Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. [A screenshot of a computer error message Description automatically generated with low confidence] Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20230605/04979993/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 33129 bytes Desc: image001.png URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20230605/04979993/attachment-0001.png>
Serious problem with R on macOS
25 messages · Calboli Federico (LUKE), Uwe Ligges, Kevin E. Thorpe +8 more
Aloha. My first thought is to check and see if you can run R from the command-line.? My second thought is to create a new user and re-install R under that user and see if it's your user environment or something system-wide. Good luck. J.
On 6/5/23 08:32, DePaolis, Fernando wrote:
Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies <https://urldefense.com/v3/__http://www.middlebury.edu/institute__;!!Mih3wA!GIE6oZkYwzBt5PoPPxbVBpthifuHm4pKyHi02HQHAvGnKu_iYdp2DZf5m2H3FKKYS3LTKCPI1guQh-OMAYbw4GPH$>?at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. *From: *DePaolis, Fernando <fdepaolis at middlebury.edu> *Date: *Monday, June 5, 2023 at 10:19 AM *To: *CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> *Subject: *Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. A screenshot of a computer error message Description automatically generated with low confidence Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies <https://urldefense.com/v3/__http://www.middlebury.edu/institute__;!!Mih3wA!GIE6oZkYwzBt5PoPPxbVBpthifuHm4pKyHi02HQHAvGnKu_iYdp2DZf5m2H3FKKYS3LTKCPI1guQh-OMAYbw4GPH$>?at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!GIE6oZkYwzBt5PoPPxbVBpthifuHm4pKyHi02HQHAvGnKu_iYdp2DZf5m2H3FKKYS3LTKCPI1guQh-OMAQh6T0nQ$
John Helly / San Diego Supercomputer Center / Scripps Institution of Oceanography https://www.sdsc.edu/~hellyj / 808 205 9882 / 760 8408660 -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20230605/86dcd665/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 33129 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20230605/86dcd665/attachment-0001.png>
If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. [A screenshot of a computer error message Description automatically generated with low confidence] Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20230606/606812d5/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 33129 bytes Desc: image001.png URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20230606/606812d5/attachment-0001.png>
On 05.06.2023 20:32, DePaolis, Fernando wrote:
Uwe Ligges (from CRAN sys admin) recommended that I post this to the list.
But he did not suggest to post in html nor to post the same mail again after he asked you whether you can start R without R Studio. And he alkso aksed you to ask here only if R also fails to start without RStudio. Uwe Ligges
Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies <http://www.middlebury.edu/institute>?at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. *From: *DePaolis, Fernando <fdepaolis at middlebury.edu> *Date: *Monday, June 5, 2023 at 10:19 AM *To: *CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> *Subject: *Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. A screenshot of a computer error message Description automatically generated with low confidence Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies <http://www.middlebury.edu/institute>?at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
On 05.06.2023 20:32, DePaolis, Fernando wrote:
Uwe Ligges (from CRAN sys admin) recommended that I post this to the list.
But he did not suggest to post in html If anyone is using the Apple store Outlook (as I am forced to do), there is no way I can see I can specify to send plain text messages. This is OT, but sending html mail might not be due to willful ignorance of netiquette. BW F nor to post the same mail again after he asked you whether you can start R without R Studio. And he alkso aksed you to ask here only if R also fails to start without RStudio. Uwe Ligges
Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.middlebury.edu%2Finstitute&data=05%7C01%7Cfederico.calboli%40luke.fi%7C48dc5c6fa7d64d5c6ccd08db666a82ab%7C7c14dfa4c0fc47259f0476a443deb095%7C0%7C0%7C638216379935416394%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=79gQKXEMWmFef4bk0ZsrR6QYf7D00DOCbvS4E%2BFBYVQ%3D&reserved=0<http://www.middlebury.edu/institute>> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. *From: *DePaolis, Fernando <fdepaolis at middlebury.edu> *Date: *Monday, June 5, 2023 at 10:19 AM *To: *CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> *Subject: *Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. A screenshot of a computer error message Description automatically generated with low confidence Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.middlebury.edu%2Finstitute&data=05%7C01%7Cfederico.calboli%40luke.fi%7C48dc5c6fa7d64d5c6ccd08db666a82ab%7C7c14dfa4c0fc47259f0476a443deb095%7C0%7C0%7C638216379935416394%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=79gQKXEMWmFef4bk0ZsrR6QYf7D00DOCbvS4E%2BFBYVQ%3D&reserved=0<http://www.middlebury.edu/institute>> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfederico.calboli%40luke.fi%7C48dc5c6fa7d64d5c6ccd08db666a82ab%7C7c14dfa4c0fc47259f0476a443deb095%7C0%7C0%7C638216379935416394%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5csS2lzYA3WyVZg40tHHxY39%2BMXw1sRsRbG59sZHzCU%3D&reserved=0<https://stat.ethz.ch/mailman/listinfo/r-sig-mac>
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I had thought there was an obvious way to send plain text from Outlook, but when I saw this I checked. All I could find is an option to reply to messages in the same format received. It may be possible to send plain text from Outlook but it is certainly not obvious how. I sent this from the Apple mail client to get plain text. Apologies to the list for a second OT post in this thread, but I thought some confirmation might be valuable.
On Jun 6, 2023, at 5:35 AM, Calboli Federico (LUKE) <federico.calboli at luke.fi> wrote: On 05.06.2023 20:32, DePaolis, Fernando wrote:
Uwe Ligges (from CRAN sys admin) recommended that I post this to the list.
But he did not suggest to post in html If anyone is using the Apple store Outlook (as I am forced to do), there is no way I can see I can specify to send plain text messages. This is OT, but sending html mail might not be due to willful ignorance of netiquette. BW F nor to post the same mail again after he asked you whether you can start R without R Studio. And he alkso aksed you to ask here only if R also fails to start without RStudio. Uwe Ligges
Kevin E. Thorpe Head of Biostatistics, Applied Health Research Centre (AHRC) Li Ka Shing Knowledge Institute of St. Michael?s Hospital Assistant Professor, Dalla Lana School of Public Health University of Toronto email: kevin.thorpe at utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016
Thank you all?it is not an RStudio issue. I cannot run R from its app or the command line?It is certainly an R issue. Next time it ?uninstalls itself? I will try to install it on another user and see what happens (although I have already tried to install it ?just for me? or for all users). Thank you again, Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: Calboli Federico (LUKE) <federico.calboli at luke.fi> Date: Tuesday, June 6, 2023 at 12:54 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: Serious problem with R on macOS You don't often get email from federico.calboli at luke.fi. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.middlebury.edu%2Finstitute&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5542d3f00bbc48c2f08408db66634fb3%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638216348966308561%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jPUL7rVaeylLyvxYHvA53PlePdTwrogwM2yM686hOJ4%3D&reserved=0> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. [A screenshot of a computer error message Description automatically generated with low confidence] Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.middlebury.edu%2Finstitute&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5542d3f00bbc48c2f08408db66634fb3%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638216348966308561%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jPUL7rVaeylLyvxYHvA53PlePdTwrogwM2yM686hOJ4%3D&reserved=0> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20230606/aaa96eec/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 33129 bytes Desc: image001.png URL: <https://stat.ethz.ch/pipermail/r-sig-mac/attachments/20230606/aaa96eec/attachment-0001.png>
OK, so - OS version? - What do you do to install? - What happens when you do it? e.g.: - Monterey 12.6.5 - Downloaded R-4.3.0-x86_64.pkg from CRAN - As user with admin privilege, open from Downloads folder and follow instructions - "The installation was succesful" - Close, move to bin. I gather that on newer OS, you may need to move the installer out of Downloads first. -pd
On 6 Jun 2023, at 17:07 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: Thank you all?it is not an RStudio issue. I cannot run R from its app or the command line?It is certainly an R issue. Next time it ?uninstalls itself? I will try to install it on another user and see what happens (although I have already tried to install it ?just for me? or for all users). Thank you again, Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: Calboli Federico (LUKE) <federico.calboli at luke.fi> Date: Tuesday, June 6, 2023 at 12:54 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: Serious problem with R on macOS You don't often get email from federico.calboli at luke.fi. Learn why this is important If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. <image001.png> Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
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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 at cbs.dk Priv: PDalgd at gmail.com
OS: Ventura 13.4 (22F66) Downloaded R-4.3.0-x86_64.pkg from CRAN Installation: Successful?everything works fine Suggestion to move the installer to Trash: Declined (because I know I will need the installer again). CRAN suggests reinstalling Xquartz, which I did a few times on the onset of the symptoms (I don?t do that anymore because there sems to be no point to it). Use: I only use RStudio and everything works fine, until at a random time a few days later (or hours in a few instances), RStudio fails to ?find R?, which doesn?t run on its own or from the console. Possible emerging conflicts: At the beginning, I thought this could be happening because other software were install afterward, but that is not the case. Looked for alternatives: I couldn?t find any reference online, so I suspect this is quite specific to my machine and/or environment. About the ?environment?, I cannot think of anything, as no changes have been made, except for routine updates (which is unlikely, but not impossible to have undesirable effects). Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 8:48 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] OK, so - OS version? - What do you do to install? - What happens when you do it? e.g.: - Monterey 12.6.5 - Downloaded R-4.3.0-x86_64.pkg from CRAN - As user with admin privilege, open from Downloads folder and follow instructions - "The installation was succesful" - Close, move to bin. I gather that on newer OS, you may need to move the installer out of Downloads first. -pd
On 6 Jun 2023, at 17:07 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: Thank you all?it is not an RStudio issue. I cannot run R from its app or the command line?It is certainly an R issue. Next time it ?uninstalls itself? I will try to install it on another user and see what happens (although I have already tried to install it ?just for me? or for all users). Thank you again, Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: Calboli Federico (LUKE) <federico.calboli at luke.fi> Date: Tuesday, June 6, 2023 at 12:54 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: Serious problem with R on macOS You don't often get email from federico.calboli at luke.fi. Learn why this is important If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. <image001.png> Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5cc979bc4733413d516e08db66a57063%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638216633105243505%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=CnoJt2MouLOzMY%2Fy2S9kxHy0lweEXf5bZQ97sfZu5uQ%3D&reserved=0<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 at cbs.dk Priv: PDalgd at gmail.com
Hum... Best I can think of is to take the hint (from Simon Urbanek) and move the .pkg file from Downloads and into another folder before installing. Some system cleaner-upper or virus checker could be moving stuff around. You haven't perchance some virus scrubber running which might be restoring your executable directories to a previous state? You might want to make a note of the location and ownership of installed files, like in Peters-Air:R pd$ ls -l `which R` lrwxr-xr-x 1 root wheel 47 Jun 6 17:41 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R Peters-Air:R pd$ ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 23:47 /Library/Frameworks/R.framework/Resources/bin/R and then, if/when it stops working, see if files have disappeared or changed owner or permissions. -pd
On 6 Jun 2023, at 18:05 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: OS: Ventura 13.4 (22F66) Downloaded R-4.3.0-x86_64.pkg from CRAN Installation: Successful?everything works fine Suggestion to move the installer to Trash: Declined (because I know I will need the installer again). CRAN suggests reinstalling Xquartz, which I did a few times on the onset of the symptoms (I don?t do that anymore because there sems to be no point to it). Use: I only use RStudio and everything works fine, until at a random time a few days later (or hours in a few instances), RStudio fails to ?find R?, which doesn?t run on its own or from the console. Possible emerging conflicts: At the beginning, I thought this could be happening because other software were install afterward, but that is not the case. Looked for alternatives: I couldn?t find any reference online, so I suspect this is quite specific to my machine and/or environment. About the ?environment?, I cannot think of anything, as no changes have been made, except for routine updates (which is unlikely, but not impossible to have undesirable effects). Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 8:48 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] OK, so - OS version? - What do you do to install? - What happens when you do it? e.g.: - Monterey 12.6.5 - Downloaded R-4.3.0-x86_64.pkg from CRAN - As user with admin privilege, open from Downloads folder and follow instructions - "The installation was succesful" - Close, move to bin. I gather that on newer OS, you may need to move the installer out of Downloads first. -pd
On 6 Jun 2023, at 17:07 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: Thank you all?it is not an RStudio issue. I cannot run R from its app or the command line?It is certainly an R issue. Next time it ?uninstalls itself? I will try to install it on another user and see what happens (although I have already tried to install it ?just for me? or for all users). Thank you again, Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: Calboli Federico (LUKE) <federico.calboli at luke.fi> Date: Tuesday, June 6, 2023 at 12:54 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: Serious problem with R on macOS You don't often get email from federico.calboli at luke.fi. Learn why this is important If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. <image001.png> Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5cc979bc4733413d516e08db66a57063%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638216633105243505%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=CnoJt2MouLOzMY%2Fy2S9kxHy0lweEXf5bZQ97sfZu5uQ%3D&reserved=0
-- 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 at cbs.dk Priv: PDalgd at gmail.com
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 at cbs.dk Priv: PDalgd at gmail.com
Thank you!! I will do that. PS: No, no additional or different scrubbers/antivirus/etc have been added. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 9:50 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hum... Best I can think of is to take the hint (from Simon Urbanek) and move the .pkg file from Downloads and into another folder before installing. Some system cleaner-upper or virus checker could be moving stuff around. You haven't perchance some virus scrubber running which might be restoring your executable directories to a previous state? You might want to make a note of the location and ownership of installed files, like in Peters-Air:R pd$ ls -l `which R` lrwxr-xr-x 1 root wheel 47 Jun 6 17:41 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R Peters-Air:R pd$ ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 23:47 /Library/Frameworks/R.framework/Resources/bin/R and then, if/when it stops working, see if files have disappeared or changed owner or permissions. -pd
On 6 Jun 2023, at 18:05 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: OS: Ventura 13.4 (22F66) Downloaded R-4.3.0-x86_64.pkg from CRAN Installation: Successful?everything works fine Suggestion to move the installer to Trash: Declined (because I know I will need the installer again). CRAN suggests reinstalling Xquartz, which I did a few times on the onset of the symptoms (I don?t do that anymore because there sems to be no point to it). Use: I only use RStudio and everything works fine, until at a random time a few days later (or hours in a few instances), RStudio fails to ?find R?, which doesn?t run on its own or from the console. Possible emerging conflicts: At the beginning, I thought this could be happening because other software were install afterward, but that is not the case. Looked for alternatives: I couldn?t find any reference online, so I suspect this is quite specific to my machine and/or environment. About the ?environment?, I cannot think of anything, as no changes have been made, except for routine updates (which is unlikely, but not impossible to have undesirable effects). Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 8:48 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] OK, so - OS version? - What do you do to install? - What happens when you do it? e.g.: - Monterey 12.6.5 - Downloaded R-4.3.0-x86_64.pkg from CRAN - As user with admin privilege, open from Downloads folder and follow instructions - "The installation was succesful" - Close, move to bin. I gather that on newer OS, you may need to move the installer out of Downloads first. -pd
On 6 Jun 2023, at 17:07 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: Thank you all?it is not an RStudio issue. I cannot run R from its app or the command line?It is certainly an R issue. Next time it ?uninstalls itself? I will try to install it on another user and see what happens (although I have already tried to install it ?just for me? or for all users). Thank you again, Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: Calboli Federico (LUKE) <federico.calboli at luke.fi> Date: Tuesday, June 6, 2023 at 12:54 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: Serious problem with R on macOS You don't often get email from federico.calboli at luke.fi. Learn why this is important If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. <image001.png> Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7Cdb2e32f6b6354231b5ff08db66ae2825%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638216670441495509%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MADUiUqcBqTzwqoAW6%2FNlk8M1hZ9dWKkxolDZPqLjIE%3D&reserved=0<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 at cbs.dk Priv: PDalgd at gmail.com
-- 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 at cbs.dk Priv: PDalgd at gmail.com
Hi, I see you've gotten all kinds of R-specific suggestions and feedback, but I wonder if this might be a more fundamental problem related to the "This file cannot be found" bug that is persisting in Mac OS cf https://forums.macrumors.com/threads/updated-to-13-1-and-now-file-cant-be-found.2373951/ I haven't encountered this problem with applications, but certainly it has been a pesky problem with files. Usually trying again resolves it for files. Sarah On Tue, Jun 6, 2023 at 3:30?AM DePaolis, Fernando
<fdepaolis at middlebury.edu> wrote:
Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Sarah Goslee (she/her) http://www.numberwright.com
Thank you, Sarah. Yes, I considered this issue and continue my investigation... eagerly awaiting an OS update/upgrade that may address it. Thank you. Fernando DePaolis Dean of Academic Operations & Integration Middlebury Institute of International Studies Sent from an iOS device. Apologies for any typos.
From: Sarah Goslee <sarah.goslee at gmail.com>
Sent: Wednesday, June 7, 2023 6:44:14 AM
To: DePaolis, Fernando <fdepaolis at middlebury.edu>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] FW: Serious problem with R on macOS
Sent: Wednesday, June 7, 2023 6:44:14 AM
To: DePaolis, Fernando <fdepaolis at middlebury.edu>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] FW: Serious problem with R on macOS
[You don't often get email from sarah.goslee at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hi, I see you've gotten all kinds of R-specific suggestions and feedback, but I wonder if this might be a more fundamental problem related to the "This file cannot be found" bug that is persisting in Mac OS cf https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforums.macrumors.com%2Fthreads%2Fupdated-to-13-1-and-now-file-cant-be-found.2373951%2F&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5f2e3459c8614b1aa1ea08db675d5958%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638217423910361537%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=4JrHrAfBf%2Bok5%2B5jNbWkrZ%2ByrVksNrOFR%2F%2FX0ZLkbss%3D&reserved=0<https://forums.macrumors.com/threads/updated-to-13-1-and-now-file-cant-be-found.2373951/> I haven't encountered this problem with applications, but certainly it has been a pesky problem with files. Usually trying again resolves it for files. Sarah On Tue, Jun 6, 2023 at 3:30?AM DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: > > Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. > > > > Thank you. > > > > > > > > Fernando DePaolis, Ph.D. > Dean of Academic Operations & Integration > > Associate Professor > > Middlebury Institute of International Studies at Monterey > ---------------------------------------------------------------------- > > [Sent from Outlook for Mac ?MacBook Pro] > > My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. > > > > From: DePaolis, Fernando <fdepaolis at middlebury.edu> > Date: Monday, June 5, 2023 at 10:19 AM > To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> > Subject: Serious problem with R on macOS > > Hello, > > For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. > > > > I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. > > Have you ever heard of a problem like this? Or do you have any suggestions? > > > > Thank you so much for your support. > > > > > > > > > > > > Fernando DePaolis, Ph.D. > Dean of Academic Operations & Integration > > Associate Professor > > Middlebury Institute of International Studies at Monterey > ---------------------------------------------------------------------- > > [Sent from Outlook for Mac ?MacBook Pro] > > My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5f2e3459c8614b1aa1ea08db675d5958%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638217423910361537%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=O%2FNlo4VTihX%2FJlBfDt71w85APPNPcCF6jAi5aQiwNvk%3D&reserved=0<https://stat.ethz.ch/mailman/listinfo/r-sig-mac> -- Sarah Goslee (she/her) https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.numberwright.com%2F&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5f2e3459c8614b1aa1ea08db675d5958%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638217423910361537%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=CIiyFlGprDx2%2BmAT5ToUyPq0jFQ8vG6%2F7CUV7%2F1hopM%3D&reserved=0<http://www.numberwright.com/>
NOTE: I only have the problem with R. No other app or file has been impacted. That's why I started the R route. Fernando DePaolis Dean of Academic Operations & Integration Middlebury Institute of International Studies Sent from an iOS device. Apologies for any typos.
From: DePaolis, Fernando <fdepaolis at middlebury.edu>
Sent: Wednesday, June 7, 2023 7:25:55 AM
To: Sarah Goslee <sarah.goslee at gmail.com>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] FW: Serious problem with R on macOS
Sent: Wednesday, June 7, 2023 7:25:55 AM
To: Sarah Goslee <sarah.goslee at gmail.com>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] FW: Serious problem with R on macOS
Thank you, Sarah. Yes, I considered this issue and continue my investigation... eagerly awaiting an OS update/upgrade that may address it. Thank you. Fernando DePaolis Dean of Academic Operations & Integration Middlebury Institute of International Studies Sent from an iOS device. Apologies for any typos. ________________________________ From: Sarah Goslee <sarah.goslee at gmail.com> Sent: Wednesday, June 7, 2023 6:44:14 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] FW: Serious problem with R on macOS [You don't often get email from sarah.goslee at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hi, I see you've gotten all kinds of R-specific suggestions and feedback, but I wonder if this might be a more fundamental problem related to the "This file cannot be found" bug that is persisting in Mac OS cf https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforums.macrumors.com%2Fthreads%2Fupdated-to-13-1-and-now-file-cant-be-found.2373951%2F&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5f2e3459c8614b1aa1ea08db675d5958%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638217423910361537%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=4JrHrAfBf%2Bok5%2B5jNbWkrZ%2ByrVksNrOFR%2F%2FX0ZLkbss%3D&reserved=0<https://forums.macrumors.com/threads/updated-to-13-1-and-now-file-cant-be-found.2373951/> I haven't encountered this problem with applications, but certainly it has been a pesky problem with files. Usually trying again resolves it for files. Sarah On Tue, Jun 6, 2023 at 3:30?AM DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: > > Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. > > > > Thank you. > > > > > > > > Fernando DePaolis, Ph.D. > Dean of Academic Operations & Integration > > Associate Professor > > Middlebury Institute of International Studies at Monterey > ---------------------------------------------------------------------- > > [Sent from Outlook for Mac ?MacBook Pro] > > My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. > > > > From: DePaolis, Fernando <fdepaolis at middlebury.edu> > Date: Monday, June 5, 2023 at 10:19 AM > To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> > Subject: Serious problem with R on macOS > > Hello, > > For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. > > > > I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. > > Have you ever heard of a problem like this? Or do you have any suggestions? > > > > Thank you so much for your support. > > > > > > > > > > > > Fernando DePaolis, Ph.D. > Dean of Academic Operations & Integration > > Associate Professor > > Middlebury Institute of International Studies at Monterey > ---------------------------------------------------------------------- > > [Sent from Outlook for Mac ?MacBook Pro] > > My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5f2e3459c8614b1aa1ea08db675d5958%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638217423910361537%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=O%2FNlo4VTihX%2FJlBfDt71w85APPNPcCF6jAi5aQiwNvk%3D&reserved=0<https://stat.ethz.ch/mailman/listinfo/r-sig-mac> -- Sarah Goslee (she/her) https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.numberwright.com%2F&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C5f2e3459c8614b1aa1ea08db675d5958%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638217423910361537%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=CIiyFlGprDx2%2BmAT5ToUyPq0jFQ8vG6%2F7CUV7%2F1hopM%3D&reserved=0<http://www.numberwright.com/>
Fernando, I don't think you posted the error you get when running R on the command line - can you copy/paste what you get when running R in the Terminal? Similarly, do you also get an error when running the R app (in Applications)? Cheers, Simon
On 6/06/2023, at 6:32 AM, DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. <image001.png> Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Hi Simon, You're right, I didn't post it...I'll make sure I do next time it happens...it's working fine for now... Thank you. Fernando DePaolis Dean Of Academic Operations & Integration Middlebury Institute of International Studies Sent from Outlook for iOS<https://aka.ms/o0ukef>. Apologies for any typos.
From: Simon Urbanek <simon.urbanek at R-project.org>
Sent: Wednesday, June 7, 2023 6:08:12 PM
To: DePaolis, Fernando <fdepaolis at middlebury.edu>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
Sent: Wednesday, June 7, 2023 6:08:12 PM
To: DePaolis, Fernando <fdepaolis at middlebury.edu>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
[You don't often get email from simon.urbanek at r-project.org. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Fernando, I don't think you posted the error you get when running R on the command line - can you copy/paste what you get when running R in the Terminal? Similarly, do you also get an error when running the R app (in Applications)? Cheers, Simon > On 6/06/2023, at 6:32 AM, DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: > > Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. > > > > Thank you. > > > > > > > > Fernando DePaolis, Ph.D. > Dean of Academic Operations & Integration > > Associate Professor > > Middlebury Institute of International Studies at Monterey > ---------------------------------------------------------------------- > > [Sent from Outlook for Mac ?MacBook Pro] > > My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. > > > > From: DePaolis, Fernando <fdepaolis at middlebury.edu> > Date: Monday, June 5, 2023 at 10:19 AM > To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> > Subject: Serious problem with R on macOS > > Hello, > > For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. > > > > I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. > > Have you ever heard of a problem like this? Or do you have any suggestions? > > > > Thank you so much for your support. > > > > > > <image001.png> > > > > > > > Fernando DePaolis, Ph.D. > Dean of Academic Operations & Integration > > Associate Professor > > Middlebury Institute of International Studies at Monterey > ---------------------------------------------------------------------- > > [Sent from Outlook for Mac ?MacBook Pro] > > My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C1933a4014d694b960ff508db67bcd820%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638217833038696753%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PmiFTg6WTZGeIn4qrF2ywWELCkxO6ennzN8XWzUvRFQ%3D&reserved=0<https://stat.ethz.ch/mailman/listinfo/r-sig-mac>
?well?here it goes again?it failed just now. This is the message I get when I try to run R from the command line on my mac
fernandodepaolis at MacBook-Pro-2 ~ % R
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.
During startup - Warning message:
package ?datasets? in options("defaultPackages") was not found
Error in loadNamespace(name) : object 'pkgInfo' not found
In addition: Warning message:
In loadNamespace(name) : package ?compiler? has no 'package.rds' in Meta/
Fatal error: unable to initialize the JIT
There was no ?message? of any sort when trying to run R.app. There was a brief flickering (like quick blinking) but nothing else.
Thank you!
Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey
----------------------------------------------------------------------
[Sent from Outlook for Mac ?MacBook Pro]
My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
From: DePaolis, Fernando <fdepaolis at middlebury.edu>
Date: Wednesday, June 7, 2023 at 9:13 PM
To: Simon Urbanek <simon.urbanek at R-project.org>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
Hi Simon,
You're right, I didn't post it...I'll make sure I do next time it happens...it's working fine for now...
Thank you.
Fernando DePaolis
Dean Of Academic Operations & Integration
Middlebury Institute of International Studies
Sent from Outlook for iOS<https://aka.ms/o0ukef>. Apologies for any typos.
From: Simon Urbanek <simon.urbanek at R-project.org>
Sent: Wednesday, June 7, 2023 6:08:12 PM
To: DePaolis, Fernando <fdepaolis at middlebury.edu>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
Sent: Wednesday, June 7, 2023 6:08:12 PM
To: DePaolis, Fernando <fdepaolis at middlebury.edu>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
[You don't often get email from simon.urbanek at r-project.org. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Fernando, I don't think you posted the error you get when running R on the command line - can you copy/paste what you get when running R in the Terminal? Similarly, do you also get an error when running the R app (in Applications)? Cheers, Simon > On 6/06/2023, at 6:32 AM, DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: > > Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. > > > > Thank you. > > > > > > > > Fernando DePaolis, Ph.D. > Dean of Academic Operations & Integration > > Associate Professor > > Middlebury Institute of International Studies at Monterey > ---------------------------------------------------------------------- > > [Sent from Outlook for Mac ?MacBook Pro] > > My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. > > > > From: DePaolis, Fernando <fdepaolis at middlebury.edu> > Date: Monday, June 5, 2023 at 10:19 AM > To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> > Subject: Serious problem with R on macOS > > Hello, > > For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. > > > > I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. > > Have you ever heard of a problem like this? Or do you have any suggestions? > > > > Thank you so much for your support. > > > > > > <image001.png> > > > > > > > Fernando DePaolis, Ph.D. > Dean of Academic Operations & Integration > > Associate Professor > > Middlebury Institute of International Studies at Monterey > ---------------------------------------------------------------------- > > [Sent from Outlook for Mac ?MacBook Pro] > > My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac at r-project.org > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7C1933a4014d694b960ff508db67bcd820%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638217833038696753%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PmiFTg6WTZGeIn4qrF2ywWELCkxO6ennzN8XWzUvRFQ%3D&reserved=0<https://stat.ethz.ch/mailman/listinfo/r-sig-mac>
This is what I get after the current failure, where neither R.app nor the call from the command line work. fernandodepaolis at MacBook-Pro-2 ~ % ls -l `which R` lrwxr-xr-x 1 root admin 47 Jun 5 10:23 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R fernandodepaolis at MacBook-Pro-2 ~ % ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 14:47 /Library/Frameworks/R.framework/Resources/bin/R which is identical to what I got when it was working fine a couple of days ago. Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Tuesday, June 6, 2023 at 10:20 AM To: peter dalgaard <pdalgd at gmail.com> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS Thank you!! I will do that. PS: No, no additional or different scrubbers/antivirus/etc have been added. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 9:50 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hum... Best I can think of is to take the hint (from Simon Urbanek) and move the .pkg file from Downloads and into another folder before installing. Some system cleaner-upper or virus checker could be moving stuff around. You haven't perchance some virus scrubber running which might be restoring your executable directories to a previous state? You might want to make a note of the location and ownership of installed files, like in Peters-Air:R pd$ ls -l `which R` lrwxr-xr-x 1 root wheel 47 Jun 6 17:41 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R Peters-Air:R pd$ ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 23:47 /Library/Frameworks/R.framework/Resources/bin/R and then, if/when it stops working, see if files have disappeared or changed owner or permissions. -pd
On 6 Jun 2023, at 18:05 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: OS: Ventura 13.4 (22F66) Downloaded R-4.3.0-x86_64.pkg from CRAN Installation: Successful?everything works fine Suggestion to move the installer to Trash: Declined (because I know I will need the installer again). CRAN suggests reinstalling Xquartz, which I did a few times on the onset of the symptoms (I don?t do that anymore because there sems to be no point to it). Use: I only use RStudio and everything works fine, until at a random time a few days later (or hours in a few instances), RStudio fails to ?find R?, which doesn?t run on its own or from the console. Possible emerging conflicts: At the beginning, I thought this could be happening because other software were install afterward, but that is not the case. Looked for alternatives: I couldn?t find any reference online, so I suspect this is quite specific to my machine and/or environment. About the ?environment?, I cannot think of anything, as no changes have been made, except for routine updates (which is unlikely, but not impossible to have undesirable effects). Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 8:48 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] OK, so - OS version? - What do you do to install? - What happens when you do it? e.g.: - Monterey 12.6.5 - Downloaded R-4.3.0-x86_64.pkg from CRAN - As user with admin privilege, open from Downloads folder and follow instructions - "The installation was succesful" - Close, move to bin. I gather that on newer OS, you may need to move the installer out of Downloads first. -pd
On 6 Jun 2023, at 17:07 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: Thank you all?it is not an RStudio issue. I cannot run R from its app or the command line?It is certainly an R issue. Next time it ?uninstalls itself? I will try to install it on another user and see what happens (although I have already tried to install it ?just for me? or for all users). Thank you again, Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: Calboli Federico (LUKE) <federico.calboli at luke.fi> Date: Tuesday, June 6, 2023 at 12:54 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: Serious problem with R on macOS You don't often get email from federico.calboli at luke.fi. Learn why this is important If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. <image001.png> Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7Cdb2e32f6b6354231b5ff08db66ae2825%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638216670441495509%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MADUiUqcBqTzwqoAW6%2FNlk8M1hZ9dWKkxolDZPqLjIE%3D&reserved=0<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 at cbs.dk Priv: PDalgd at gmail.com
-- 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 at cbs.dk Priv: PDalgd at gmail.com
On Thu, Jun 8, 2023 at 10:43?AM DePaolis, Fernando <fdepaolis at middlebury.edu> wrote:
This is what I get after the current failure, where neither R.app nor the call from the command line work. fernandodepaolis at MacBook-Pro-2 ~ % ls -l `which R` lrwxr-xr-x 1 root admin 47 Jun 5 10:23 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R .... If you open up the "Console" app you should have access to the system
logs, which might have some useful hints about what is actually failing, or leading up to the failure.
This is what I got when trying to run R from the console
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.
During startup - Warning message:
package ?datasets? in options("defaultPackages") was not found
Error in loadNamespace(name) : object 'pkgInfo' not found
In addition: Warning message:
In loadNamespace(name) : package ?compiler? has no 'package.rds' in Meta/
Fatal error: unable to initialize the JIT
Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey
----------------------------------------------------------------------
[Sent from Outlook for Mac ?MacBook Pro]
My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
From: Keith Bierman <khbkhb at gmail.com>
Date: Thursday, June 8, 2023 at 9:51 AM
To: DePaolis, Fernando <fdepaolis at middlebury.edu>
Cc: peter dalgaard <pdalgd at gmail.com>, r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
You don't often get email from khbkhb at gmail.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
On Thu, Jun 8, 2023 at 10:43?AM DePaolis, Fernando <fdepaolis at middlebury.edu<mailto:fdepaolis at middlebury.edu>> wrote:
This is what I get after the current failure, where neither R.app nor the call from the command line work. fernandodepaolis at MacBook-Pro-2 ~ % ls -l `which R` lrwxr-xr-x 1 root admin 47 Jun 5 10:23 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R .... If you open up the "Console" app you should have access to the system logs, which might have some useful hints about what is actually failing, or leading up to the failure.
Not clear why there is a symbolic link.? Maybe try using the fullpath name to invoke R and see if that works.? It seems to me that 'sometimes', on OSX, some symbolic links behave oddly.? This may be related to the Privacy/Security settings but I don't have any clear understanding of what's going on. J.
On 6/8/23 06:37, DePaolis, Fernando wrote:
This is what I get after the current failure, where neither R.app nor the call from the command line work. fernandodepaolis at MacBook-Pro-2 ~ % ls -l `which R` lrwxr-xr-x 1 root admin 47 Jun 5 10:23 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R fernandodepaolis at MacBook-Pro-2 ~ % ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 14:47 /Library/Frameworks/R.framework/Resources/bin/R which is identical to what I got when it was working fine a couple of days ago. Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<https://urldefense.com/v3/__http://www.middlebury.edu/institute__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26qcicJyf$ > at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Tuesday, June 6, 2023 at 10:20 AM To: peter dalgaard <pdalgd at gmail.com> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS Thank you!! I will do that. PS: No, no additional or different scrubbers/antivirus/etc have been added. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<https://urldefense.com/v3/__http://www.middlebury.edu/institute__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26qcicJyf$ > at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 9:50 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26tXIOdrG$ ] Hum... Best I can think of is to take the hint (from Simon Urbanek) and move the .pkg file from Downloads and into another folder before installing. Some system cleaner-upper or virus checker could be moving stuff around. You haven't perchance some virus scrubber running which might be restoring your executable directories to a previous state? You might want to make a note of the location and ownership of installed files, like in Peters-Air:R pd$ ls -l `which R` lrwxr-xr-x 1 root wheel 47 Jun 6 17:41 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R Peters-Air:R pd$ ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 23:47 /Library/Frameworks/R.framework/Resources/bin/R and then, if/when it stops working, see if files have disappeared or changed owner or permissions. -pd
On 6 Jun 2023, at 18:05 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: OS: Ventura 13.4 (22F66) Downloaded R-4.3.0-x86_64.pkg from CRAN Installation: Successful?everything works fine Suggestion to move the installer to Trash: Declined (because I know I will need the installer again). CRAN suggests reinstalling Xquartz, which I did a few times on the onset of the symptoms (I don?t do that anymore because there sems to be no point to it). Use: I only use RStudio and everything works fine, until at a random time a few days later (or hours in a few instances), RStudio fails to ?find R?, which doesn?t run on its own or from the console. Possible emerging conflicts: At the beginning, I thought this could be happening because other software were install afterward, but that is not the case. Looked for alternatives: I couldn?t find any reference online, so I suspect this is quite specific to my machine and/or environment. About the ?environment?, I cannot think of anything, as no changes have been made, except for routine updates (which is unlikely, but not impossible to have undesirable effects). Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 8:48 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26tXIOdrG$ ] OK, so - OS version? - What do you do to install? - What happens when you do it? e.g.: - Monterey 12.6.5 - Downloaded R-4.3.0-x86_64.pkg from CRAN - As user with admin privilege, open from Downloads folder and follow instructions - "The installation was succesful" - Close, move to bin. I gather that on newer OS, you may need to move the installer out of Downloads first. -pd
On 6 Jun 2023, at 17:07 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: Thank you all?it is not an RStudio issue. I cannot run R from its app or the command line?It is certainly an R issue. Next time it ?uninstalls itself? I will try to install it on another user and see what happens (although I have already tried to install it ?just for me? or for all users). Thank you again, Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: Calboli Federico (LUKE) <federico.calboli at luke.fi> Date: Tuesday, June 6, 2023 at 12:54 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: Serious problem with R on macOS You don't often get email from federico.calboli at luke.fi. Learn why this is important If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. <image001.png> Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
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-- 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 at cbs.dk Priv: PDalgd at gmail.com
-- 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 at cbs.dk Priv: PDalgd at gmail.com [[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26vBFIhq6$
John Helly / San Diego Supercomputer Center / Scripps Institution of Oceanography https://www.sdsc.edu/~hellyj / 808 205 9882 / 760 8408660
The symbolic link is the standard way R is installed on a Mac. It's
installed as a "framework", but the symlink in /usr/local/bin/R makes
Unix-like tools see it as a standard program, which is what you want
from the terminal.
The warnings and errors Fernando was seeing, like
package ?datasets? in options("defaultPackages") was not found
make it look as though the framework is broken. I have no idea how that
would happen. Maybe he'll learn more by running
.libPaths()
in R. It should print something like
[1] "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library"
but maybe not identical to that. Running ls on that directory in the
terminal should list all the installed packages (including datasets and
everything else that is supposed to be installed).
Duncan Murdoch
On 08/06/2023 3:16 p.m., John Helly via R-SIG-Mac wrote:
Not clear why there is a symbolic link.? Maybe try using the fullpath name to invoke R and see if that works.? It seems to me that 'sometimes', on OSX, some symbolic links behave oddly.? This may be related to the Privacy/Security settings but I don't have any clear understanding of what's going on. J. On 6/8/23 06:37, DePaolis, Fernando wrote:
This is what I get after the current failure, where neither R.app nor the call from the command line work. fernandodepaolis at MacBook-Pro-2 ~ % ls -l `which R` lrwxr-xr-x 1 root admin 47 Jun 5 10:23 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R fernandodepaolis at MacBook-Pro-2 ~ % ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 14:47 /Library/Frameworks/R.framework/Resources/bin/R which is identical to what I got when it was working fine a couple of days ago. Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<https://urldefense.com/v3/__http://www.middlebury.edu/institute__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26qcicJyf$ > at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Tuesday, June 6, 2023 at 10:20 AM To: peter dalgaard <pdalgd at gmail.com> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS Thank you!! I will do that. PS: No, no additional or different scrubbers/antivirus/etc have been added. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies<https://urldefense.com/v3/__http://www.middlebury.edu/institute__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26qcicJyf$ > at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 9:50 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26tXIOdrG$ ] Hum... Best I can think of is to take the hint (from Simon Urbanek) and move the .pkg file from Downloads and into another folder before installing. Some system cleaner-upper or virus checker could be moving stuff around. You haven't perchance some virus scrubber running which might be restoring your executable directories to a previous state? You might want to make a note of the location and ownership of installed files, like in Peters-Air:R pd$ ls -l `which R` lrwxr-xr-x 1 root wheel 47 Jun 6 17:41 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R Peters-Air:R pd$ ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 23:47 /Library/Frameworks/R.framework/Resources/bin/R and then, if/when it stops working, see if files have disappeared or changed owner or permissions. -pd
On 6 Jun 2023, at 18:05 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: OS: Ventura 13.4 (22F66) Downloaded R-4.3.0-x86_64.pkg from CRAN Installation: Successful?everything works fine Suggestion to move the installer to Trash: Declined (because I know I will need the installer again). CRAN suggests reinstalling Xquartz, which I did a few times on the onset of the symptoms (I don?t do that anymore because there sems to be no point to it). Use: I only use RStudio and everything works fine, until at a random time a few days later (or hours in a few instances), RStudio fails to ?find R?, which doesn?t run on its own or from the console. Possible emerging conflicts: At the beginning, I thought this could be happening because other software were install afterward, but that is not the case. Looked for alternatives: I couldn?t find any reference online, so I suspect this is quite specific to my machine and/or environment. About the ?environment?, I cannot think of anything, as no changes have been made, except for routine updates (which is unlikely, but not impossible to have undesirable effects). Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 8:48 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26tXIOdrG$ ] OK, so - OS version? - What do you do to install? - What happens when you do it? e.g.: - Monterey 12.6.5 - Downloaded R-4.3.0-x86_64.pkg from CRAN - As user with admin privilege, open from Downloads folder and follow instructions - "The installation was succesful" - Close, move to bin. I gather that on newer OS, you may need to move the installer out of Downloads first. -pd
On 6 Jun 2023, at 17:07 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: Thank you all?it is not an RStudio issue. I cannot run R from its app or the command line?It is certainly an R issue. Next time it ?uninstalls itself? I will try to install it on another user and see what happens (although I have already tried to install it ?just for me? or for all users). Thank you again, Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: Calboli Federico (LUKE) <federico.calboli at luke.fi> Date: Tuesday, June 6, 2023 at 12:54 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: Serious problem with R on macOS You don't often get email from federico.calboli at luke.fi. Learn why this is important If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. <image001.png> Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://urldefense.com/v3/__https://nam02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fstat.ethz.ch*2Fmailman*2Flistinfo*2Fr-sig-mac&data=05*7C01*7Cfdepaolis*40middlebury.edu*7Cdb2e32f6b6354231b5ff08db66ae2825*7Ca1bb0a191576421dbe93b3a7d4b6dcaa*7C1*7C0*7C638216670441495509*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=MADUiUqcBqTzwqoAW6*2FNlk8M1hZ9dWKkxolDZPqLjIE*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26tAaI22e$ <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26vBFIhq6$ >
-- 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 at cbs.dk Priv: PDalgd at gmail.com
-- 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 at cbs.dk Priv: PDalgd at gmail.com [[alternative HTML version deleted]]
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!Fr3HvZOZi4Vn9PoE48tKxAfj3AtOpcj4qLfq1EJ9yNCh3wNtCoPAjKvY7X98gkORFUN5nZHSXmGRARZ26vBFIhq6$
Yes, this is consistent with the fact that R starts for you. Some other files seem to have gone missing though, notably the datasets and compiler package, so that R does not get very far before givinng up the ghost. The pattern of recently created files disappearing is worrying, but not likely due to anything that R itself is doing. It is quite possible that you have a disk error, either physical or logical (inconsistent file system state), or it could be the OS error that Sarah was alluding to. You might want to try the First Aid option in the Disc Utility app (possibly enlist a local expert). - Peter
On 8 Jun 2023, at 18:37 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: This is what I get after the current failure, where neither R.app nor the call from the command line work. fernandodepaolis at MacBook-Pro-2 ~ % ls -l `which R` lrwxr-xr-x 1 root admin 47 Jun 5 10:23 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R fernandodepaolis at MacBook-Pro-2 ~ % ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 14:47 /Library/Frameworks/R.framework/Resources/bin/R which is identical to what I got when it was working fine a couple of days ago. Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Tuesday, June 6, 2023 at 10:20 AM To: peter dalgaard <pdalgd at gmail.com> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS Thank you!! I will do that. PS: No, no additional or different scrubbers/antivirus/etc have been added. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 9:50 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hum... Best I can think of is to take the hint (from Simon Urbanek) and move the .pkg file from Downloads and into another folder before installing. Some system cleaner-upper or virus checker could be moving stuff around. You haven't perchance some virus scrubber running which might be restoring your executable directories to a previous state? You might want to make a note of the location and ownership of installed files, like in Peters-Air:R pd$ ls -l `which R` lrwxr-xr-x 1 root wheel 47 Jun 6 17:41 /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R Peters-Air:R pd$ ls -l /Library/Frameworks/R.framework/Resources/bin/R -rwxrwxr-x 1 root admin 9196 Apr 21 23:47 /Library/Frameworks/R.framework/Resources/bin/R and then, if/when it stops working, see if files have disappeared or changed owner or permissions. -pd
On 6 Jun 2023, at 18:05 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: OS: Ventura 13.4 (22F66) Downloaded R-4.3.0-x86_64.pkg from CRAN Installation: Successful?everything works fine Suggestion to move the installer to Trash: Declined (because I know I will need the installer again). CRAN suggests reinstalling Xquartz, which I did a few times on the onset of the symptoms (I don?t do that anymore because there sems to be no point to it). Use: I only use RStudio and everything works fine, until at a random time a few days later (or hours in a few instances), RStudio fails to ?find R?, which doesn?t run on its own or from the console. Possible emerging conflicts: At the beginning, I thought this could be happening because other software were install afterward, but that is not the case. Looked for alternatives: I couldn?t find any reference online, so I suspect this is quite specific to my machine and/or environment. About the ?environment?, I cannot think of anything, as no changes have been made, except for routine updates (which is unlikely, but not impossible to have undesirable effects). Thank you Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: peter dalgaard <pdalgd at gmail.com> Date: Tuesday, June 6, 2023 at 8:48 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu> Cc: Calboli Federico (LUKE) <federico.calboli at luke.fi>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS [You don't often get email from pdalgd at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] OK, so - OS version? - What do you do to install? - What happens when you do it? e.g.: - Monterey 12.6.5 - Downloaded R-4.3.0-x86_64.pkg from CRAN - As user with admin privilege, open from Downloads folder and follow instructions - "The installation was succesful" - Close, move to bin. I gather that on newer OS, you may need to move the installer out of Downloads first. -pd
On 6 Jun 2023, at 17:07 , DePaolis, Fernando <fdepaolis at middlebury.edu> wrote: Thank you all?it is not an RStudio issue. I cannot run R from its app or the command line?It is certainly an R issue. Next time it ?uninstalls itself? I will try to install it on another user and see what happens (although I have already tried to install it ?just for me? or for all users). Thank you again, Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: Calboli Federico (LUKE) <federico.calboli at luke.fi> Date: Tuesday, June 6, 2023 at 12:54 AM To: DePaolis, Fernando <fdepaolis at middlebury.edu>, r-sig-mac at r-project.org <r-sig-mac at r-project.org> Subject: Re: Serious problem with R on macOS You don't often get email from federico.calboli at luke.fi. Learn why this is important If you can use R.app or R on the terminal, it is a R studio bug. Have you tested? Also, ?reinstall? works best after removing all actual files, such as the whole ~/.R, all the ~/.R* files, and whatever R studio might add. BW F Federico Calboli Tutkija Genomiikka ja jalostus Luonnonvarakeskus Uwe Ligges (from CRAN sys admin) recommended that I post this to the list. Thank you. Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated. From: DePaolis, Fernando <fdepaolis at middlebury.edu> Date: Monday, June 5, 2023 at 10:19 AM To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org> Subject: Serious problem with R on macOS Hello, For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R. I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either. Have you ever heard of a problem like this? Or do you have any suggestions? Thank you so much for your support. <image001.png> Fernando DePaolis, Ph.D. Dean of Academic Operations & Integration Associate Professor Middlebury Institute of International Studies at Monterey ---------------------------------------------------------------------- [Sent from Outlook for Mac ?MacBook Pro] My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-mac&data=05%7C01%7Cfdepaolis%40middlebury.edu%7Cdb2e32f6b6354231b5ff08db66ae2825%7Ca1bb0a191576421dbe93b3a7d4b6dcaa%7C1%7C0%7C638216670441495509%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MADUiUqcBqTzwqoAW6%2FNlk8M1hZ9dWKkxolDZPqLjIE%3D&reserved=0
-- 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 at cbs.dk Priv: PDalgd at gmail.com
-- 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 at cbs.dk Priv: PDalgd at gmail.com
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 at cbs.dk Priv: PDalgd at gmail.com
On 6/8/23 09:33, DePaolis, Fernando wrote:
?well?here it goes again?it failed just now. This is the message I get when I try to run R from the command line on my mac
You were advised to try using Disk Utility / First Aid. Have you done so yet? ?(You are getting intermittent errors accessing base packages. So this may just be a flakey disk sector.)
David.
>
>
> fernandodepaolis at MacBook-Pro-2 ~ % R
>
>
>
> R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
>
> Copyright (C) 2023 The R Foundation for Statistical Computing
>
> Platform: x86_64-apple-darwin20 (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.
>
>
>
> During startup - Warning message:
>
> package ?datasets? in options("defaultPackages") was not found
>
> Error in loadNamespace(name) : object 'pkgInfo' not found
>
> In addition: Warning message:
>
> In loadNamespace(name) : package ?compiler? has no 'package.rds' in Meta/
>
> Fatal error: unable to initialize the JIT
>
>
>
> There was no ?message? of any sort when trying to run R.app. There was a brief flickering (like quick blinking) but nothing else.
>
> Thank you!
>
>
> Fernando DePaolis, Ph.D.
> Dean of Academic Operations & Integration
> Associate Professor
> Middlebury Institute of International Studies<http://www.middlebury.edu/institute> at Monterey
> ----------------------------------------------------------------------
> [Sent from Outlook for Mac ?MacBook Pro]
> My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
>
> From: DePaolis, Fernando <fdepaolis at middlebury.edu>
> Date: Wednesday, June 7, 2023 at 9:13 PM
> To: Simon Urbanek <simon.urbanek at R-project.org>
> Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
> Hi Simon,
> You're right, I didn't post it...I'll make sure I do next time it happens...it's working fine for now...
>
> Thank you.
>
>
>
> Fernando DePaolis
> Dean Of Academic Operations & Integration
> Middlebury Institute of International Studies
>
> Sent from Outlook for iOS<https://aka.ms/o0ukef>. Apologies for any typos.
>
> ________________________________
> From: Simon Urbanek <simon.urbanek at R-project.org>
> Sent: Wednesday, June 7, 2023 6:08:12 PM
> To: DePaolis, Fernando <fdepaolis at middlebury.edu>
> Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
> Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
>
> [You don't often get email from simon.urbanek at r-project.org. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
>
> Fernando,
>
> I don't think you posted the error you get when running R on the command line - can you copy/paste what you get when running R in the Terminal? Similarly, do you also get an error when running the R app (in Applications)?
>
> Cheers,
> Simon
>
>
>
>> On 6/06/2023, at 6:32 AM, DePaolis, Fernando <fdepaolis at middlebury.edu> wrote:
>>
>> Uwe Ligges (from CRAN sys admin) recommended that I post this to the list.
>>
>>
>>
>> Thank you.
>>
>>
>>
>>
>>
>>
>>
>> Fernando DePaolis, Ph.D.
>> Dean of Academic Operations & Integration
>>
>> Associate Professor
>>
>> Middlebury Institute of International Studies at Monterey
>> ----------------------------------------------------------------------
>>
>> [Sent from Outlook for Mac ?MacBook Pro]
>>
>> My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
>>
>>
>>
>> From: DePaolis, Fernando <fdepaolis at middlebury.edu>
>> Date: Monday, June 5, 2023 at 10:19 AM
>> To: CRAN-sysadmin at R-project.org <CRAN-sysadmin at R-project.org>
>> Subject: Serious problem with R on macOS
>>
>> Hello,
>>
>> For a few months now, I?ve been having an odd and rather annoying problem. I use RStudio and it frequently cannot start R, producing the error message attached below. This is clearly not the, as I worked on it the night before or even just a few hours earlier. What is clear is that R is not available on my system, although all the files are still there (in /Library/Frameworks/R.framework). It could be that a critical file becomes corrupted, or the system can?t find it. I have not been able to determine whether that is the case, or which file could be affected. I might have re-installed R dozens of times in the last month. This is something that never happened in the previous more than 15 years of using R.
>>
>>
>>
>> I?ve tried everything I can think of, and the problem persists?and haven?t found any satisfactory feedback online either.
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>> Have you ever heard of a problem like this? Or do you have any suggestions?
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>>
>>
>> Thank you so much for your support.
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>>
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>>
>> <image001.png>
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>>
>>
>>
>>
>> Fernando DePaolis, Ph.D.
>> Dean of Academic Operations & Integration
>>
>> Associate Professor
>>
>> Middlebury Institute of International Studies at Monterey
>> ----------------------------------------------------------------------
>>
>> [Sent from Outlook for Mac ?MacBook Pro]
>>
>> My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
>>
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Fernando, that looks like something is deleting files on your disk - that sounds pretty bad. I would probably recommend re-installing a fresh macOS as you may have some malware (or over-eager anti-virus or corporate software?) on your machine. Given that R works after installation it really seems like some issue on your OS and not with R itself. Cheers, Simon
On 9/06/2023, at 4:33 AM, DePaolis, Fernando <fdepaolis at middlebury.edu> wrote:
?well?here it goes again?it failed just now. This is the message I get when I try to run R from the command line on my mac
fernandodepaolis at MacBook-Pro-2 ~ % R
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.
During startup - Warning message:
package ?datasets? in options("defaultPackages") was not found
Error in loadNamespace(name) : object 'pkgInfo' not found
In addition: Warning message:
In loadNamespace(name) : package ?compiler? has no 'package.rds' in Meta/
Fatal error: unable to initialize the JIT
There was no ?message? of any sort when trying to run R.app. There was a brief flickering (like quick blinking) but nothing else.
Thank you!
Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International Studies at Monterey
----------------------------------------------------------------------
[Sent from Outlook for Mac ?MacBook Pro]
My working hours (US Pacific time zone) may not be your working hours. Please do not feel obligated to respond outside your normal work hours, unless otherwise indicated.
From: DePaolis, Fernando <fdepaolis at middlebury.edu>
Date: Wednesday, June 7, 2023 at 9:13 PM
To: Simon Urbanek <simon.urbanek at R-project.org>
Cc: r-sig-mac at r-project.org <r-sig-mac at r-project.org>
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
Hi Simon,
You're right, I didn't post it...I'll make sure I do next time it happens...it's working fine for now...
Thank you.
Fernando DePaolis
Dean Of Academic Operations & Integration
Middlebury Institute of International Studies
Sent from Outlook for iOS. Apologies for any typos.