Bioequivalence and Bioavailability Forum • Fail to install BEAR package for R

SerhiiP
☆

Ukraine,
2020-06-23 11:15
(1563 d 10:58 ago)

Posting: # 21564
Views: 10,961

Fail to install BEAR package for R [🇷 for BE/BA]

Hello everyone!
I really wanted to try BEAR package, I had following this guide about it's installation https://sourceforge.net/projects/yjlee-r-packages/files/bear/
but i've got this problem:

…

package ‘cairoDevice’ successfully unpacked and MD5 sums checked



The downloaded binary packages are in

   C:\Users\123456\AppData\Local\Temp\RtmpKEbBNj\downloaded_packages

Error in install.packages : cannot open the connection



 Now checking installation error of package 'bear'...

 failed to install 'gWidgets'



 failed to install 'gWidgetsRGtk2'



 failed to install 'bear'





 -> Sorry, 'bear' is not successfully installed.

Can someone explain what is going on here? :confused:

Tried to restart everything,but still the same error occures

Windows 10, R 4.0.1, bear 2.8.8

help!

krish85 ☆ India, 2020-06-29 07:32 (1557 d 14:41 ago) @ SerhiiP Posting: # 21588 Views: 9,325	Fail to install BEAR package for R Post reply
	Hi, I am also getting similar error while installing ivivc0.3.3. `Now checking installation error of package 'ivivc'... failed to install 'gWidgets' failed to install 'gWidgetsRGtk2' -> Sorry, 'ivivc' is not successfully installed.` May be, we are missing something....idk...

yjlee168 ★★★ Kaohsiung, Taiwan, 2020-06-29 12:56 (1557 d 09:17 ago) @ krish85 Posting: # 21593 Views: 9,354	Fail to install 'ivivc' package for R Post reply
	Hi krish85 OK. But could you reveal more info (OS, error messages et al.) first about failing installation of BEAR (your subject title) or ivivc (your messages)? I will see if I can help. — All the best, -- Yung-jin Lee bear v2.9.1:- created by Hsin-ya Lee & Yung-jin Lee Kaohsiung, Taiwan https://www.pkpd168.com/bear Download link (updated) -> here

krish85
☆

India,
2020-06-29 13:10
(1557 d 09:03 ago)

@ yjlee168
Posting: # 21594
Views: 9,389

Fail to install 'ivivc' package for R

Post reply

❝ OK. But could you reveal more info (OS, error messages et al.) first about failing installation of BEAR (your subject title) or ivivc (your messages)? I will see if I can help.

I am using R 4.0.2 on windows 10. I have never installed bear or ivivc before. first i tried to instrall ivivic as per the instruction provided by you on
https://sourceforge.net/projects/yjlee-r-packages/files/bear/

so, i had kept preinst and ivivc_0.3.3.zip file in my wd and after starting r as admin, "source("preinst.r") and do("ivivc", "ivivc_0.3.3.zip"), started installing varios packages.. but then messege on r displayes as below.

If the following package installations fail, please browse

http://forum.bebac.at/mix_entry.php?id=19734 for more info.

Press Enter to continue



i press enter and then



package ‘ivivc’ successfully unpacked and MD5 sums checked



Now checking installation error of package 'ivivc'...

failed to install 'gWidgets'



failed to install 'gWidgetsRGtk2'



-> Sorry, 'ivivc' is not successfully installed.

yjlee168 ★★★ Kaohsiung, Taiwan, 2020-06-29 13:30 (1557 d 08:43 ago) @ krish85 Posting: # 21595 Views: 9,331	Fail to install 'ivivc' package for R Post reply
	Hi krish85, Try to run install.packages("RGkt2") under R console as system administrator. Then show me the error messages. Thanks. — All the best, -- Yung-jin Lee bear v2.9.1:- created by Hsin-ya Lee & Yung-jin Lee Kaohsiung, Taiwan https://www.pkpd168.com/bear Download link (updated) -> here

krish85 ☆ India, 2020-06-29 13:47 (1557 d 08:26 ago) @ yjlee168 Posting: # 21596 Views: 9,366	Fail to install 'ivivc' package for R Post reply
	❝ Try to run install.packages("RGkt2") under R console as system administrator. Then show me the error messages. Thanks. I got this.. `--- Please select a CRAN mirror for use in this session ---` ( i select first one, cloud) `Warning message: package ‘RGkt2’ is not available (for R version 4.0.2)` Edit: Please follow the Forum’s Policy. [Helmut]

Helmut
★★★

Vienna, Austria,
2020-06-29 14:49
(1557 d 07:23 ago)

@ krish85
Posting: # 21597
Views: 9,384

Fail to install 'ivivc' package for R

Post reply

Hi krish85,

❝ --- Please select a CRAN mirror for use in this session --- ( i select first one, cloud)

❝ Warning message:

❝ package ‘RGkt2’ is not available (for R version 4.0.2)

Very strange. It was built under R4.0.0 though it should work with later releases. Download the Windows-binary from CRAN and install the package from the local zip-file.

Package: RGtk2

Version: 2.20.36

Title: R Bindings for Gtk 2.8.0 and Above

Author: Michael Lawrence <[email protected]> and Duncan Temple Lang <[email protected]>

Depends: R (>= 3.4.0)

Imports: methods

SystemRequirements: Cairo (>= 1.0.0), ATK (>= 1.10.0), Pango (>= 1.10.0), GTK+ (>= 2.8.0), GLib (>= 2.8.0)

Maintainer: Michael Lawrence <[email protected]>

Description: Facilities in the R language for programming

  graphical interfaces using Gtk, the Gimp Tool Kit.

License: GPL

URL: http://www.ggobi.org/rgtk2, http://www.omegahat.net

Encoding: UTF-8

NeedsCompilation: yes

Packaged: 2019-03-03 23:20:52 UTC; larman

Repository: CRAN

Date/Publication: 2019-03-08 15:32:41 UTC

Built: R 4.0.0; x86_64-w64-mingw32; 2020-04-26 13:30:29 UTC; windows

Archs: i386, x64

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
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zizou ★ Plzeň, Czech Republic, 2020-06-29 14:57 (1557 d 07:16 ago) @ yjlee168 Posting: # 21598 Views: 9,272	Fail to install 'ivivc' package for R Post reply
	❝ Try to run install.packages("RGkt2") under R console as system administrator. Then show me the error messages. Thanks. Hi, try also install.packages("RGtk2"). Best regards, zizou

krish85
☆

India,
2020-06-29 15:20
(1557 d 06:52 ago)

@ zizou
Posting: # 21599
Views: 9,287

Fail to install 'ivivc' package for R

Post reply

❝ Hi, try also install.packages("RGtk2").

ooops....its RGtk2....thanks...

--- Please select a CRAN mirror for use in this session ---

trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.0/RGtk2_2.20.36.zip'

Content type 'application/zip' length 16529627 bytes (15.8 MB)

downloaded 15.8 MB



package ‘RGtk2’ successfully unpacked and MD5 sums checked



The downloaded binary packages are in

C:\Users\Admin\AppData\Local\Temp\Rtmpy43zWs\downloaded_packages

there is no error/warning in this..

but again while installing, same error shows.

Now checking installation error of package 'ivivc'...

failed to install 'gWidgets'



failed to install 'gWidgetsRGtk2'



-> Sorry, 'ivivc' is not successfully installed.

Edit: Please follow the Forum’s Policy. [Helmut]

Helmut
★★★

Vienna, Austria,
2020-06-29 15:47
(1557 d 06:25 ago)

@ krish85
Posting: # 21600
Views: 9,402

Packages retired from CRAN

Post reply

Hi krish85,

❝ Now checking installation error of package 'ivivc'...

❝ failed to install 'gWidgets'

❝

❝ failed to install 'gWidgetsRGtk2'

These two packages were retired from CRAN (see here and there). After Jan 2019 their maintainer did not respond to update requests by CRAN. Brian Ripley made corrections in the last release (April 2020), built them under R4.0.0, and tagged them ORPHANED in the DESCRIPTION files. Now they are history.

To quote CRAN:

Orphaned packages have no active maintainer: they have Maintainer: ORPHANED in their DESCRIPTON file. Orphaned packages remain in the main CRAN packages section as long as they pass "R CMD check" for the current release version of R. Everybody is more than welcome to take over as maintainer of an orphaned package. Simply download the package sources, make changes if necessary (respecting original author and license!) and resubmit the package to CRAN with your name as maintainer in the DESCRIPTION file of the package. Possible reasons for orphanizing a package:

The current maintainer actively wants to orphanize the package, e.g., due to no longer having time or interest to act as package maintainer.
Emails sent to the current maintainer by the CRAN admins bounced, or were not answered for longer periods of time.

The current orphanizing process:

File PACKAGES.in in CRAN's src/contrib directory (the repository package metadata file) adds a Maintainer: ORPHANED override and an X-CRAN-Comment entry providing information about the original maintainer, and the date and reason for orphanizing.
Package sources and binaries are updated on CRAN without increasing the version number.
If the package cleanly passes R CMD check for the current release version of R, it remains in CRAN's src/contrib directory. Otherwise, it is moved to the Archive.

I think you have three options:

If you have the devtools and all dependent packages (a lot!), you can build the packages from their latest archived sources (gWidgets 0.0-54.2, gWidgetsRGtk2 0.0-86.1). Not something I would recommend an inexperienced RUser. See also the note at the end.
Install gWidgets2, gWidgets2RGtk2, and gWidgets2tcltk. These packages have the same maintainer as the retired packages. Try whether ivivc runs with them. If not:
Since the original GUI-packages are retired, it’s up to Yung-jin to deal with the problem (i.e., adapt his packages to work with the gWidgets*2 packages).
@Yung-jin:
- “The gWidgets2 package provides a programming interface for making graphical user interfaces within R. The package is a rewrite of the gWidgets package, introducing a few external changes but a significant number of internal ones.”
(my emphasis; sorry…)

Note:

The packages didn’t pass CRAN’s checks without error(s) on R4.0.1 (otherwise, there wouldn’t be a reason to archive them). Even if you succeed in building them from the sources, there is no guarantee to work as intended on your R4.0.2 installation.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
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Science Quotes

yjlee168
★★★

Kaohsiung, Taiwan,
2020-06-29 18:21
(1557 d 03:51 ago)

@ Helmut
Posting: # 21602
Views: 9,235

Packages retired from CRAN

Post reply

Dear Helmut,

❝ ❝ failed to install 'gWidgets'

❝ ❝ failed to install 'gWidgetsRGtk2'

❝

❝ These two packages were retired from CRAN ...

I don't know that. :-(

Thank Helmut. I am totally doomed and the party is over now.

❝ ... Not something I would recommend an inexperienced RUser.

Haha~ still joking.

❝ ... Since the original GUI-packages are retired, it’s up to Yung-jin to deal with the problem (i.e., adapt his packages to work with the gWidgets*2 packages).

It's not retired. It was removed from CRAN since the author did not respond, though it still works well under R v4.0.x. Hopefully it will come back again soon. It happened before as far as I can remember.

❝ @Yung-jin: “The gWidgets2 package provides a programming interface for making graphical user interfaces within R. The package is a rewrite of the gWidgets package...

gWidgets2 is a disaster to me. It's not upgraded version of gWidgets at all. It's like an add-on to gWidgets. I have tried it and the GUI just looked messed up.

—
All the best,
-- Yung-jin Lee
bear v2.9.1:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

Helmut
★★★

Vienna, Austria,
2020-06-29 19:31
(1557 d 02:41 ago)

@ yjlee168
Posting: # 21604
Views: 9,210

Packages retired from CRAN

Post reply

Hi Yung-jin,

❝ I am totally doomed and the party is over now.

Don’t Give Up

❝ ❝ ... Since the original GUI-packages are retired, …

❝ It's not retired. It was removed from CRAN since the author did not respond,…

That’s the same thing.
Retired = archived = only old sources available on CRAN = bad luck for [image]

Users requiring binaries for their OS.

❝ … though it still works well under R v4.0.x.

I believe it. I have no problems with bear 2.8.8 under R4.0.2. However, there are errors in functions (or arguments) you don’t call in you packages.

❝ Hopefully it will come back again soon. It happened before as far as I can remember.

Only if the maintainer would do what the word implies. Fix the error(s) and re-submit. Since in this case the maintainer of gWidgets* and gWidgets*2 is the same person, the last version of the former was of January 2019 and the first one the latter submitted at the same time, chances are close to nil that he will exhume the former and take care about both in parallel.

❝ gWidgets2 is a disaster to me. It's not upgraded version of gWidgets at all. It's like an add-on to gWidgets. I have tried it and the GUI just looked messed up.

My knowledge about GUIs is close to zero. I think you have still some options:

Fix the errors and submit the packages as the new maintainer. Then it would mean back to the stressful life which was a reason why you don’t host your packages at CRAN for years.
As above but host binaries (for Windows and MacOS) and the source (for Linuxes) at your site.
Jump in at the deep end and adapt your code-base to gWidgets*2. Nasty first though not that bad on the long run.

PS: Cheer up! Two stories of this year:

There was an error in package pbkrtest. CRAN’s Kurt Hornik repeatedly asked the maintainer for a fix with no reply. On Feb 19^th maintainers of dependent packages were notified that ours will be archived on Mar 4^th as well. Panic. E-mails to and fro, fixed on Feb 20^th. What if the maintainer would have been on vacation?
In the transition for R3.6.3 to R4.0.0 some tests of our package replicateBE suddenly failed and I was asked by CRAN for a fix. Why the heck? It turned out that the default singularity tolerance in package lme4 changed. Was a kind of scavenger hunt to figure that out.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

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Science Quotes

yjlee168
★★★

Kaohsiung, Taiwan,
2020-06-30 01:18
(1556 d 20:55 ago)

@ Helmut
Posting: # 21607
Views: 9,186

Packages retired from CRAN

Post reply

Dear Helmut,

❝ ❝ … though it still works well under R v4.0.x.

❝

❝ I believe it. I have no problems with bear 2.8.8 under R4.0.2. However, there are errors in functions (or arguments) you don’t call in you packages.

Good points. I just found that the source of package gWidgetRGtk2 cannot be compiled under R v4.0.2. However, the package of gWidgets can.

❝ ❝ Hopefully it will come back again soon. It happened before as far as I can remember.

❝

❝ Only if the maintainer would do what the word implies. Fix the error(s) and re-submit. Since in this case the maintainer of gWidgets* and gWidgets*2 is the same person

Correct. same author.

❝ ...

❝ Fix the errors and submit the packages as the new maintainer. Then it would mean back to the stressful life which was a reason why you don’t host your packages at CRAN for years.

right.

❝ As above but host binaries (for Windows and MacOS) and the source (for Linuxes) at your site.

I pick up this option for now.

❝ Jump in at the deep end and adapt your code-base to gWidgets*2. Nasty first though not that bad on the long run.

I am thinking tcltk since it's default GUI for R. Therefore, no extra driver is required. However, it just looks even more ugly than RGtk2 under Windows.

❝ Two stories of this year... What if the maintainer would have been on vacation?

Rule#1: no vacation for all R package developers!

❝ In the transition for R3.6.3 to R4.0.0 some tests of our package replicateBE...

really? Then I guess that it could be much more packages removed from CRAN since switching to R v4.0.0.

—
All the best,
-- Yung-jin Lee
bear v2.9.1:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

Helmut
★★★

Vienna, Austria,
2020-06-30 01:55
(1556 d 20:18 ago)

@ yjlee168
Posting: # 21608
Views: 9,132

Packages retired from CRAN

Post reply

Hi Yung-jin,

❝ I am thinking tcltk since it's default GUI for R. Therefore, no extra driver is required. However, it just looks even more ugly than RGtk2 under Windows.

Beauty is in the eye of the beholder. ;-)

❝ ❝ In the transition for R3.6.3 to R4.0.0 some tests of our package replicateBE...

❝

❝ really? Then I guess that it could be much more packages removed from CRAN since switching to R v4.0.0.

Duno. On R-help and esp. R-pkg-devel there were some confused discussions. We were very happy that the default in data.frame() is since R4.0.0 StringsAsFactors = FALSE. However, it had side-effects. If a library reads data and requires factors in a model, the old default worked. The same code in R4.0.0 terminated with an error (have to either read with StringsAsFactors = TRUE or factorize later).

Since 4.0.2 was released just 16 days after 4.0.1 I wonder whether this is all which was changed under the hood. The name “Taking Off Again” is telling.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

yjlee168
★★★

Kaohsiung, Taiwan,
2020-06-30 02:15
(1556 d 19:58 ago)

@ Helmut
Posting: # 21610
Views: 9,187

short life of R v4.0.1

Post reply

Dear Helmut,

❝ ... Since 4.0.2 was released just 16 days after 4.0.1 I wonder whether this is all which was changed under the hood. The name “Taking Off Again” is telling.

It's also about the errors of tcltk. :-D

Here are the quotes of e-mails from [email protected].

Dear Peter,



Thank you very much for this.



To clarify slightly, the bug affects not just the Rcmdr package but use of the tcltk package on Windows more generally.



Best,

 John



  -----------------------------

  John Fox, Professor Emeritus

  McMaster University

  Hamilton, Ontario, Canada

  Web: http::/socserv.mcmaster.ca/jfox



> On Jun 9, 2020, at 5:28 PM, Peter Dalgaard via R-help <[email protected]> wrote:

>

> Unfortunatly, a memory allocation bug prevented the R Commander package from working on Windows. This is fixed in R-patched, but we cannot have this not working in the official release when IT departments start installing for the Fall semester, so we need to issue a new release.

>

> Full schedule is available on developer.r-project.org.

>

> --

> Peter Dalgaard, Professor,

> Center for Statistics, Copenhagen Business School

> Solbjerg Plads 3, 2000 Frederiksberg, Denmark

> Phone: (+45)38153501

> Office: A 4.23

> Email: [email protected]  Priv: [email protected]

—
All the best,
-- Yung-jin Lee
bear v2.9.1:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

Helmut
★★★

Vienna, Austria,
2020-06-30 14:40
(1556 d 07:32 ago)

@ yjlee168
Posting: # 21616
Views: 9,132

stringsAsFactors (again)

Post reply

Hi Yung-jin,

❝ Here are the quotes of e-mails from [email protected]. […]

Not only this one…

Coming back to stringsAsFactors. A history by Kurt Hornik. The Developer Blog is interesting to get insights about ‘hidden gems’.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

yjlee168
★★★

Kaohsiung, Taiwan,
2020-07-01 03:33
(1555 d 18:40 ago)

@ Helmut
Posting: # 21625
Views: 9,038

list of removed R packages as requires 'gWidgets' or 'gWidgetsRGtk2' from CRAN

Post reply

Dear all

I just Googled around and found the following R packages were also retired/removed/archived (n = 24) together with gWidgets & gWidgetsRGtk2 (not include gWidgetstcltk) from CRAN.


removed R packages        archived on

-------------------------------------

SeqGrapheR                2020-05-20

stacomiR                  2020-05-20

CONS                      2020-05-20

ProgGUIinR                2020-04-30

WMCapacity                2020-05-20

reshapeGUI                2020-05-20

fit4NM                    2020-05-20

pcrsim                    2020-05-20

BAYESDEF                  2020-05-20

AtelieR                   2020-06-04

MissingDataGUI            2020-06-04

PKgraph                   2020-06-04

DCM                       2020-05-20

GrammR                    2020-05-20

MetSizeR                  2020-05-20

NPMOD                     2020-05-20

QVM                       2020-05-20

RQDA                      2020-05-20

Ricetl                    2020-05-20

RunuranGUI                2020-05-20

cppcor                    2020-05-20

melviewr                  2020-05-20

pcrsim                    2020-05-20

plfMA                     2020-05-20

-------------------------------------

midrangeMCP               2020-05-20

(and Unarchived/Unorphaned on 2020-06-23)

ref. link.

—
All the best,
-- Yung-jin Lee
bear v2.9.1:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

yjlee168
★★★

Kaohsiung, Taiwan,
2020-06-30 01:57
(1556 d 20:16 ago)

@ krish85
Posting: # 21609
Views: 9,389

solutions for installation 'ivivc'

Post reply

Hi krish85,

❝ ❝ Hi, try also install.packages("RGtk2").

Thank @zizou. That's correct. My fault.

Here are solutions:

download gWidgets and gWidgetsRGtk2 binary files from my Google cloud drive:
gWidgets (Windows, binary, v0.0-54.2) & gWidgetsRGtk2 (Windows, binary, v0.0-86.1). And place both zip files under your working directory. Please do not unzip these two zip files;
open R console as the system administrator. Type
install.packages("gWidgets.zip", repos=NULL)
install.packages("gWidgetsRGtk2.zip", repos=NULL)
close R console and re-open R console as the system administrator again. Then type library(RGtk2). This will pop-up a dialogue asking if install GTK+ driver. Click "install GTK+ driver." Then close R console.
finally you can install ivivc for R now. Open R console and type install.packages("ivivc_0.3.3.zip", repos=NULL)

It should work now. Sorry for the delay of these messages.

—
All the best,
-- Yung-jin Lee
bear v2.9.1:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

krish85 ☆ India, 2020-06-30 12:15 (1556 d 09:58 ago) @ yjlee168 Posting: # 21613 Views: 9,118	solutions for installation 'ivivc' Post reply
	Hi Yung-jin, Now it worked !!!!!!! Thank you so much for support and assistance !!

yjlee168 ★★★ Kaohsiung, Taiwan, 2020-06-30 16:24 (1556 d 05:49 ago) @ krish85 Posting: # 21619 Views: 9,074	solutions for installation 'ivivc' Post reply
	Hi krish85, Great to hear that. And very sorry about forgetting to turn on the function of 'file sharing' for both files. — All the best, -- Yung-jin Lee bear v2.9.1:- created by Hsin-ya Lee & Yung-jin Lee Kaohsiung, Taiwan https://www.pkpd168.com/bear Download link (updated) -> here