Re: [R-SIG-Mac] Blank help window
Not born that way. I've migrated several laptops. This is the first time I lost /etc/hosts. > On 2018-10-19, at 05:01, Peter Dalgaard wrote: > > What? Are they born that way, or does Migration Assistent bungle things up? > Or maybe OpenVPN does? > > Anyways, try adding a line saying > > 127.0.0.1 localhost > > -pd > >> On 19 Oct 2018, at 00:34 , Ben Tupper wrote: >> >> Hi, >> >> >> ben@gale ~ $ ping localhost >> ping: cannot resolve localhost: Unknown host >> >> Here's /etc/hosts in its entirety. >> >> ben@gale ~ $ more /etc/hosts >> # BEGIN section for OpenVPN Client SSL sites >> 127.94.0.1 client.openvpn.net >> 127.94.0.2 openvpn-client.vpn.bigelow.org >> # END section for OpenVPN Client SSL sites >> >> I'm not currently using VPN. >> >> >>> On Oct 18, 2018, at 6:29 PM, peter dalgaard wrote: >>> >>> Cannot _find_ localhost?? Can you do this (in a Terminal window) ? >>> >>> Peter-Dalgaards-MacBook-Air:STAT pd$ ping localhost >>> PING localhost (127.0.0.1): 56 data bytes >>> Request timeout for icmp_seq 0 >>> Request timeout for icmp_seq 1 >>> ^C >>> --- localhost ping statistics --- >>> 3 packets transmitted, 0 packets received, 100.0% packet loss >>> >>> If not, what is in the first couple of lines in /etc/hosts? >>> >>> -pd >>> On 19 Oct 2018, at 00:09 , Ben Tupper wrote: Just a little followup. Switching the default browser from Firefox to Safari yields a similar message in the browser after... Browse[2]> browseURL(x) 'Safari can't open the page "localhost:29682/library/utils/html/help.html" because Safari can't find the server "localhost".' >>> >>> -- >>> Peter Dalgaard, Professor, >>> Center for Statistics, Copenhagen Business School >>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark >>> Phone: (+45)38153501 >>> Office: A 4.23 >>> Email: pd@cbs.dk Priv: pda...@gmail.com >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> Ben Tupper >> Bigelow Laboratory for Ocean Sciences >> 60 Bigelow Drive, P.O. Box 380 >> East Boothbay, Maine 04544 >> http://www.bigelow.org >> >> Ecological Forecasting: https://eco.bigelow.org/ >> >> >> >> >> > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Office: A 4.23 > Email: pd@cbs.dk Priv: pda...@gmail.com > > > > > > > > > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Blank help window
Ha! My /etc/hosts was empty (perhaps an error by Migration Assistant?). Populating it with the /etc/hosts from the host computer (particularly defining localhost) solves the problem. Many, many thanks for all your timely efforts and considerable help, > On 2018-10 -18, at 19:52, Marc Schwartz wrote: > > Hi, > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Blank help window
> On 2018-10-17, at 22:29, Marc Schwartz wrote: > > Ok, strange. I figured that there was some conflict/corruption in place with > R.app that was not immediately clear. > > Peter raised the possibility of a firewall issue, but I am curious as to why > that would affect the use of help in R.app, but not via other environments, > like the Mac Terminal app. Theoretically, it should be via similar protocols > and ports in each setting, unless there is something specific that R.app does > to the OS environment when running, that would inhibit the dynamic generation > of the HTML pages. But if so, why just for the two of you? > > It seems like the server is starting up ok, but the help pages are not being > generated by Rd2HTML() in R.app. > > However, it sparked a thought in my head, which is always risky, and that is, > do you guys have any anti-virus/malware software running? I may be grasping > at straws here, but such applications have been known to cause all kinds of > flaky behaviors, that are not immediately evident nor associated with them. No firewall; no anti-virus or other malware software > > One other thought. When you get the blank HTML page, presumably white > background, drag the cursor around the page to try to highlight text, as if > the text was also white, thus not showing against the white background. > Another straw Nope. Blank is blank. No invisible text detected. > > Regards, > > Marc > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Blank help window
> On 2018-10 -17, at 17:42, Peter Dalgaard wrote:
>
> Hmm, when trying from R.app, do you see the following?
>
>> ?data.frame
> starting httpd help server ... done
>> (tools::startDynamicHelp(NA))
> [1] 26163
R> ?mean
starting httpd help server ... done
R> (tools::startDynamicHelp(NA))
[1] 10116
http://127.0.0.1:10116/NEWS yields the “R News” page in my browser.
>
> (The last bit is the port number of the HTTP server and will differ between
> invokations. I think you get 0 if the server isn't running and -1 if it
> failed to start.)
>
> If the server is there, you could try connecting from your favourite browser
> at (say) http://127.0.0.1:26163/NEWS
>
> If the server is there, but you cannot talk to it, then I suspect that a
> firewall is getting in the way.
>
> -pd
>
>
>> On 17 Oct 2018, at 20:53 , Ben Tupper wrote:
>>
>> Hi,
>>
>> The behavior I see is identical to what you describe regardless of the
>> function (I used ?data.frame as an example). The help commands
>>
>>> ?
>>
>> and
>>
>>> help("something")
>>
>> both bring up a blank help window. All of the other steps you have taken
>> yield the same result on my system.
>>
>>
>> R version 3.5.1 (2018-07-02) -- "Feather Spray"
>> Copyright (C) 2018 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin15.6.0 (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.
>>
>> [R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]
>>
>>> sessionInfo()
>> R version 3.5.1 (2018-07-02)
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> Running under: macOS Sierra 10.12.6
>>
>> Matrix products: default
>> BLAS:
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
>> LAPACK:
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.5.1
>>
>>
>>> capabilities()
>> jpeg pngtiff tcltk X11aqua
>> http/ftp sockets libxmlfifo
>> TRUETRUETRUETRUETRUETRUE
>> TRUETRUETRUETRUE
>> cledit iconv NLS profmem cairo ICU
>> long.double libcurl
>> TRUETRUETRUETRUETRUETRUE
>> TRUETRUE
>>
>>
>>
>>
>>
>>> On Oct 17, 2018, at 1:48 PM, zListserv wrote:
>>>
>>> Many thanks for your suggestions. Not sure whether Ben’s issue is the same
>>> as mine. Ben has problems with ?data.frame. My issue is a blank help
>>> window when typing ?mean (or any other function).
>>>
>>> Peter suggested checking capabilities(). They are all TRUE.
>>>
>>> You both suggested checking configuration files. Removing .Rprofile,
>>> .Rdata, and .Rapp.history made no difference.
>>>
>>> Simon suggested:
>>>
>>>> On 2018-10 -17, at 08:57, Simon Urbanek
>>>> wrote:
>>>>
>>>> Few things to try:
>>>>
>>>> - do you see anything in the error console?
>>>
>>> Nothing noticeable in the error console, though I’m inexpert at reading it.
>>>>
>>>> - remove (rename) any and all customization files like ~/.Rprofle ~/.RData
>>>> etc.
>>>
>>> No effect
>>>
>>>>
>>>> - try running R from the console and starting the html help by hand to see
>>>> if it works at all:
>>>> tools::startDynamicHelp()
>>>> help.start
Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 187, Issue 8
> > I am not sure whether the following may cause the problem: > > When I used the Migration Assistant I had some problem with X11, > and realized that the Migration Assistant did create the symbolic link: > /usr/X11 -> /opt/X11 > but did not create the symbolic link: > /usr/X11R6 -> /opt/X11 You are right about Migration Assistant. I defined both of these symbolic links manually while I was trying to solve the problem. My help window is still blank despite their presence. > > Best regards, > Christian > > > > > -- > > Message: 5 > Date: Wed, 17 Oct 2018 13:48:12 -0400 > From: zListserv > To: Simon Urbanek , pda...@gmail.com, > r-sig-mac@r-project.org, btup...@bigelow.org > Subject: Re: [R-SIG-Mac] Blank help window > Message-ID: <963deb05-07e5-44d3-86fd-36bd1a257...@gmail.com> > Content-Type: text/plain; charset="utf-8" > > Many thanks for your suggestions. Not sure whether Ben’s issue is the same > as mine. Ben has problems with ?data.frame. My issue is a blank help window > when typing ?mean (or any other function). > > Peter suggested checking capabilities(). They are all TRUE. > > You both suggested checking configuration files. Removing .Rprofile, .Rdata, > and .Rapp.history made no difference. > > Simon suggested: > >> On 2018-10 -17, at 08:57, Simon Urbanek wrote: >> >> Few things to try: >> >> - do you see anything in the error console? > > Nothing noticeable in the error console, though I’m inexpert at reading it. >> >> - remove (rename) any and all customization files like ~/.Rprofle ~/.RData >> etc. > > No effect > >> >> - try running R from the console and starting the html help by hand to see >> if it works at all: >> tools::startDynamicHelp() >> help.start(browser="/usr/bin/open”) >> > > Help works when running R from console > >> - if that works try the same from the R.app gui *before* using help: >> help.start(browser="/usr/bin/open”) > > No effect in R (except it opens my default browser). > >> >> Cheers, >> Simon >> >> >>> On Oct 16, 2018, at 7:11 PM, zListserv wrote: >>> >>> >>> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration >>> Assistant. Everything went well, though there are always a few things that >>> don't transfer such as applications installed by Brew which I installed >>> manually. >>> >>> An issue with R arose I can't solve. The help systen opens with a blank >>> window. >>> >>> Help works when I run R from the terminal so I know the files are >>> installed. Help works fine on the Macintosh I used a the source for the >>> migration so it isn't a problem I inherited. Re-installing R (see >>> sessionInfo below) didn't solve the problem. >>> >>> Anyone have any suggestions how I can get help to work? >>> >>> R version 3.5.1 (2018-07-02) >>> Platform: x86_64-apple-darwin15.6.0 (64-bit) >>> Running under: macOS High Sierra 10.13.6 >>> >>> Matrix products: default >>> BLAS: >>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib >>> LAPACK: >>> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods >>> [7] base >>> >>> other attached packages: >>> [1] HANDLS_0.34 zUtil_0.121 >>> >>> loaded via a namespace (and not attached): >>> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15 MASS_7.3-50 >>> [5] chron_2.3-52grid_3.5.1 plyr_1.8.4 xtable_1.8-2 >>> [9] DBI_1.0.0 RSQLite_2.1.1 sqldf_0.4-11blob_1.1.1 >>> [13] sp_1.3-1gsubfn_0.7 proto_1.0.0 tools_3.5.1 >>> [17] Matching_4.9-3 bit64_0.9-7 foreign_0.8-70 bit_1.1-14 >>> [21] compiler_3.5.1 maptools_0.9-2 memoise_1.1.0 >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > > > > -- > > Subject: Digest Footer > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > -- > > End of R-SIG-Mac Digest, Vol 187, Issue 8 > * ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Blank help window
Many thanks for your suggestions. Not sure whether Ben’s issue is the same as mine. Ben has problems with ?data.frame. My issue is a blank help window when typing ?mean (or any other function). Peter suggested checking capabilities(). They are all TRUE. You both suggested checking configuration files. Removing .Rprofile, .Rdata, and .Rapp.history made no difference. Simon suggested: > On 2018-10 -17, at 08:57, Simon Urbanek wrote: > > Few things to try: > > - do you see anything in the error console? Nothing noticeable in the error console, though I’m inexpert at reading it. > > - remove (rename) any and all customization files like ~/.Rprofle ~/.RData > etc. No effect > > - try running R from the console and starting the html help by hand to see if > it works at all: > tools::startDynamicHelp() > help.start(browser="/usr/bin/open”) > Help works when running R from console > - if that works try the same from the R.app gui *before* using help: > help.start(browser="/usr/bin/open”) No effect in R (except it opens my default browser). > > Cheers, > Simon > > >> On Oct 16, 2018, at 7:11 PM, zListserv wrote: >> >> >> I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration >> Assistant. Everything went well, though there are always a few things that >> don't transfer such as applications installed by Brew which I installed >> manually. >> >> An issue with R arose I can't solve. The help systen opens with a blank >> window. >> >> Help works when I run R from the terminal so I know the files are installed. >> Help works fine on the Macintosh I used a the source for the migration so >> it isn't a problem I inherited. Re-installing R (see sessionInfo below) >> didn't solve the problem. >> >> Anyone have any suggestions how I can get help to work? >> >> R version 3.5.1 (2018-07-02) >> Platform: x86_64-apple-darwin15.6.0 (64-bit) >> Running under: macOS High Sierra 10.13.6 >> >> Matrix products: default >> BLAS: >> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib >> LAPACK: >> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> [7] base >> >> other attached packages: >> [1] HANDLS_0.34 zUtil_0.121 >> >> loaded via a namespace (and not attached): >> [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15 MASS_7.3-50 >> [5] chron_2.3-52grid_3.5.1 plyr_1.8.4 xtable_1.8-2 >> [9] DBI_1.0.0 RSQLite_2.1.1 sqldf_0.4-11blob_1.1.1 >> [13] sp_1.3-1gsubfn_0.7 proto_1.0.0 tools_3.5.1 >> [17] Matching_4.9-3 bit64_0.9-7 foreign_0.8-70 bit_1.1-14 >> [21] compiler_3.5.1 maptools_0.9-2 memoise_1.1.0 >> >> ___ >> 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
[R-SIG-Mac] Blank help window
I recently migrated to a MacBook Pro (15-inch, 2018) using the Migration Assistant. Everything went well, though there are always a few things that don't transfer such as applications installed by Brew which I installed manually. An issue with R arose I can't solve. The help systen opens with a blank window. Help works when I run R from the terminal so I know the files are installed. Help works fine on the Macintosh I used a the source for the migration so it isn't a problem I inherited. Re-installing R (see sessionInfo below) didn't solve the problem. Anyone have any suggestions how I can get help to work? R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] HANDLS_0.34 zUtil_0.121 loaded via a namespace (and not attached): [1] Rcpp_0.12.17lattice_0.20-35 digest_0.6.15 MASS_7.3-50 [5] chron_2.3-52grid_3.5.1 plyr_1.8.4 xtable_1.8-2 [9] DBI_1.0.0 RSQLite_2.1.1 sqldf_0.4-11blob_1.1.1 [13] sp_1.3-1gsubfn_0.7 proto_1.0.0 tools_3.5.1 [17] Matching_4.9-3 bit64_0.9-7 foreign_0.8-70 bit_1.1-14 [21] compiler_3.5.1 maptools_0.9-2 memoise_1.1.0 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Problem updating packages
In MacOS 10.12.3 (Sierra), I can't update packages (though it worked on the same computer in MacOS 10.11): update.packages( lib = lib <- .libPaths()[1], pkgs = as.data.frame(installed.packages(lib), stringsAsFactors=FALSE)$Package, type = 'source') Warning: unable to access index for repository https://cloud.r-project.org/src/contrib: cannot open the connection Warning message: In read.dcf(file = tmpf) : cannot open compressed file '/tmp/RtmpS3f5mS/file959038dcc8eb', probable reason 'No such file or directory' --- My internet connection works fine; updating hasn't worked since I upgraded MacOS to 10.12 from 10.11. Confusingly, on a new MacBook Pro with 10.12.3 & R 3.3.3, updating works without error. It feels as though something changed in the upgrade and now I can't get to where I got before. I'd appreciate help in resolving this. --- Here's my configuration: R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.3 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets [6] methods base other attached packages: [1] HANDLS_0.30zUtil_0.94 sysMods_0.01 [4] foreign_0.8-67 car_2.1-3 loaded via a namespace (and not attached): [1] Rcpp_0.12.8maptools_0.8-40 [3] splines_3.3.3 MASS_7.3-45 [5] xtable_1.8-2 lattice_0.20-34 [7] minqa_1.2.4plyr_1.8.4 [9] tools_3.3.3nnet_7.3-12 [11] parallel_3.3.3 pbkrtest_0.4-6 [13] grid_3.3.3 nlme_3.1-131 [15] mgcv_1.8-17quantreg_5.29 [17] DBI_0.5-1 MatrixModels_0.4-1 [19] lme4_1.1-12Matrix_1.2-8 [21] nloptr_1.0.4 RSQLite_1.0.0 [23] gsubfn_0.6-6 Matching_4.9-2 [25] sp_1.2-3 SparseM_1.74 [27] chron_2.3-47 sqldf_0.4-10 [29] proto_1.0.0 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Mavericks CMD install error
I’ve done my best to follow Prof Ripley’s instructions (30 Oct 2013) for installing packages after upgrading to Mavericks. I’m stuck with an error in a package that installed without error under 10.8 (with the most recent version of Xcode 5.0.2). I installed the command line tools (late Oct 2013) for Mavericks and updated XQuartz. I inserted definitions for CC, CXX, CFLAGS, CXXFLAGS, FLIBS in ~/.R.Makevars: CC=clang CXX=clang++ CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion” FLIBS=-lgfortran though xcode-select —install generated an error (“Can’t install software because it is not currently available from the Software Update server”). Here’s the error: $ r CMD install zStat * installing to library ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library’ * installing *source* package ‘zStat’ ... ** libs clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o zStat.so zCor.o SHLIB_LIBADD = -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation clang: error: no such file or directory: 'SHLIB_LIBADD' clang: error: no such file or directory: '=' make: *** [zStat.so] Error 1 ERROR: compilation failed for package ‘zStat’ * removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zStat’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zStat’ I would appreciate any guidance you can offer. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Tab setting in R.app editor
Is there a way to change to default tab stop setting from the present 4 characters (stops at 5, 9, etc) to 8 characters (stops at 9, 17, etc)? ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
