[R-SIG-Mac] damned Catalina - kaspersky as well!
R. Mark Sharp
rm@h@rp @end|ng |rom me@com
Sun Dec 22 06:08:38 CET 2019
I am not getting any error with Catalina 10.15.2
> install.packages("regtools", repo = "https://cloud.r-project.org")
also installing the dependency ‘dummies’
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/dummies_1.5.6.tgz'
Content type 'application/x-gzip' length 27294 bytes (26 KB)
==================================================
downloaded 26 KB
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/regtools_1.1.0.tgz'
Content type 'application/x-gzip' length 1596328 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
The downloaded binary packages are in
/var/folders/y3/5z1skj6s5tq0pktmsq6x80v80000gn/T//RtmpMKeXpC/downloaded_packages
System Software Overview:
System Version: macOS 10.15.2 (19C57)
Kernel Version: Darwin 19.2.0
Boot Volume: Macintosh HD
Boot Mode: Normal
Computer Name: prefect
User Name: R. Mark Sharp (msharp)
Secure Virtual Memory: Enabled
System Integrity Protection: Enabled
Time since boot: 3 days 19:36
Model Name: MacBook Pro
Model Identifier: MacBookPro11,3
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 157.0.0.0.0
SMC Version (system): 2.19f12
Serial Number (system): C02NN2F0G3QP
Hardware UUID: 5E2ECC0B-E7EC-5E58-97BB-2513010E6DA8
R. Mark Sharp, Ph.D.
Data Scientist and Biomedical Statistical Consultant
7526 Meadow Green St.
San Antonio, TX 78251
mobile: 210-218-2868
rmsharp using me.com
> On Dec 21, 2019, at 12:31 PM, bruno apolloni <apolloni using di.unimi.it> wrote:
>
> The antivirus kaspersky blocks the direct connection to the cloud repo. Removed antivirus -> install.packages() works.
>
> Thanks for all
>
> Bruno
>
>> Il giorno 19 dic 2019, alle ore 21:54, bruno apolloni <apolloni using di.unimi.it> ha scritto:
>>
>> Maybe, dear Luis.
>>
>> All the best
>>
>> Bruno
>>
>>> Il giorno 19 dic 2019, alle ore 20:45, Luis Puerto <luiss.puerto using gmail.com> ha scritto:
>>>
>>> Bruno, I doubt Apple is going to patch anything because the problem seems to be either on your computer or on your network.
>>>
>>> It smells to me that for example your host file, or something else, has been modified, or something in your network has also change that is blocking your access to that repository for some reason.
>>>
>>> I'm also on Catalina and as the rest I can access that repo on the browser, or any other, without a trouble.
>>>
>>> Anyhow, if you really think that the problem is on Apple side, you should contact them if you really expect them to produce any fix.
>>>
>>> Best of the lucks!
>>>
>>> Cheers!
>>> Luis
>>>
>>>> On 19 Dec 2019, at 18:50, bruno apolloni <apolloni using di.unimi.it <mailto:apolloni using di.unimi.it>> wrote:
>>>>
>>>> Ok, I surrend!
>>>>
>>>> Waiting for necessary patches by Apple, for the moment I’m comfortably running R on a Windows system.
>>>>
>>>> Thanks for all.
>>>>
>>>> Bruno
>>>>
>>>>> Il giorno 18 dic 2019, alle ore 16:46, Bob Rudis <bob using rud.is <mailto:bob using rud.is>> ha scritto:
>>>>>
>>>>> Something else changed on your system as Catalina does no domain/IP/URL blocking without user-intervention and those repo URLs work fine on all my (many) Catalina systems.
>>>>>
>>>>> What else changed after you did the Catalina install?
>>>>>
>>>>> There's a great deal wrong with Catalina, this is not one of those things.
>>>>>
>>>>>> On Dec 18, 2019, at 10:43, peter dalgaard <pdalgd using gmail.com <mailto:pdalgd using gmail.com>> wrote:
>>>>>>
>>>>>> Hmm, my best guess is that file downloads are failing somehow. It's not like, e.g.,
>>>>>>
>>>>>> https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES.gz <https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES.gz>
>>>>>>
>>>>>> is not on the website.
>>>>>>
>>>>>> Time to get scientific: Try putting a debug(download.file) and/or debug(available.packages), retry the install (or maybe just do available.packages(repos=....)), and single-step through the call to see where it goes wrong. One possibility is that you don't have write permission for the directory that it wants to download into, so figure out what the exact target is.
>>>>>>
>>>>>> -pd
>>>>>>
>>>>>>
>>>>>>> On 18 Dec 2019, at 16:05 , bruno apolloni <apolloni using di.unimi.it> wrote:
>>>>>>>
>>>>>>> Thanks for the clarification. I did it, but with the same result
>>>>>>>
>>>>>>>> install.packages("regtools", repo = "https://cloud.r-project.org")
>>>>>>> Installing package into ‘/Users/blapo_nuovo/Library/R/3.6/library’
>>>>>>> Warning: unable to access index for repository https://cloud.r-project.org/src/contrib:
>>>>>>> Warning: unable to access index for repository https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6:
>>>>>>> Warning message:
>>>>>>> package ‘regtools’ is not available (for R version 3.6.2)
>>>>>>>
>>>>>>> Cave Catalina! Me too have no problem with el-captain.
>>>>>>>
>>>>>>> Bruno
>>>>>>>
>>>>>>>> Il giorno 18 dic 2019, alle ore 15:52, Duncan Murdoch <murdoch.duncan using gmail.com> ha scritto:
>>>>>>>>
>>>>>>>> On 18/12/2019 8:43 a.m., bruno apolloni wrote:
>>>>>>>>> Do you mean that it does not work locally on my computer, but only in the cloud?
>>>>>>>>
>>>>>>>> I think he meant
>>>>>>>>
>>>>>>>> install.packages("regtools", repo = "https://cloud.r-project.org")
>>>>>>>>
>>>>>>>> which works for me (but I'm not on Catalina, I'm still on High Sierra).
>>>>>>>>
>>>>>>>> Duncan Murdoch
>>>>>>>>
>>>>>>>>> Thanks for the collaboration
>>>>>>>>> Bruno
>>>>>>>>>> Il giorno 18 dic 2019, alle ore 14:37, Rainer M Krug <Rainer using krugs.de> ha scritto:
>>>>>>>>>>
>>>>>>>>>> Just works out of the box, i.e. the cloud repo.
>>>>>>>>>>
>>>>>>>>>> PS: please CC the list in - thanks
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> On 18 Dec 2019, at 14:34, bruno apolloni <apolloni using di.unimi.it <mailto:apolloni using di.unimi.it>> wrote:
>>>>>>>>>>>
>>>>>>>>>>> I tried from many repo:
>>>>>>>>>>>
>>>>>>>>>>> https://cran.r-project.org <https://cran.r-project.org/>
>>>>>>>>>>> https://pbil.univ-lyon1.fr/CRAN/ <https://pbil.univ-lyon1.fr/CRAN/>
>>>>>>>>>>> https://cran.stat.unipd.it <https://cran.stat.unipd.it/>
>>>>>>>>>>> http://cran.mirror.garr.it/mirrors/CRAN/ <http://cran.mirror.garr.it/mirrors/CRAN/>
>>>>>>>>>>>
>>>>>>>>>>> always with the same answer:
>>>>>>>>>>>
>>>>>>>>>>> package ‘regtools’ is not available (for R version 3.6.2) .
>>>>>>>>>>>
>>>>>>>>>>> Which URL you refer to? The above links are opened in Safari.
>>>>>>>>>>>
>>>>>>>>>>> Thanks for your cooperation
>>>>>>>>>>>
>>>>>>>>>>> Bruno
>>>>>>>>>>>
>>>>>>>>>>>> Il giorno 18 dic 2019, alle ore 13:41, Rainer M Krug <Rainer using krugs.de <mailto:Rainer using krugs.de>> ha scritto:
>>>>>>>>>>>>
>>>>>>>>>>>> Also on Catalena: I can install without problems. Try a different repo? Can you open the URL in Safari?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>
>>>>>>>>>>>> Rainer
>>>>>>>>>>>>
>>>>>>>>>>>>> On 18 Dec 2019, at 13:32, bruno apolloni <apolloni using di.unimi.it <mailto:apolloni using di.unimi.it>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Any help after the Ken answer?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks a lot
>>>>>>>>>>>>> Bruno
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Inizio messaggio inoltrato:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Da: bruno apolloni <apolloni using di.unimi.it <mailto:apolloni using di.unimi.it>>
>>>>>>>>>>>>>> Oggetto: Re: [R-SIG-Mac] damned Catalina
>>>>>>>>>>>>>> Data: 18 dicembre 2019 13:30:54 CET
>>>>>>>>>>>>>> A: Ken Beath <ken using kjbeath.com.au <mailto:ken using kjbeath.com.au>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Actually, in https://cran.r-project.org/bin/macosx/ <https://cran.r-project.org/bin/macosx/> <https://cran.r-project.org/bin/macosx/ <https://cran.r-project.org/bin/macosx/>> I read;
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> For discussion of Mac-related topics and reporting Mac-specific bugs, please use the R-SIG-Mac <https://stat.ethz.ch/mailman/listinfo/r-sig-mac <https://stat.ethz.ch/mailman/listinfo/r-sig-mac>> mailing list.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Did something went wrong? Should I remove the first line of my mail? Actually, what I need is to run “regtools” on Cran R insalled on my computer. Thanks for your unsderstanding, all the best
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Bruno
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Bruno Apolloni
>>>>>>>>>>>>>> (Full Professor )
>>>>>>>>>>>>>> Dipartimento di Informatica
>>>>>>>>>>>>>> University of Milano
>>>>>>>>>>>>>> Via Comelico 39
>>>>>>>>>>>>>> 20135 Milano (Italy)
>>>>>>>>>>>>>> Tel. +39(0)2-50316284
>>>>>>>>>>>>>> Fax. +39(0)2-50316228
>>>>>>>>>>>>>> Mobile +39 333 7469878
>>>>>>>>>>>>>> e-mail: apolloni using di.unimi.it <mailto:apolloni using di.unimi.it> <mailto:apolloni using di.unimi.it <mailto:apolloni using di.unimi.it>>
>>>>>>>>>>>>>> http://homes.di.unimi.it/apolloni <http://homes.di.unimi.it/apolloni> <http://homes.di.unimi.it/apolloni <http://homes.di.unimi.it/apolloni>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Il giorno 18 dic 2019, alle ore 13:08, Ken Beath <ken using kjbeath.com.au <mailto:ken using kjbeath.com.au> <mailto:ken using kjbeath.com.au <mailto:ken using kjbeath.com.au>>> ha scritto:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Try another repository. It works fine with the main CRAN and teh RStudio repositories.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Ken
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On 18 Dec 2019, at 10:50 pm, bruno apolloni <apolloni using di.unimi.it <mailto:apolloni using di.unimi.it> <mailto:apolloni using di.unimi.it <mailto:apolloni using di.unimi.it>>> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Dear All
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> among disasters of the new operating system Catalina, this one concerns R.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Trying to install “regtools" the answer by Crane R consolle is
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> unable to access index for repository https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> The same for “devtools”. This happens on my Mac with Catalina OS. The same installation on same Crane R but on a laptop of colleauge of mine endowed with previous OS (el captain) succeeds without any problem.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Any remedy to suggest?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks a lot
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Bruno
>>>>>>>>>>>>>>>> [[alternative HTML version deleted]]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>>>>>>>> R-SIG-Mac using r-project.org <mailto:R-SIG-Mac using r-project.org> <mailto:R-SIG-Mac using r-project.org <mailto:R-SIG-Mac using r-project.org>>
>>>>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac <https://stat.ethz.ch/mailman/listinfo/r-sig-mac>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> [[alternative HTML version deleted]]
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>>>>> R-SIG-Mac using r-project.org <mailto:R-SIG-Mac using r-project.org>
>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac <https://stat.ethz.ch/mailman/listinfo/r-sig-mac>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>>>>>>>>>>>
>>>>>>>>>>>> Orcid ID: 0000-0002-7490-0066
>>>>>>>>>>>>
>>>>>>>>>>>> Department of Evolutionary Biology and Environmental Studies
>>>>>>>>>>>> University of Zürich
>>>>>>>>>>>> Office Y34-J-74
>>>>>>>>>>>> Winterthurerstrasse 190
>>>>>>>>>>>> 8075 Zürich
>>>>>>>>>>>> Switzerland
>>>>>>>>>>>>
>>>>>>>>>>>> Office: +41 (0)44 635 47 64
>>>>>>>>>>>> Cell: +41 (0)78 630 66 57
>>>>>>>>>>>> email: Rainer.Krug using uzh.ch <mailto:Rainer.Krug using uzh.ch>
>>>>>>>>>>>> Rainer using krugs.de <mailto:Rainer using krugs.de>
>>>>>>>>>>>> Skype: RMkrug
>>>>>>>>>>>>
>>>>>>>>>>>> PGP: 0x0F52F982
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>>>>>>>>>
>>>>>>>>>> Orcid ID: 0000-0002-7490-0066
>>>>>>>>>>
>>>>>>>>>> Department of Evolutionary Biology and Environmental Studies
>>>>>>>>>> University of Zürich
>>>>>>>>>> Office Y34-J-74
>>>>>>>>>> Winterthurerstrasse 190
>>>>>>>>>> 8075 Zürich
>>>>>>>>>> Switzerland
>>>>>>>>>>
>>>>>>>>>> Office: +41 (0)44 635 47 64
>>>>>>>>>> Cell: +41 (0)78 630 66 57
>>>>>>>>>> email: Rainer.Krug using uzh.ch <mailto:Rainer.Krug using uzh.ch>
>>>>>>>>>> Rainer using krugs.de <mailto:Rainer using krugs.de>
>>>>>>>>>> Skype: RMkrug
>>>>>>>>>>
>>>>>>>>>> PGP: 0x0F52F982
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> [[alternative HTML version deleted]]
>>>>>>>>> _______________________________________________
>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>> R-SIG-Mac using r-project.org
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> R-SIG-Mac using r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>> --
>>>>>> Peter Dalgaard, Professor,
>>>>>> Center for Statistics, Copenhagen Business School
>>>>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>>>>> Phone: (+45)38153501
>>>>>> Office: A 4.23
>>>>>> Email: pd.mes using cbs.dk Priv: PDalgd using gmail.com
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac using r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>
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