[R-SIG-Mac] Fail to install Rserve 1.8-6
Hi all,
Configuration is as follows
MacOS Catalina 10.15.5
R version 4.0.1
I try
install.packages('Rserve',,'http://www.rforge.net/‘)
And then attempt to install from sources. At the end I get the following message
ld: library not found for -lssl
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [forward] Error 1
make: *** [all] Error 2
ERROR: compilation failed for package ‘Rserve’
* removing
‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rserve’
The downloaded source packages are in
‘/private/var/folders/lr/dz6qc47x3zg_2d_dzd5jtq5mgn/T/RtmpeSL5uH/downloaded_packages’
Warning message:
In install.packages("Rserve", , "http://www.rforge.net/";) :
installation of package ‘Rserve’ had non-zero exit status
Any help on this?
Many thanks in advance
Stavros
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Re: [R-SIG-Mac] Labels not displaying in R plots
Bingo, Simon. Thanks. Running Validate Font on all my fonts on my iMac did indeed result in "Warnings and Errors" that there were duplicates -- including key 'default' fonts like Arial and Palatino. Some of those fonts were in: ~/Library/Fonts/ Duplicates were in: /Users/*username*/Library/Fonts/ The directory on my iMac: /Users/*username*/Library/Fonts/ is chock full of fonts. Notably: In my MacBook, the directory: /Users/*username*/Library/Fonts/ - has not got a single file in it! So back on my iMac, I removed the duplicate fonts in the /Users/*username*/Library/Fonts/ directory. And, firing up R, running demo=(topic="graphics") -- I am now seeing labels! Just to close this off then -- where does R look for font information when it goes to plot something? On Mon, Jun 8, 2020 at 5:51 PM Simon Urbanek wrote: > David, > > that is typically a sign of damaged fonts in your system. Open the Font > Book (in Applications), select User and see if there are any broken fonts > and remove them. You can also select fonts and run File -> Validate Font. > Either way, you can compare your font configuration on both machines using > Font Book. > > I hope it helps. > > Cheers, > Simon > > > > > On Jun 9, 2020, at 6:37 AM, David Akin wrote: > > > > Hey listers -- > > > > I'm a journalist and an R newbie but do I know my way around a Mac. > > > > Got a weird problem I'm trying to troubleshoot > > > > Both my Macbook Air and my iMac are running the same OS: Mojave 10.14.6 > > > > But each one is running different versions of R. > > > > The iMac is running v 4.0.0 "Arbor Day" > > > > The Macbook is running 3.6.0 "Planting of a Tree" > > > > PROBLEM: Labels do not display in plots run on the iMac. Labels do > display properly on the MacBook. > > > > Example: > > Here's the colour wheel example from demo(topic="graphics") on the iMac. > No labels. > > > > > > And here's the same plot as it displays on the Macbook. With Labels. > > > > > > Looking a little closer at the fine print in the console when I fire up > R, there is this line on my iMac: > > > > [R.app GUI 1.71 (7827) x86_64-apple-darwin17.0] > > > > But we have different version numbers on my Macbook: > > > > [R.app GUI 1.70 (7657) x86_64-apple-darwin15.6.0] > > > > Attempted the following on the iMac: > > > > 1. Uninstalled R 4.0.0 > > 2. Grab the R 3.6.3 from http://mac.r-project.org/ > > 3. Installed R 3.6.3. > > 4. Ran demo(topics="Graphics") again -- and got the same result -- no > labels on any plots. > > > > Help? > > > > > > > > -- > > David Akin > > --- > > http://www.davidakin.com > > ___ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > -- David Akin --- http://www.davidakin.com [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] labels on plots
You sure you don't have a font or fontsize missing? Or possibly a screen resolution-setting mismatch? On 6/8/20 5:11 PM, r-sig-mac-requ...@r-project.org wrote: 1. Labels not displaying in R plots (David Akin) -- Message: 1 Date: Mon, 8 Jun 2020 14:37:46 -0400 From: David Akin To: r-sig-mac@r-project.org Subject: [R-SIG-Mac] Labels not displaying in R plots Message-ID: Content-Type: text/plain; charset="utf-8" Hey listers -- I'm a journalist and an R newbie but do I know my way around a Mac. Got a weird problem I'm trying to troubleshoot Both my Macbook Air and my iMac are running the same OS: Mojave 10.14.6 But each one is running different versions of R. The iMac is running v 4.0.0 "Arbor Day" The Macbook is running 3.6.0 "Planting of a Tree" *PROBLEM:* Labels do not display in plots run on the iMac. Labels do display properly on the MacBook. Example: Here's the colour wheel example from demo(topic="graphics") on the iMac. No labels. [image: image.png] And here's the same plot as it displays on the Macbook. With Labels. [image: Image 2020-06-08 at 9.11 AM.jpg] Looking a little closer at the fine print in the console when I fire up R, there is this line on my iMac: [R.app GUI 1.71 (7827) x86_64-apple-darwin17.0] But we have different version numbers on my Macbook: [R.app GUI 1.70 (7657) x86_64-apple-darwin15.6.0] Attempted the following on the iMac: 1. Uninstalled R 4.0.0 2. Grab the R 3.6.3 from http://mac.r-project.org/ 3. Installed R 3.6.3. 4. Ran demo(topics="Graphics") again -- and got the same result -- no labels on any plots. Help? -- Carl Witthoft c...@witthoft.com resume: https://app.box.com/file/498153801347 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Labels not displaying in R plots
David, that is typically a sign of damaged fonts in your system. Open the Font Book (in Applications), select User and see if there are any broken fonts and remove them. You can also select fonts and run File -> Validate Font. Either way, you can compare your font configuration on both machines using Font Book. I hope it helps. Cheers, Simon > On Jun 9, 2020, at 6:37 AM, David Akin wrote: > > Hey listers -- > > I'm a journalist and an R newbie but do I know my way around a Mac. > > Got a weird problem I'm trying to troubleshoot > > Both my Macbook Air and my iMac are running the same OS: Mojave 10.14.6 > > But each one is running different versions of R. > > The iMac is running v 4.0.0 "Arbor Day" > > The Macbook is running 3.6.0 "Planting of a Tree" > > PROBLEM: Labels do not display in plots run on the iMac. Labels do display > properly on the MacBook. > > Example: > Here's the colour wheel example from demo(topic="graphics") on the iMac. No > labels. > > > And here's the same plot as it displays on the Macbook. With Labels. > > > Looking a little closer at the fine print in the console when I fire up R, > there is this line on my iMac: > > [R.app GUI 1.71 (7827) x86_64-apple-darwin17.0] > > But we have different version numbers on my Macbook: > > [R.app GUI 1.70 (7657) x86_64-apple-darwin15.6.0] > > Attempted the following on the iMac: > > 1. Uninstalled R 4.0.0 > 2. Grab the R 3.6.3 from http://mac.r-project.org/ > 3. Installed R 3.6.3. > 4. Ran demo(topics="Graphics") again -- and got the same result -- no labels > on any plots. > > Help? > > > > -- > David Akin > --- > http://www.davidakin.com > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01
Simon, When I removed these two I did get a slightly different behavior on my MBA. In the past I would get the pinwheel of death and R would peg at 100%, but now when I try and load a second file it simply crashes R immediately. Debug Console log here: https://gist.github.com/bhive01/1421f464ce5d345644878cd41309f647 Separately I loaded up R from my applications folder and then clicked on a file to load it and it did the same thing: https://gist.github.com/bhive01/d7791d0070a43d73de2489f6cab9211f The same crashing behavior if you load it from the Open Recents in the menu: https://gist.github.com/bhive01/1bae74d6cbcbb8c014415d47ac9fe456 In the first instance I double clicked the file from Finder and it would open with R-GUI/R. But a second file would not, once R was loaded. I don't know if that gets us any closer, but apparently there is some difference in that it crashes immediately rather than a pinwheel of death. The only thing I can think of is that I did have my own custom color palette and you reference changing the color scheme. Seems unlikely, but perhaps there's a connection there? As Carl says, I'm happy to try other things if you have suggestions or have ideas on more information. I've been using BBEdit to open other scripts, but often forget and end up with a crash because I double-click on a file. I might try to get BBEdit to work with R more intimately as Carl pointed out. B On Sun, Jun 7, 2020 at 3:46 PM Simon Urbanek wrote: > Thanks for the reports. Unfortunately, I still cannot reproduce it on > Catalina - neither with 4.0.1 nor 4.0.0. > Can someone post exactly how to replicate? (How do exactly you open the > file? - the Open dialog works fine for me...) > > Note that the GUI is independent of R and compatible up to the patch > version, i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also > just download the GUI from > https://mac.R-project.org > and run it from the image, you don’t even have to install it. > > The only changes in the GUI for 4.0.1 were in the colours for dark mode, > so file handling behaviour didn’t really change. > > Some places to remove to try if it has any effect: > > rm -rf ~/Library/Caches/org.R-project.R > rm ~/Library/Preferences/org.R-project.R.plist > > Thanks, > Simon > > > > > On Jun 8, 2020, at 10:22 AM, Brandon Hurr > wrote: > > > > This sounds exactly like the issue I am still having when I run to open > > more than one R script file in R-GUI’s editor. Perhaps it has got worse > > with the newer builds? > > > > On Sun, Jun 7, 2020 at 15:16 Carl Witthoft wrote: > > > >> I'm not sure what to look for in the Reports sections of Console.app, > >> but I did find this report of R exceeding a diagnostic limit of CPU > >> usage, which most likely is related to one of the hangs - R.app always > >> goes full throttle on one CPU core. > >> > >> Date/Time:2020-06-05 18:58:36 -0400 > >> End time: 2020-06-05 19:00:16 -0400 > >> OS Version: Mac OS X 10.15.5 (Build 19F101) > >> Architecture: x86_64h > >> Report Version: 29 > >> Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B > >> > >> Data Source: Microstackshots > >> Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535 > >> > >> Command: R > >> Path: /Applications/R.app/Contents/MacOS/R > >> Identifier: org.R-project.R > >> Version: R 4.0.0 GUI 1.71 Catalina build (7827) > >> PID: 21391 > >> > >> Event:cpu usage > >> Action taken: none > >> CPU: 90 seconds cpu time over 100 seconds (90% cpu > >> average), exceeding limit of 50% cpu over 180 seconds > >> CPU limit:90s > >> Limit duration: 180s > >> CPU used: 90s > >> CPU duration: 100s > >> Duration: 100.35s > >> Duration Sampled: 87.74s > >> Steps:51 > >> > >> Hardware model: iMac19,2 > >> Active cpus: 4 > >> > >> Fan speed:1200 rpm > >> > >> Heaviest stack for the target process: > >> 51 start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9] > >> 51 main + 720 (R + 8032) [0x105c66f60] > >> 51 -[NSApplication finishLaunching] + 2601 (AppKit + 207160) > >> [0x7fff2dc1c938] > >> 51 -[NSApplication _postDidFinishNotification] + 312 (AppKit + > >> 306403) [0x7fff2dc34ce3] > >> 51 -[NSNotificationCenter postNotificationName:object:userInfo:] + > >> 59 (Foundation + 38790) [0x7fff32ff6786] > >> 51 _CFXNotificationPost + 1351 (CoreFoundation + 297529) > >> [0x7fff3097ba39] > >> 51 -[_CFXNotificationRegistrar find:object:observer:enumerator:] + > >> 1554 (CoreFoundation + 300429) [0x7fff3097c58d] > >> 51 ___CFXNotificationPost_block_invoke + 80 (CoreFoundation + > >> 496660) [0x7fff309ac414] > >> 51 _CFXRegistrationPost1 + 372 (CoreFoundation + 497576) > >> [0x7fff309ac7a8] > >> 51 ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation + > >> 497715) [0x7fff309ac833] > >> 51 __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12 > >>
Re: [R-SIG-Mac] Update to versions GEOS 3.8.0, GDAL 3.0.4 and PROJ 7.0.0 in macOS Catalina
Thank you very much Alberto,
I tried:
brew tap osgeo/osgeo4mac
brew unlink gdal
brew unlink proj
brew install osgeo-gdal
brew install osgeo-proj
brew link osgeo-gdal
brew link osgeo-proj
install.packages("rgdal", type = "source")
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file,
DLLpath = DLLpath, ...):
unable to load shared object
'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so,
6): Symbol not found: ___addtf3
Referenced from: /usr/local/opt/gcc/lib/gcc/9/libquadmath.0.dylib
Expected in: /usr/lib/libSystem.B.dylib
in /usr/local/opt/gcc/lib/gcc/9/libquadmath.0.dylib
Error: loading failed
Execution halted
After trying to find a solution, some people suggested me to wait for the
binary packages.
Manuel
El dom., 7 jun. 2020 a las 4:47, Alberto Lázaro-López ()
escribió:
> Hi all,
>
> I got in touch with Manuel Spínola in R-sig-geo mailing list, I didn’t
> keep an eye on this list though.
> I’ve seen some mails regarding issues with PROJ and GDAL in macOS
> following Homebrew versions.
>
> We are maintaining a Homebrew tap focused on OSGeo projects called
> OSGeo4Mac.
> At this moment, it’s serving bottles for GDAL 3.1.0 and PROJ 6.3.2, but
> also other GIS software as PostGIS or SAGA.
> They are intended to be more flexible and provide more functionality than
> those available as core versions too.
>
> We are also looking for collaborators to discuss and support formulas they
> are interested in.
> You are really welcome.
>
> Best regards,
>
> Alberto D. Lázaro López
> about.me/alazarolop
>
> [[alternative HTML version deleted]]
>
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COSTA RICA
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Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01
It sounds a little as if the R.app is somehow damaged. What do the commands ls -ls $(which R) ls -las $(which Rscript) issued from a terminal show? Mine show (abbreviated) [...] /usr/local/bin/R -> ../Cellar/r/4.0.0_1/bin/R [...] /usr/local/bin/Rscript -> ../Cellar/r/4.0.0_1/bin/Rscript I use homebrew and the plain (command line) R, ie not the App (installed as cask), with RStudio (installed as cask). I have the following first line in most of my R scripts #!/usr/bin/env Rscript and they all run currently. I will wait for 4.0.1 to pitch up on homebrew and see that that does. The editor scripts have nothing to do with this, they just reference the command line R (above). There are equally comfortable ones for TextMate2 and AlphaX, and others. greetings, el On 08/06/2020 14:13, Carl Witthoft wrote: > In the meantime, there is a decent alternative. I found some scripts > for BBEdit which let you execute code or "source" code directly from > BBEdit. See http://bearak.org/code/text/index.html > > On 6/7/20 11:39 PM, John Helly wrote: >> Fails for me 100%. If you want to zoom to look at it, I can arrange. >> Hard to explain how to replicate since it happens right away as soon >> as I try to do anything. Running Catalina on a brand-new Mac Pro. >> >> J. >> ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01
In the meantime, there is a decent alternative. I found some scripts for BBEdit which let you execute code or "source" code directly from BBEdit. See http://bearak.org/code/text/index.html On 6/7/20 11:39 PM, John Helly wrote: Fails for me 100%. If you want to zoom to look at it, I can arrange. Hard to explain how to replicate since it happens right away as soon as I try to do anything. Running Catalina on a brand-new Mac Pro. J. On 6/7/20 15:46, Simon Urbanek wrote: Thanks for the reports. Unfortunately, I still cannot reproduce it on Catalina - neither with 4.0.1 nor 4.0.0. Can someone post exactly how to replicate? (How do exactly you open the file? - the Open dialog works fine for me...) Note that the GUI is independent of R and compatible up to the patch version, i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also just download the GUI from https://urldefense.com/v3/__https://mac.R-project.org__;!!Mih3wA!ReiXSbqAjm6U4nbE1g9kiDWBjuTDcKsZfnp69eK0Ey0VZg4-UB24sxHHdM6_uVk$ and run it from the image, you don’t even have to install it. The only changes in the GUI for 4.0.1 were in the colours for dark mode, so file handling behaviour didn’t really change. Some places to remove to try if it has any effect: rm -rf ~/Library/Caches/org.R-project.R rm ~/Library/Preferences/org.R-project.R.plist Thanks, Simon On Jun 8, 2020, at 10:22 AM, Brandon Hurr wrote: This sounds exactly like the issue I am still having when I run to open more than one R script file in R-GUI’s editor. Perhaps it has got worse with the newer builds? On Sun, Jun 7, 2020 at 15:16 Carl Witthoft wrote: I'm not sure what to look for in the Reports sections of Console.app, but I did find this report of R exceeding a diagnostic limit of CPU usage, which most likely is related to one of the hangs - R.app always goes full throttle on one CPU core. Date/Time:2020-06-05 18:58:36 -0400 End time: 2020-06-05 19:00:16 -0400 OS Version: Mac OS X 10.15.5 (Build 19F101) Architecture: x86_64h Report Version: 29 Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B Data Source: Microstackshots Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535 Command: R Path: /Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: R 4.0.0 GUI 1.71 Catalina build (7827) PID: 21391 Event:cpu usage Action taken: none CPU: 90 seconds cpu time over 100 seconds (90% cpu average), exceeding limit of 50% cpu over 180 seconds CPU limit:90s Limit duration: 180s CPU used: 90s CPU duration: 100s Duration: 100.35s Duration Sampled: 87.74s Steps:51 Hardware model: iMac19,2 Active cpus: 4 Fan speed:1200 rpm Heaviest stack for the target process: 51 start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9] 51 main + 720 (R + 8032) [0x105c66f60] 51 -[NSApplication finishLaunching] + 2601 (AppKit + 207160) [0x7fff2dc1c938] 51 -[NSApplication _postDidFinishNotification] + 312 (AppKit + 306403) [0x7fff2dc34ce3] 51 -[NSNotificationCenter postNotificationName:object:userInfo:] + 59 (Foundation + 38790) [0x7fff32ff6786] 51 _CFXNotificationPost + 1351 (CoreFoundation + 297529) [0x7fff3097ba39] 51 -[_CFXNotificationRegistrar find:object:observer:enumerator:] + 1554 (CoreFoundation + 300429) [0x7fff3097c58d] 51 ___CFXNotificationPost_block_invoke + 80 (CoreFoundation + 496660) [0x7fff309ac414] 51 _CFXRegistrationPost1 + 372 (CoreFoundation + 497576) [0x7fff309ac7a8] 51 ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation + 497715) [0x7fff309ac833] 51 __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12 (CoreFoundation + 497823) [0x7fff309ac89f] 51 -[RController applicationDidFinishLaunching:] + 1176 (R + 15960) [0x105c68e58] 51 -[REngine executeString:] + 286 (R + 76926) [0x105c77c7e] 51 -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212 (Foundation + 393672) [0x7fff3304d1c8] 51 CFRunLoopRunSpecific + 462 (CoreFoundation + 532174) [0x7fff309b4ece] 51 __CFRunLoopRun + 874 (CoreFoundation + 534677) [0x7fff309b5895] 51 __CFRunLoopDoObservers + 457 (CoreFoundation + 537335) [0x7fff309b62f7] 51 __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 23 (CoreFoundation + 537541) [0x7fff309b63c5] 51 ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 (AppKit + 9439312) [0x7fff2e4ea850] 51 __62+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayLink]_block_invoke + 266 (AppKit + 1971601) [0x7fff2ddcb591] 51 CA::Transaction::commit() + 644 (QuartzCore + 8352) [0x7fff3c47a0a0] 51 CA::Context::commit_transaction(CA::Transaction*, double) + 334 (QuartzCore + 13494) [0x7fff3c47b4b6] 51 CA::Layer::display_if_needed(CA::Transaction*) + 757 (QuartzCore + 152061) [0x7fff3c49d1fd] 51 -[_NSViewBackingLayer display] + 800 (AppKit + 1231223) [0x7fff2dd1
