Problem installing hexbin?
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Sander Oom ▴ 30
@sander-oom-1695
Last seen 10.3 years ago
Dear R-bioconductor users, I have a problem installing hexbin from bioconductor: > biocLite(c("hexbin")) Running bioCLite version 0.1 with R version 2.2.1 Running biocinstall version 1.1 with R version 2.2.1 trying URL 'http://www.bioconductor.org/packages/bioc/1.7/src/contrib/hexbin_1.4. 0.tar.gz' Content type 'application/x-gzip' length 491520 bytes opened URL ================================================== downloaded 480Kb * Installing *source* package 'hexbin' ... ** libs gfortran -fPIC -c hbin.f -o hbin.o In file hbin.f:1 subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape, 1 Error: Symbol 'shape' at (1) has no IMPLICIT type make: *** [hbin.o] Error 1 ERROR: compilation failed for package 'hexbin' ** Removing '/usr/lib/R/library/hexbin' The downloaded packages are in /tmp/RtmpZ12736/downloaded_packages Warning message: installation of package 'hexbin' had non-zero exit status in: install.packages(pkgs = "hexbin", repos = c("http://www.bioconductor.org/packages/bioc/1.7", > Any suggestions? Thanks in advance for your help, Sander. PS.... I am using R on SUSE10: > > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 2.1 year 2005 month 12 day 20 svn rev 36812 language R > >
hexbin hexbin • 3.5k views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.3 years ago
Hi Sander, Sander Oom <slist at="" oomvanlieshout.net=""> writes: > I have a problem installing hexbin from bioconductor: > >> biocLite(c("hexbin")) > > Running bioCLite version 0.1 with R version 2.2.1 > > Running biocinstall version 1.1 with R version 2.2.1 > trying URL > 'http://www.bioconductor.org/packages/bioc/1.7/src/contrib/hexbin_1. 4.0.tar.gz' > Content type 'application/x-gzip' length 491520 bytes > opened URL > ================================================== > downloaded 480Kb > > * Installing *source* package 'hexbin' ... > ** libs > gfortran -fPIC -c hbin.f -o hbin.o > In file hbin.f:1 > > subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape, > 1 > Error: Symbol 'shape' at (1) has no IMPLICIT type > make: *** [hbin.o] Error 1 > ERROR: compilation failed for package 'hexbin' > ** Removing '/usr/lib/R/library/hexbin' I suspect the issue is with your Fortran compiler. What does gfortran --version report?
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Hi Seth and Sander: > > gfortran -fPIC -c hbin.f -o hbin.o > > In file hbin.f:1 > > > > subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape, > > 1 > > Error: Symbol 'shape' at (1) has no IMPLICIT type > > make: *** [hbin.o] Error 1 > > ERROR: compilation failed for package 'hexbin' > > ** Removing '/usr/lib/R/library/hexbin' > > I suspect the issue is with your Fortran compiler. What does gfortran > --version report? I have seen this before and the problem is that gfortran is more strict about the 80 character column width than g77 was. I think moving the shape variable to the next line with a new type declaration, i.e. something like: INTEGER shape, will fix the problem. Good Luck!! Dave H -- David A. Henderson, Ph.D. Research Scientist Insightful Corporation 1700 Westlake Avenue North, Suite 500 Seattle, WA 98109-3044 Tel: 206-802-2307 Fax: 206-283-8691 DNADave at Insightful.Com http://www.insightful.com
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David Henderson wrote: > Hi Seth and Sander: > >>> gfortran -fPIC -c hbin.f -o hbin.o >>> In file hbin.f:1 >>> >>> subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape, >>> 1 >>> Error: Symbol 'shape' at (1) has no IMPLICIT type >>> make: *** [hbin.o] Error 1 >>> ERROR: compilation failed for package 'hexbin' >>> ** Removing '/usr/lib/R/library/hexbin' >> I suspect the issue is with your Fortran compiler. What does gfortran >> --version report? > > I have seen this before and the problem is that gfortran is more strict > about the 80 character column width than g77 was. I think moving the > shape variable to the next line with a new type declaration, i.e. > something like: INTEGER shape, will fix the problem. > > Good Luck!! > > Dave H Hi Seth and Dave, ~> gfortran --version GNU Fortran 95 (GCC 4.0.2 20050901 (prerelease) (SUSE Linux)) Copyright (C) 2005 Free Software Foundation, Inc. Would not know where to start looking for the 'shape' declaration. Hopefully the developer will be following the mailing list and know the answer.... Thanks, Sander.
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it seems fine on our Suse Box with rgentlem at gladstone:~> gfortran --version GNU Fortran 95 (GCC 4.0.2 20050901 (prerelease) (SUSE Linux)) Copyright (C) 2005 Free Software Foundation, Inc. and: gfortran -fPIC -c hbin.f -o hbin.o does what I think it is supposed to do. So I suspect that something else is wrong. I do see tabs not spaces in the file (which could cause some problems I suspect). To find the source down load the package, untar it and look in hexbin/src you could try changing all tabs to the right number of spaces and see if that fixes things. note the file also declares implicit none and then does define a type for shape. best wishes Robert Sander Oom wrote: > David Henderson wrote: > >>Hi Seth and Sander: >> >> >>>>gfortran -fPIC -c hbin.f -o hbin.o >>>> In file hbin.f:1 >>>> >>>> subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape, >>>> 1 >>>>Error: Symbol 'shape' at (1) has no IMPLICIT type >>>>make: *** [hbin.o] Error 1 >>>>ERROR: compilation failed for package 'hexbin' >>>>** Removing '/usr/lib/R/library/hexbin' >>> >>>I suspect the issue is with your Fortran compiler. What does gfortran >>>--version report? >> >>I have seen this before and the problem is that gfortran is more strict >>about the 80 character column width than g77 was. I think moving the >>shape variable to the next line with a new type declaration, i.e. >>something like: INTEGER shape, will fix the problem. >> >>Good Luck!! >> >>Dave H > > > Hi Seth and Dave, > > ~> gfortran --version > GNU Fortran 95 (GCC 4.0.2 20050901 (prerelease) (SUSE Linux)) > Copyright (C) 2005 Free Software Foundation, Inc. > > Would not know where to start looking for the 'shape' declaration. > Hopefully the developer will be following the mailing list and know the > answer.... > > Thanks, > > Sander. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Hi Robert: > it seems fine on our Suse Box with > rgentlem at gladstone:~> gfortran --version > GNU Fortran 95 (GCC 4.0.2 20050901 (prerelease) (SUSE Linux)) > Copyright (C) 2005 Free Software Foundation, Inc. > and: > gfortran -fPIC -c hbin.f -o hbin.o > > does what I think it is supposed to do. > So I suspect that something else is wrong. Here's what I see on my SuSE 10.0 laptop: minime{david}103: gfortran --version GNU Fortran 95 (GCC 4.0.2 20050901 (prerelease) (SUSE Linux)) Copyright (C) 2005 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING minime{david}104: R CMD INSTALL hexbin_1.4.0.tar.gz * Installing *source* package 'hexbin' ... ** libs gfortran -fPIC -O2 -c hbin.f -o hbin.o In file hbin.f:1 subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape, 1 Error: Symbol 'shape' at (1) has no IMPLICIT type make: *** [hbin.o] Error 1 ERROR: compilation failed for package 'hexbin' ** Removing '/usr/local/lib/R/library/hexbin' ** Restoring previous '/usr/local/lib/R/library/hexbin' > I do see tabs not spaces in the file (which could cause some problems I > suspect). > > To find the source down load the package, untar it and look in > hexbin/src > you could try changing all tabs to the right number of spaces and see if > that fixes things. > > note the file also declares > implicit none > and then does define a type for shape. Here's a snippet from the code in hbin.f viewed in vi: double precision x(n), y(n), xcm(*),ycm(*), rx(2),ry(2), size,shape integer i, i1, i2, iinc integer j1, j2, jinc integer L, lmax, lat double precision c1, c2, con1, con2, dist1 double precision sx, sy, xmin, ymin, xr, yr "hbin.f" 87L, 1938C 18,63-70 Top The 18,63-70 on the last line indicates that I have my cursor on column 70 of line 18. The cursor is in fact placed upon the comma right before the shape parameter is defined to be a double precision variable. I'll perform one edit to the file as follows: double precision x(n), y(n), xcm(*),ycm(*), rx(2),ry(2), size,shape will change to: double precision x(n), y(n), xcm(*),ycm(*), rx(2),ry(2), size double precision shape Now, here's the result of trying to install hexbin on my laptop following the above edit: minime{david}113: R CMD INSTALL hexbin * Installing *source* package 'hexbin' ... ** libs gfortran -fPIC -O2 -c hbin.f -o hbin.o gfortran -fPIC -O2 -c hcell.f -o hcell.o gfortran -fPIC -O2 -c herode.f -o herode.o gfortran -fPIC -O2 -c hsm.f -o hsm.o gcc -shared -L/usr/local/lib -o hexbin.so hbin.o hcell.o herode.o hsm.o -lgfortran -lm -lgcc_s ** R ** data ** inst ** preparing package for lazy loading Creating a new generic function for 'plot' in 'hexbin' Creating a new generic function for 'summary' in 'hexbin' ** help >>> Building/Updating help pages for package 'hexbin' Formats: text html latex example ** building package indices ... * DONE (hexbin) I've written to the maintainer in the past and he indicated that this would be fixed in new versions. Evidently it has not. There is likely a compiler flag that allows for sloppy column widths in fortran programs and I'll bet that you used this to compile R which is why it works for you and notfor me or Sander. Thanks!! Dave H -- David A. Henderson, Ph.D. Research Scientist Insightful Corporation 1700 Westlake Avenue North, Suite 500 Seattle, WA 98109-3044 Tel: 206-802-2307 Fax: 206-283-8691 DNADave at Insightful.Com http://www.insightful.com
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.3 years ago
David Henderson <dnadave at="" insightful.com=""> writes: > Hi Robert: > > > Here's what I see on my SuSE 10.0 laptop: > > minime{david}103: gfortran --version > GNU Fortran 95 (GCC 4.0.2 20050901 (prerelease) (SUSE Linux)) > Copyright (C) 2005 Free Software Foundation, Inc. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > minime{david}104: R CMD INSTALL hexbin_1.4.0.tar.gz > * Installing *source* package 'hexbin' ... > ** libs > gfortran -fPIC -O2 -c hbin.f -o hbin.o > In file hbin.f:1 > > subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape, > 1 > Error: Symbol 'shape' at (1) has no IMPLICIT type Dave, I think you have an old version of the hexbin code. hexbin> svn log -v -r 14557 ------------------------------------------------------------------ ------ r14557 | nikko at hailmail.net | 2005-10-24 09:11:18 -0700 (Mon, 24 Oct 2005) | 3 lines Changed paths: M /trunk/madman/Rpacks/hexbin/R/hexplom.R M /trunk/madman/Rpacks/hexbin/src/hbin.f debugging, fixed hbin.f to comply with gfortran error messages. Now it compiles ~/hexbin/src> svn diff -r 14556:HEAD Index: hbin.f =================================================================== --- hbin.f (.../trunk/madman/Rpacks/hexbin/src) (revision 14556) +++ hbin.f (.../branches/RELEASE_1_8/madman/Rpacks/hexbin/src) (revision 17729) @@ -15,7 +15,8 @@ integer n, nc, cell(*), cnt(*), bnd(2), cellid(*) c cellid(*): length 1 or n - double precision x(n), y(n), xcm(*),ycm(*), rx(2),ry(2), size,shape + double precision x(n), y(n), xcm(*),ycm(*), rx(2),ry(2), size + double precision shape integer i, i1, i2, iinc integer j1, j2, jinc integer L, lmax, lat Can you try with the latest: http://bioconductor.org/packages/1.8/bioc/html/hexbin.html + seth
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Seth Falcon wrote: > David Henderson <dnadave at="" insightful.com=""> writes: > >> Hi Robert: >> >> >> Here's what I see on my SuSE 10.0 laptop: >> >> minime{david}103: gfortran --version >> GNU Fortran 95 (GCC 4.0.2 20050901 (prerelease) (SUSE Linux)) >> Copyright (C) 2005 Free Software Foundation, Inc. >> >> GNU Fortran comes with NO WARRANTY, to the extent permitted by law. >> You may redistribute copies of GNU Fortran >> under the terms of the GNU General Public License. >> For more information about these matters, see the file named COPYING >> minime{david}104: R CMD INSTALL hexbin_1.4.0.tar.gz >> * Installing *source* package 'hexbin' ... >> ** libs >> gfortran -fPIC -O2 -c hbin.f -o hbin.o >> In file hbin.f:1 >> >> subroutine hbin(x,y,cell,cnt,xcm,ycm, size, shape, >> 1 >> Error: Symbol 'shape' at (1) has no IMPLICIT type > > Dave, I think you have an old version of the hexbin code. > > hexbin> svn log -v -r 14557 > ---------------------------------------------------------------- -------- > r14557 | nikko at hailmail.net | 2005-10-24 09:11:18 -0700 (Mon, 24 Oct 2005) | 3 lines > Changed paths: > M /trunk/madman/Rpacks/hexbin/R/hexplom.R > M /trunk/madman/Rpacks/hexbin/src/hbin.f > > debugging, fixed hbin.f to comply with gfortran error messages. Now it > compiles > > > ~/hexbin/src> svn diff -r 14556:HEAD > Index: hbin.f > =================================================================== > --- hbin.f (.../trunk/madman/Rpacks/hexbin/src) (revision 14556) > +++ hbin.f (.../branches/RELEASE_1_8/madman/Rpacks/hexbin/src) (revision 17729) > @@ -15,7 +15,8 @@ > > integer n, nc, cell(*), cnt(*), bnd(2), cellid(*) > c cellid(*): length 1 or n > - double precision x(n), y(n), xcm(*),ycm(*), rx(2),ry(2), size,shape > + double precision x(n), y(n), xcm(*),ycm(*), rx(2),ry(2), size > + double precision shape > integer i, i1, i2, iinc > integer j1, j2, jinc > integer L, lmax, lat > > Can you try with the latest: > http://bioconductor.org/packages/1.8/bioc/html/hexbin.html > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Hi Seth, Thanks for your help! A little progress was achieved, but still no correct result: > srcHexbin <- "http://bioconductor.org/packages/1.8/bioc/src/contrib/" > install.packages("hexbin", contriburl=srcHexbin) trying URL 'http://bioconductor.org/packages/1.8/bioc/src/contrib//hexbin_1.6.0.t ar.gz' Content type 'application/x-gzip' length 512021 bytes opened URL ================================================== downloaded 500Kb * Installing *source* package 'hexbin' ... ** libs gfortran -fPIC -c hbin.f -o hbin.o gfortran -fPIC -c hcell.f -o hcell.o gfortran -fPIC -c herode.f -o herode.o gfortran -fPIC -c hsm.f -o hsm.o gcc -shared -L/usr/local/lib -o hexbin.so hbin.o hcell.o herode.o hsm.o -lgfortran -lm -lgcc_s -L/usr/lib/R/lib -lR ** R ** data ** inst ** preparing package for lazy loading Error in setMethod("plot", signature(x = "hexbin", y = "missing"), gplot.hexbin) : no existing definition for function 'plot' Error: unable to load R code in package 'hexbin' Execution halted ERROR: lazy loading failed for package 'hexbin' ** Removing '/usr/lib/R/library/hexbin' The downloaded packages are in /tmp/RtmpeM8437/downloaded_packages Warning message: installation of package 'hexbin' had non-zero exit status in: install.packages("hexbin", contriburl = srcHexbin) > I regularly run this code to keep up tot date: options(repos = "http://cran.r-project.org/") ( theNew <- new.packages(ask=FALSE) ) install.packages(theNew) update.packages(ask=FALSE, checkBuilt=T) Thanks, Sander. > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 2.1 year 2005 month 12 day 20 svn rev 36812 language R >
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.3 years ago
Sander Oom <slist at="" oomvanlieshout.net=""> writes: > Hi Seth, > > Thanks for your help! A little progress was achieved, but still no > correct result: > >> srcHexbin <- "http://bioconductor.org/packages/1.8/bioc/src/contrib/" >> install.packages("hexbin", contriburl=srcHexbin) That is the URL for the 1.8 release (which was released _yesterday_) and is only compatible with R 2.3.x. You are using R 2.2.1. In general, it is better to install Bioc packages like this: source("http://bioconductor.org/biocLite.R") biocLite("hexbin") But the bug fix you need is not in the previous release. So please try upgrading to the latest R release (and then you _can_ use biocLite). + seth
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