I am not an expert in configure scripts, but it looks to me as though the next thing in R's configure script deals with java. Maybe java is broken on your system badly enough that it halts the configure script? You could try this:
- copy the flies java and javac from SAGE_ROOT/build/pkgs/r/patches/ to SAGE_ROOT/local/bin. This installs intentionally "broken" versions of java and javac, to prevent any system versions from interfering with R's installation process. - run 'make r' (which will try to install R). - then delete the files java and javac from SAGE_ROOT/local/bin. I'm really just taking guesses, though. John On Tuesday, September 4, 2018 at 12:40:38 PM UTC-7, Nagesh Adluru wrote: > > Hi Dima and John, > > I got the libstd++-static installed. I did not use screen this time. I am > not sure how to make "check ...static libraries" to yes. The gcc, g++ and > gfortran are all version 7.3.1 20180303 (Red Hat 7.3.1-5). > > I am still getting the error for r. I am attaching the fresh log again > just in case. Also I was thinking, the latest version of R available is > r.3.5.1 and sage is trying to install r.3.4.4. Would upgrading it to > r.3.5.1 resolve this mysterious issue? > > Thanks so much for your insights and help! > Sincerely, > Nagesh > On Mon, Sep 3, 2018 at 5:49 PM Nagesh Adluru <nagesh...@gmail.com > <javascript:>> wrote: > >> 1) I realized recently that libstd++-static is missing. I will try to get >> those and also try to make "check....static libraries" to yes for gfortran. >> 2) I will try without screen just to check Dima's hypothesis. >> 3) Thanks for sharing your input about paperconf, John! >> >> I will report back once I try these. >> Thanks so much everyone! >> Best, >> Nagesh >> >> On Mon, Sep 3, 2018 at 5:17 PM John H Palmieri <jhpalm...@gmail.com >> <javascript:>> wrote: >> >>> On my OS X machine, I do not have paperconf, and R builds just fine. I >>> wonder if screen is getting in the way somehow. Can you try without using >>> it? >>> >>> (According to the log file, gfortran seems to be there. There is no >>> working ObjC++ compiler, but I don't think that should be an issue, right?) >>> >>> >>> >>> On Monday, September 3, 2018 at 2:33:22 PM UTC-7, Dima Pasechnik wrote: >>>> >>>> you do have gfortran installed, right? >>>> (usually R is one of the last packages to be built, but perhaps you >>>> overlooked some errors) >>>> >>>> The R install log after paperconf would go as follows: >>>> >>>> ... >>>> checking for lpr... lpr >>>> checking for paperconf... /usr/bin/paperconf >>>> checking whether we are using the GNU Fortran compiler... yes >>>> checking whether gfortran accepts -g... yes >>>> checking if libtool supports shared libraries... yes >>>> checking whether to build shared libraries... yes >>>> checking whether to build static libraries... no >>>> ... >>>> >>>> and so I suspect that it misreports a fortran error... >>>> >>>> >>>> >>>> On Mon, Sep 3, 2018 at 11:52 PM Nagesh Adluru <nagesh...@gmail.com> >>>> wrote: >>>> > >>>> > It is bash and >>>> > the output of echo $SHELL is /bin/bash >>>> > >>>> > >>>> > >>>> > On Mon, Sep 3, 2018 at 3:44 PM Dima Pasechnik <dim...@gmail.com> >>>> wrote: >>>> >> >>>> >> looks puzzling. >>>> >> What is your default shell? >>>> >> If it is not bash, then there might be strange problems like this. >>>> What is the output of >>>> >> >>>> >> echo $SHELL >>>> >> >>>> >> >>>> >> >>>> >> On Mon, 3 Sep 2018, 19:48 Nagesh Adluru, <nagesh...@gmail.com> >>>> wrote: >>>> >>> >>>> >>> Hi Dima, >>>> >>> >>>> >>> I am also getting the output letter just like in your case. It is >>>> not crashing. So what would you think is the problem? >>>> >>> >>>> >>> Also thanks for clarifying about screen! >>>> >>> >>>> >>> Thanks so much. >>>> >>> Nagesh >>>> >>> >>>> >>> On Mon, Sep 3, 2018 at 5:03 AM Dima Pasechnik <dim...@gmail.com> >>>> wrote: >>>> >>>> >>>> >>>> On Sun, Sep 2, 2018 at 11:20 PM Nagesh Adluru <nagesh...@gmail.com> >>>> wrote: >>>> >>>> > >>>> >>>> > Hi David, >>>> >>>> > >>>> >>>> > Thanks for sharing that insight. I did install the anaconda in >>>> between for a different purpose which explains the new problem with >>>> libcurl >>>> that I did not have before the libpaper issue. Based on your advice I >>>> removed anaconda from the path and I did a full make distclean and >>>> reinstall and now the libcurl is gone but it still errors after paperconf >>>> message (log attached) even though we have libpaper installed (screenshot >>>> attached). >>>> >>>> > Please let me know what should I try next since libcurl seems no >>>> longer to be a problem and libpaper is installed! >>>> >>>> > >>>> >>>> what is the output of 'paperconf' ? >>>> >>>> Could you try running paperconf at shell prompt, to see if it >>>> outputs >>>> >>>> anything meaningful, e.g. for me it >>>> >>>> outputs 'letter'. It looks as if it either crashes, or outputs >>>> >>>> something R is not happy about... >>>> >>>> >>>> >>>> $ paperconf >>>> >>>> letter >>>> >>>> >>>> >>>> >>>> >>>> > Thank you all so much for the help! >>>> >>>> > Sincerely, >>>> >>>> > Nagesh >>>> >>>> > >>>> >>>> > On Sun, Sep 2, 2018 at 10:06 AM David Einstein <dei...@gmail.com> >>>> wrote: >>>> >>>> >> >>>> >>>> >> I don't know about centos, but on OSX this situation occurs >>>> when anaconda is installed, and the anaconda directories occur earlier in >>>> the path than the system directories. Removing anaconda from the path >>>> before building sage fixes the problem. >>>> >>>> >> >>>> >>>> >> On Sunday, September 2, 2018 at 8:15:33 AM UTC-4, Nagesh Adluru >>>> wrote: >>>> >>>> >>> >>>> >>>> >>> I had actually thought of that but the sys admin thought we >>>> had the devel installed. I will pursue this line with more pressure now >>>> that I have your suggestion as well. >>>> >>>> >>> >>>> >>>> >>> Thanks again so much for the prompt help! >>>> >>>> >>> Best, >>>> >>>> >>> Nagesh >>>> >>>> >>> >>>> >>>> >>> On Sun, Sep 2, 2018, 2:12 AM Dima Pasechnik <dim...@gmail.com> >>>> wrote: >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Sunday, September 2, 2018 at 1:27:46 AM UTC+3, Nagesh >>>> Adluru wrote: >>>> >>>> >>>>> >>>> >>>> >>>>> Hi Dima, >>>> >>>> >>>>> >>>> >>>> >>>>> Between the delays from our IT admin and me trying to >>>> resolve the issue by myself since in the original log there was no issue >>>> of >>>> libcurl, I got delayed in getting back. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> The log says: >>>> >>>> >>>> >>>> >>>> >>>> configure: error: libcurl >= 7.22.0 library and headers are >>>> required >>>> >>>> >>>> >>>> >>>> >>>> You need libcurl-devel package, which includes headers. >>>> >>>> >>>> >>>> >>>> >>>> HTH >>>> >>>> >>>> Dima >>>> >>>> >>>> >>>> >>>> >>>>> >>>> >>>> >>>>> I am really sorry for the delay. I was however not able to >>>> resolve this issue by myself. If you see the new log (attached) for >>>> r-3.4.4.p0 you would see that it is not seeing the libcurl that we have. >>>> Our yum info on libcurl says we have 7.26 (screenshot attached) but the R >>>> configuration does not seem to find the necessary library headers for >>>> above >>>> 7.22. >>>> >>>> >>>>> >>>> >>>> >>>>> Could you kindly look into this? Again I am really sorry for >>>> the delay. >>>> >>>> >>>>> Thank you so much. >>>> >>>> >>>>> Nagesh >>>> >>>> >>>>> >>>> >>>> >>>>> On Mon, Aug 27, 2018 at 1:27 AM Dima Pasechnik < >>>> dim...@gmail.com> wrote: >>>> >>>> >>>>>> >>>> >>>> >>>>>> if you still have the failed Sage install, all you need to >>>> do after libpaper installation is to run make again. >>>> >>>> >>>>>> >>>> >>>> >>>>>> -- >>>> >>>> >>>>>> You received this message because you are subscribed to the >>>> Google Groups "sage-devel" group. >>>> >>>> >>>>>> To unsubscribe from this group and stop receiving emails >>>> from it, send an email to sage-devel+...@googlegroups.com. >>>> >>>> >>>>>> To post to this group, send email to >>>> sage-...@googlegroups.com. >>>> >>>> >>>>>> Visit this group at >>>> https://groups.google.com/group/sage-devel. >>>> >>>> >>>>>> For more options, visit https://groups.google.com/d/optout. >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> >>>> >>>> You received this message because you are subscribed to the >>>> Google Groups "sage-devel" group. >>>> >>>> >>>> To unsubscribe from this group and stop receiving emails from >>>> it, send an email to sage-devel+...@googlegroups.com. >>>> >>>> >>>> To post to this group, send email to >>>> sage-...@googlegroups.com. >>>> >>>> >>>> Visit this group at >>>> https://groups.google.com/group/sage-devel. >>>> >>>> >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>>> >> >>>> >>>> >> -- >>>> >>>> >> You received this message because you are subscribed to the >>>> Google Groups "sage-devel" group. >>>> >>>> >> To unsubscribe from this group and stop receiving emails from >>>> it, send an email to sage-devel+...@googlegroups.com. >>>> >>>> >> To post to this group, send email to sage-...@googlegroups.com. >>>> >>>> >>>> >> Visit this group at https://groups.google.com/group/sage-devel. >>>> >>>> >>>> >> For more options, visit https://groups.google.com/d/optout. >>>> >>>> > >>>> >>>> > -- >>>> >>>> > You received this message because you are subscribed to the >>>> Google Groups "sage-devel" group. >>>> >>>> > To unsubscribe from this group and stop receiving emails from >>>> it, send an email to sage-devel+...@googlegroups.com. >>>> >>>> > To post to this group, send email to sage-...@googlegroups.com. >>>> >>>> > Visit this group at https://groups.google.com/group/sage-devel. >>>> >>>> > For more options, visit https://groups.google.com/d/optout. >>>> >>>> >>>> >>>> -- >>>> >>>> You received this message because you are subscribed to the Google >>>> Groups "sage-devel" group. >>>> >>>> To unsubscribe from this group and stop receiving emails from it, >>>> send an email to sage-devel+...@googlegroups.com. >>>> >>>> To post to this group, send email to sage-...@googlegroups.com. >>>> >>>> Visit this group at https://groups.google.com/group/sage-devel. >>>> >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>>> >>> -- >>>> >>> You received this message because you are subscribed to the Google >>>> Groups "sage-devel" group. >>>> >>> To unsubscribe from this group and stop receiving emails from it, >>>> send an email to sage-devel+...@googlegroups.com. >>>> >>> To post to this group, send email to sage-...@googlegroups.com. >>>> >>> Visit this group at https://groups.google.com/group/sage-devel. >>>> >>> For more options, visit https://groups.google.com/d/optout. >>>> >> >>>> >> -- >>>> >> You received this message because you are subscribed to the Google >>>> Groups "sage-devel" group. >>>> >> To unsubscribe from this group and stop receiving emails from it, >>>> send an email to sage-devel+...@googlegroups.com. >>>> >> To post to this group, send email to sage-...@googlegroups.com. >>>> >> Visit this group at https://groups.google.com/group/sage-devel. >>>> >> For more options, visit https://groups.google.com/d/optout. >>>> > >>>> > -- >>>> > You received this message because you are subscribed to the Google >>>> Groups "sage-devel" group. >>>> > To unsubscribe from this group and stop receiving emails from it, >>>> send an email to sage-devel+...@googlegroups.com. >>>> > To post to this group, send email to sage-...@googlegroups.com. >>>> > Visit this group at https://groups.google.com/group/sage-devel. >>>> > For more options, visit https://groups.google.com/d/optout. >>>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "sage-devel" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to sage-devel+...@googlegroups.com <javascript:>. >>> To post to this group, send email to sage-...@googlegroups.com >>> <javascript:>. >>> Visit this group at https://groups.google.com/group/sage-devel. >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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