.9.4 version (the one that is still on CRAN and gets installed with install.packages()), having to do with data frames called "data". Then simply renaming your data frame should do the trick.

If however you installed st using remotes' or devtools' install_github(), could you post a reproducible example (including a sample of your data frame)? Maybe something specific to your data is happening here...

Thx

chrispenshumba commented 4 years ago

ERROR (probably on Mac),

error: X11 library is missing: install XQuartz from xquartz.macosforge.org

SOLUTION:

Hope it helps all the best.

venturinbru commented 4 years ago

Hello,

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun system might not have X11 capabilities; in case of errors when using dfSummary(), set st_options(use.x11 = FALSE)

Results from capabilities() are X11 FALSE

My system Mac OS Catalina 10.15.6

how to solve this?

dcomtois commented 4 years ago

Hi,

What led to this error? Updating? Installing from the first time? Using what method?

On Mon, 14 Sep 2020 at 22:05, venturinbru notifications@github.com wrote:

Hello,

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun system might not have X11 capabilities; in case of errors when using dfSummary(), set st_options(use.x11 = FALSE)

Results from capabilities() are X11 FALSE

My system Mac OS Catalina 10.15.6

how to solve this?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dcomtois/summarytools/issues/67#issuecomment-692416565, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNVLA3GX27XZ7Y5242BZ3DSF3DV5ANCNFSM4HFSHIIQ .

rockycore commented 3 years ago

System: macOS Catalina 10.15.7, RStudio 1.3.1093, XQuartz 2.7.11 My steps to get it work: (1) Install XQuartz (2) re-install summarytools: install.packages("summarytools") (3) re-import library(summarytools)

Thanks for the help