tcltk package failure with Bioconductor #1863

verdurin · 2015-08-14T13:56:52Z

I'm trying to install R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb on EB 2.2.0.

The build is failing because it is unable to find the 'tcltk' package:

== 2015-08-14 09:43:56,016 main.Bundle DEBUG Installing extension widgetTools with default class RPackage (from easybuild.easyblocks.generic.rpackage)
== 2015-08-14 09:43:56,017 main.Bundle DEBUG Installing R package widgetTools version 1.46.0.
== 2015-08-14 09:43:56,017 main.Bundle DEBUG make_cmdline_cmd returns R CMD INSTALL /home/operations/.local/easybuild/sources/r/R-bundle-Bioconductor/extensions/widgetTools_1.46.0.tar.gz   --library=/srv/data/sw/eb/software/R-bundle-Bioconductor/3.1-goolf-1.7.20-R-3.2.0 --no-clean-on-error
== 2015-08-14 09:43:56,017 main.run DEBUG run_cmd: running cmd R CMD INSTALL /home/operations/.local/easybuild/sources/r/R-bundle-Bioconductor/extensions/widgetTools_1.46.0.tar.gz   --library=/srv/data/sw/eb/software/R-bundle-Bioconductor/3.1-goolf-1.7.20-R-3.2.0 --no-clean-on-error (in /home/operations/src/github/easybuild-easyconfigs)
== 2015-08-14 09:43:56,296 main.run DEBUG cmd "R CMD INSTALL /home/operations/.local/easybuild/sources/r/R-bundle-Bioconductor/extensions/widgetTools_1.46.0.tar.gz   --library=/srv/data/sw/eb/software/R-bundle-Bioconductor/3.1-goolf-1.7.20-R-3.2.0 --no-clean-on-error" exited with exitcode 1 and output:
* installing *source* package 'widgetTools' ...
** R
** inst
** preparing package for lazy loading
Warning: S3 methods 'as.character.tclObj', 'as.character.tclVar', 'as.double.tclObj', 'as.integer.tclObj', 'as.logical.tclObj', 'as.raw.tclObj', 'print.tclObj', '[[.tclArray', '[[<-.tclArray', '$.tclArray', '$<-.tclArray', 'names.tclArray', 'names<-.tclArray', 'length.tclArray', 'length<-.tclArray', 'tclObj.tclVar', 'tclObj<-.tclVar', 'tclvalue.default', 'tclvalue.tclObj', 'tclvalue.tclVar', 'tclvalue<-.default', 'tclvalue<-.tclVar', 'close.tkProgressBar' were declared in NAMESPACE but not found
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: Tcl/Tk support is not available on this system
Error : package 'tcltk' could not be loaded
ERROR: lazy loading failed for package 'widgetTools'

== 2015-08-14 09:43:56,331 main ERROR cmd "R CMD INSTALL /home/operations/.local/easybuild/sources/r/R-bundle-Bioconductor/extensions/widgetTools_1.46.0.tar.gz   --library=/srv/data/sw/eb/software/R-bundle-Bioconductor/3.1-goolf-1.7.20-R-3.2.0 --no-clean-on-error" exited with exitcode 1 and output:
* installing *source* package 'widgetTools' ...
** R
** inst
** preparing package for lazy loading
Warning: S3 methods 'as.character.tclObj', 'as.character.tclVar', 'as.double.tclObj', 'as.integer.tclObj', 'as.logical.tclObj', 'as.raw.tclObj', 'print.tclObj', '[[.tclArray', '[[<-.tclArray', '$.tclArray', '$<-.tclArray', 'names.tclArray', 'names<-.tclArray', 'length.tclArray', 'length<-.tclArray', 'tclObj.tclVar', 'tclObj<-.tclVar', 'tclvalue.default', 'tclvalue.tclObj', 'tclvalue.tclVar', 'tclvalue<-.default', 'tclvalue<-.tclVar', 'close.tkProgressBar' were declared in NAMESPACE but not found
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: Tcl/Tk support is not available on this system
Error : package 'tcltk' could not be loaded
ERROR: lazy loading failed for package 'widgetTools'
 (at easybuild/tools/run.py:360 in parse_cmd_output)
== 2015-08-14 09:43:56,332 main.easyblock WARNING build failed (first 300 chars): cmd "R CMD INSTALL /home/operations/.local/easybuild/sources/r/R-bundle-Bioconductor/extensions/widgetTools_1.46.0.tar.gz   --library=/srv/data/sw/eb/software/R-bundle-Bioconductor/3.1-goolf-1.7.20-R-3.2.0 --no-clean-on-error" exited with exitcode 1 and output:
* installing *source* package 'widgetT
== 2015-08-14 09:43:56,332 main.Bundle INFO Closing log for application name R-bundle-Bioconductor version 3.1

The text was updated successfully, but these errors were encountered:

verdurin · 2015-08-14T13:58:14Z

There may have been a problem with the initial R build:

[operations@snap-boot-test-2 easybuild-easyconfigs]$ R

R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (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.

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.

> library("tcltk")
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: Tcl/Tk support is not available on this system
In addition: Warning message:
S3 methods 'as.character.tclObj', 'as.character.tclVar', 'as.double.tclObj', 'as.integer.tclObj', 'as.logical.tclObj', 'as.raw.tclObj', 'print.tclObj', '[[.tclArray', '[[<-.tclArray', '$.tclArray', '$<-.tclArray', 'names.tclArray', 'names<-.tclArray', 'length.tclArray', 'length<-.tclArray', 'tclObj.tclVar', 'tclObj<-.tclVar', 'tclvalue.default', 'tclvalue.tclObj', 'tclvalue.tclVar', 'tclvalue<-.default', 'tclvalue<-.tclVar', 'close.tkProgressBar' were declared in NAMESPACE but not found
Error: package or namespace load failed for 'tcltk'
> capabilities("tcltk")
tcltk
FALSE

verdurin · 2015-08-14T13:59:16Z

These are the only available build logs for the tcltk package:

make[3]: Entering directory `/home/operations/.local/easybuild/build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
make[4]: Entering directory `/home/operations/.local/easybuild/build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk'
mkdir -p -- ../../../library/tcltk/exec
make[4]: Leaving directory `/home/operations/.local/easybuild/build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk'
make[3]: Leaving directory `/home/operations/.local/easybuild/build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk'

boegel · 2015-08-14T14:06:35Z

This is what I have in the log for the same R installation (same version/toolchain).

Seems like you're missing tcltk.so, not sure why it's not getting built...

building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
make[4]: Entering directory `/tmp/vsc40023/easybuild_build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk'
mkdir -p -- ../../../library/tcltk/exec
make[4]: Leaving directory `/tmp/vsc40023/easybuild_build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk'
make[4]: Entering directory `/tmp/vsc40023/easybuild_build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk/src'
gcc -std=gnu99 -I../../../../include -DNDEBUG -I/usr/include -I/usr/include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/OpenBLAS/0.2.13-GCC-4.8.4-LAPACK-3.5.0/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/FFTW/3.3.4-gompi-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libreadline/6.3-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/ncurses/5.9-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libpng/1.6.17-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libjpeg-turbo/1.4.0-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Java/1.7.0_80/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Tcl/8.6.4-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Tk/8.6.4-goolf-1.7.20-no-X11/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/cURL/7.43.0-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libxml2/2.9.2-goolf-1.7.20/include    -fpic  -O2 -march=native  -c init.c -o init.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I/usr/include -I/usr/include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/OpenBLAS/0.2.13-GCC-4.8.4-LAPACK-3.5.0/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/FFTW/3.3.4-gompi-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libreadline/6.3-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/ncurses/5.9-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libpng/1.6.17-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libjpeg-turbo/1.4.0-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Java/1.7.0_80/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Tcl/8.6.4-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Tk/8.6.4-goolf-1.7.20-no-X11/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/cURL/7.43.0-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libxml2/2.9.2-goolf-1.7.20/include    -fpic  -O2 -march=native  -c tcltk.c -o tcltk.o
gcc -std=gnu99 -I../../../../include -DNDEBUG -I/usr/include -I/usr/include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/OpenBLAS/0.2.13-GCC-4.8.4-LAPACK-3.5.0/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/FFTW/3.3.4-gompi-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libreadline/6.3-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/ncurses/5.9-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libpng/1.6.17-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libjpeg-turbo/1.4.0-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Java/1.7.0_80/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Tcl/8.6.4-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Tk/8.6.4-goolf-1.7.20-no-X11/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/cURL/7.43.0-goolf-1.7.20/include -I/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libxml2/2.9.2-goolf-1.7.20/include    -fpic  -O2 -march=native  -c tcltk_unix.c -o tcltk_unix.o
making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_unix.d from tcltk_unix.c
gcc -std=gnu99 -shared -L../../../../lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/GCC/4.8.4/lib64 -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/GCC/4.8.4/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/OpenBLAS/0.2.13-GCC-4.8.4-LAPACK-3.5.0/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-1.7.20-OpenBLAS-0.2.13-LAPACK-3.5.0/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/FFTW/3.3.4-gompi-1.7.20/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libreadline/6.3-goolf-1.7.20/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/ncurses/5.9-goolf-1.7.20/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libpng/1.6.17-goolf-1.7.20/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libjpeg-turbo/1.4.0-goolf-1.7.20/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Java/1.7.0_80/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Tcl/8.6.4-goolf-1.7.20/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Tk/8.6.4-goolf-1.7.20-no-X11/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/cURL/7.43.0-goolf-1.7.20/lib -L/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/libxml2/2.9.2-goolf-1.7.20/lib -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.5 -L/usr/lib64 -ltk8.5 -lX11 -lm -L../../../../lib -lR
make[5]: Entering directory `/tmp/vsc40023/easybuild_build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk/src'
mkdir -p -- ../../../../library/tcltk/libs
make[5]: Leaving directory `/tmp/vsc40023/easybuild_build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk/src'
make[4]: Leaving directory `/tmp/vsc40023/easybuild_build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk/src'
make[4]: Entering directory `/tmp/vsc40023/easybuild_build/R/3.2.0/goolf-1.7.20/R-3.2.0/src/library/tcltk'
byte-compiling package 'tcltk'

boegel · 2015-08-14T21:08:16Z

@verdurin: let us know whether installing both X11 headers and libs resolved this issue... I'd love to get a good view on this.

verdurin · 2015-08-17T09:21:58Z

I've tried a complete rebuild but with the same result. However, I suspect local misconfiguration may be in part to blame, so I've tried to fix that and will now rebuild everything again.

verdurin · 2015-08-17T11:53:49Z

Still the same problem after a complete rebuild, with fixed local configuration. The R build doesn't include the tcltk capability.

boegel · 2015-08-17T12:07:54Z

@verdurin: do you have more details about OS, etc.? Can you share the full R debug log with me (bzipped via mail, or uploaded somewhere)?

verdurin · 2015-08-17T13:01:27Z

This is all on a CentOS 7.1 instance, fully updated. I've just started another instance, on which I'm running the whole pipeline again and I'll put the log online for you.

boegel · 2015-08-17T13:07:13Z

OK, I have access to CentOS 7.1 too, I can see if I can reproduce the problem there.

verdurin · 2015-08-17T13:12:30Z

I've just mailed you a link to the two log files - R and R-bundle-Bioconductor. Thanks again.

boegel · 2015-08-17T14:41:47Z

I can't reproduce this issue on CentOS 7.1:

-bash-4.2$ cat /etc/redhat-release 
CentOS Linux release 7.1.1503 (Core) 
-bash-4.2$ ls $EASYBUILD_PREFIX/software/R/3.2.0-goolf-1.7.20/lib64/R/library/tcltk/libs
tcltk.so

verdurin · 2015-08-17T14:45:44Z

Hmmph. Can you send me the history of how you installed it, so I can try that? (in case I've done it wrong somehow)

verdurin · 2015-08-17T15:01:49Z

All I have in the directory is a single file 'tcltk', with the contents:

.onLoad <- function(libname, pkgname)
stop("Tcl/Tk support is not available on this system", domain = "R-tcltk")

boegel · 2015-08-17T15:04:27Z

I didn't do anything special, just "eb R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb -dr".

I did use 2.3.0dev, but that shouldn't matter, nothing has changed that could affect the R installation, afaik (see https://github.com/hpcugent/easybuild-easyconfigs/commits/develop/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb and https://github.com/hpcugent/easybuild-easyblocks/commits/develop/easybuild/easyblocks/r/r.py)

verdurin · 2015-08-17T15:08:51Z

Well, difficult to get that wrong. I wonder whether it's to do with system dependencies? What did you install on the system before invoking eb?

boegel · 2015-08-17T15:56:54Z

In yours logs, I find this at the end of the output of the configure command:

R is now configured for x86_64-unknown-linux-gnu

  Source directory:          .
  Installation directory:    /srv/data/sw/eb/software/R/3.2.0-goolf-1.7.20

  C compiler:                gcc -std=gnu99  -O2 -march=native
  Fortran 77 compiler:       gfortran  -O2 -march=native

  C++ compiler:              g++  -O2 -march=native
  C++ 11 compiler:           g++  -std=c++11 -O2 -march=native
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:         

  Interfaces supported:      
  External libraries:        readline, BLAS(OpenBLAS), LAPACK(generic), zlib, PCRE, curl
  Additional capabilities:   PNG, JPEG, NLS
  Options enabled:           shared R library, R profiling

  Capabilities skipped:      TIFF, cairo, ICU
  Options not enabled:       shared BLAS, memory profiling

  Recommended packages:      no

configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages

In my logs, I have this (note mention of tcltk here):

R is now configured for x86_64-unknown-linux-gnu

  Source directory:          .
  Installation directory:    /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/CO7/haswell-ib/software/R/3.2.0-goolf-1.7.20

  C compiler:                gcc -std=gnu99  -O2 -march=native
  Fortran 77 compiler:       gfortran  -O2 -march=native

  C++ compiler:              g++  -O2 -march=native
  C++ 11 compiler:           g++  -std=c++11 -O2 -march=native
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:         

  Interfaces supported:      tcltk
  External libraries:        readline, BLAS(OpenBLAS), LAPACK(generic), zlib, bzlib, lzma, PCRE, curl
  Additional capabilities:   PNG, JPEG, NLS, cairo
  Options enabled:           shared R library, R profiling

  Capabilities skipped:      TIFF, ICU
  Options not enabled:       shared BLAS, memory profiling

  Recommended packages:      no

configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer

So, you have some dependency that is required for tcltk missing in the OS. No clue which one though...

boegel · 2015-08-17T16:05:11Z

From https://support.bioconductor.org/p/43061/:

Required stuff:
 make
 libc6-dev
 gfortran
 gfortran-4.2
 g++
 g++-4.2
 libreadline5-dev
 libx11-dev
 libxt-dev

Other highly recommended stuff (TeX/LaTeX, tcltk, PNG, JPEG, cairo,
Java):
 texlive-full
 tcl8.5-dev
 tk8.5-dev
 libxss-dev
 libpng12-dev
 libjpeg62-dev
 libcairo2-dev
 gcj
 gcj-4.2

libpng and libjpeg are covered by EB itself via dependencies, and I don't have cairo or libxss (which is screensaver related) in the OS. I sure hope texlive is not to blame. ;-)

Do you have libXt stuff installed? And which libX11 packages are installed exactly?

verdurin · 2015-08-17T16:10:35Z

I've just installed libXt, libXt-devel and will try rebuilding just R.

libX11 and libX11-devel are installed.

verdurin · 2015-08-17T16:17:30Z

Okay, libXt wasn't sufficient on its own.

verdurin · 2015-08-17T16:26:11Z

Right, I've installed tk-devel and tcl-devel and it looks as though it might work. The 'Interfaces' line in the configure output looks like yours. I'll let you know once it's finished...

verdurin · 2015-08-17T16:32:19Z

Yes, trying that on two different instances, the 'Interfaces' line after ./configure looks better. One has a lot more memory and CPUs so will hopefully finish before I have to leave for the day. I'll check from home tonight, anyway.

verdurin · 2015-08-17T16:34:42Z

Can't see a tcltk.so yet but the small 'tcltk' file looks better:

local({
    info <- loadingNamespaceInfo()
    pkg <- info$pkgname
    ns <- .getNamespace(as.name(pkg))
    if (is.null(ns))
        stop("cannot find namespace environment for ", pkg, domain = NA);
    dbbase <- file.path(info$libname, pkg, "R", pkg)
    lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
})

boegel · 2015-08-17T16:52:03Z

OK, that basically means something is wrong or incomplete with the Tcl/Tk that are included as dependencies... Yikes.

verdurin · 2015-08-17T21:07:41Z

Can confirm that on both instances Bioconductor built successfully after installation of tk and tcl devel RPMs. It loads without any errors.

verdurin · 2015-09-13T06:55:50Z

Just to confirm that with 2.3.0 I still had to install tk-devel and tcl-devel.

boegel · 2015-09-22T18:20:29Z

Yeah, we'll need to figure this out at some point...

@verdurin: can you check whether R needs to be told where Tcl/Tk are available, since they're installed in a non-standard prefix with EB?

verdurin · 2015-09-24T16:42:14Z

@boegel: will do

boegel · 2016-03-11T16:04:09Z

@verdurin ping? Is this still an issue with #2102 in place?

verdurin · 2016-03-12T10:23:22Z

Running a test build now, @boegel

verdurin · 2016-03-12T11:12:58Z

Hmm, running the test in a Fedora 23 vagrant box, and saw this error with binutils:

configure:5978: result: no
configure:5998: checking for version 0.12 of ISL
configure:6017: gcc -o conftest -g -O2      conftest.c /home/vagrant/.local/easybuild/software/zlib/1.2.8/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib -lisl >&5
conftest.c:10:25: fatal error: isl/version.h: No such file or directory
compilation terminated.
configure:6017: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h.  */
| #include <isl/version.h>
|    #include <string.h>
| int
| main ()
| {
| if (strncmp (isl_version (), "isl-0.12", strlen ("isl-0.12")) != 0)
|      return 1;
|
|   ;
|   return 0;
| }

verdurin · 2016-03-12T11:13:41Z

This is with R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb

boegel · 2016-03-12T12:22:34Z

@verdurin: this is when installing GCC?

@wpoely86: any idea?

verdurin · 2016-03-12T12:28:56Z

It's a brand new Vagrant box so there's nothing on there. This is with binutils, specifically:

== processing EasyBuild easyconfig /home/vagrant/EasyBuild-Whl34Y/easybuild-easyconfigs/easybuild/easyconfigs/b/binutils/binutils-2.25.eb
== building and installing binutils/2.25...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== FAILED: Installation ended unsuccessfully (build directory: /home/vagrant/.local/easybuild/build/binutils/2.25/dummy-): build failed (first 300 chars): cmd "LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath=/usr/lib"
 make -j 2 " exited with exitcode 2 and output:
make[1]: Entering directory '/home/vagrant/.local/easybuild/build/binutils/2.25/dummy-/binutils-2.25'
Configuring in ./intl
Configuring in ./l
== Results of the build can be found in the log file /tmp/eb-mfiV6D/easybuild-binutils-2.25-20160312.103706.TeBrY.log
ERROR: Build of /home/vagrant/EasyBuild-Whl34Y/easybuild-easyconfigs/easybuild/easyconfigs/b/binutils/binutils-2.25.eb failed (err: 'build failed (first 300 chars): cmd "LIBS="$EBROOTZLIB/lib/libz.a -Wl,-rpath=/lib64 -Wl,-rpath=/usr/lib64 -Wl,-rpath=/lib -Wl,-rpath
=/usr/lib" make -j 2 " exited with exitcode 2 and output:\nmake[1]: Entering directory \'/home/vagrant/.local/easybuild/build/binutils/2.25/dummy-/binutils-2.25\'\nConfiguring in ./intl\nConfiguring in ./l')

boegel · 2016-03-12T12:51:15Z

fixed with #2681?

verdurin · 2016-03-12T22:13:56Z

No, that's already in the tree I'm using, which is a brand new develop as of this morning.

boegel · 2016-03-14T17:37:21Z

@verdurin Then I'll need more details, can you share a full debug log on the binutils install issue?

verdurin · 2016-03-14T21:37:21Z

@boegel - trying to reproduce now. I suspect it's a change in the Fedora RPM groups.

verdurin · 2016-03-14T23:08:44Z

Okay, the ISL error has gone, but the X11 error is still there:

== 2016-03-13 09:12:36,399 templates.py:173 DEBUG version found in easyconfig is 8.6.4
== 2016-03-13 09:12:36,399 templates.py:210 DEBUG name: name, config: Tk
== 2016-03-13 09:12:36,399 templates.py:210 DEBUG name: version, config: 8.6.4
== 2016-03-13 09:12:36,399 templates.py:210 DEBUG name: versionsuffix, config: -no-X11
== 2016-03-13 09:12:36,400 templates.py:210 DEBUG name: versionprefix, config:
== 2016-03-13 09:12:36,400 easyblock.py:2067 INFO Running method build_step part of step build
== 2016-03-13 09:12:36,400 run.py:99 DEBUG run_cmd: running cmd  make -j 2  (in /home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix)
== 2016-03-13 09:12:36,443 run.py:392 DEBUG cmd " make -j 2 " exited with exitcode 2 and output:
gcc -c -O2 -I/home/vagrant/.local/easybuild/software/Tcl/8.6.4-foss-2016a/include -pipe -I/home/vagrant/.local/easybuild/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/include -I/home/vagrant/.local/easybuild/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/include -I/home/vagrant/.local/easybuild/software/FFTW/3.3.4-gompi-2016a/include -I/home/vagrant/.local/easybuild/software/Tcl/8.6.4-foss-2016a/include -Wall -fPIC -DBUILD_tk -I/home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../unix -I/home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic -I/home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../bitmaps -I/home/vagrant/.local/easybuild/build/Tcl/8.6.4/foss-2016a/tcl8.6.4/generic -I/home/vagrant/.local/easybuild/build/Tcl/8.6.4/foss-2016a/tcl8.6.4/unix  -DPACKAGE_NAME=\"tk\" -DPACKAGE_TARNAME=\"tk\" -DPACKAGE_VERSION=\"8.6\" -DPACKAGE_STRING=\"tk\ 8.6\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DUSE_THREAD_ALLOC=1 -D_REENTRANT=1 -D_THREAD_SAFE=1 -DHAVE_PTHREAD_ATTR_SETSTACKSIZE=1 -DHAVE_PTHREAD_ATFORK=1 -DTCL_THREADS=1 -DMODULE_SCOPE=extern\ __attribute__\(\(__visibility__\(\"hidden\"\)\)\) -DHAVE_HIDDEN=1 -DHAVE_CAST_TO_UNION=1 -DTCL_SHLIB_EXT=\".so\" -DNDEBUG=1 -DTCL_CFG_OPTIMIZED=1 -D_LARGEFILE64_SOURCE=1 -DTCL_WIDE_INT_IS_LONG=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_INTPTR_T=1 -DHAVE_UINTPTR_T=1 -DHAVE_PW_GECOS=1 -DXKEYCODETOKEYSYM_IS_DEPRECATED=1      -DTCL_NO_DEPRECATED  -DUSE_TCL_STUBS /home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic/tkStubLib.cgcc -c -O2 -I/home/vagrant/.local/easybuild/software/Tcl/8.6.4-foss-2016a/include -pipe -I/home/vagrant/.local/easybuild/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/include -I/home/vagrant/.local/easybuild/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/include -I/home/vagrant/.local/easybuild/software/FFTW/3.3.4-gompi-2016a/include -I/home/vagrant/.local/easybuild/software/Tcl/8.6.4-foss-2016a/include -Wall -fPIC -DBUILD_tk -I/home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../unix -I/home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic -I/home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../bitmaps -I/home/vagrant/.local/easybuild/build/Tcl/8.6.4/foss-2016a/tcl8.6.4/generic -I/home/vagrant/.local/easybuild/build/Tcl/8.6.4/foss-2016a/tcl8.6.4/unix  -DPACKAGE_NAME=\"tk\" -DPACKAGE_TARNAME=\"tk\" -DPACKAGE_VERSION=\"8.6\" -DPACKAGE_STRING=\"tk\ 8.6\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DUSE_THREAD_ALLOC=1 -D_REENTRANT=1 -D_THREAD_SAFE=1 -DHAVE_PTHREAD_ATTR_SETSTACKSIZE=1 -DHAVE_PTHREAD_ATFORK=1 -DTCL_THREADS=1 -DMODULE_SCOPE=extern\ __attribute__\(\(__visibility__\(\"hidden\"\)\)\) -DHAVE_HIDDEN=1 -DHAVE_CAST_TO_UNION=1 -DTCL_SHLIB_EXT=\".so\" -DNDEBUG=1 -DTCL_CFG_OPTIMIZED=1 -D_LARGEFILE64_SOURCE=1 -DTCL_WIDE_INT_IS_LONG=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_INTPTR_T=1 -DHAVE_UINTPTR_T=1 -DHAVE_PW_GECOS=1 -DXKEYCODETOKEYSYM_IS_DEPRECATED=1      -DTCL_NO_DEPRECATED  -DUSE_TCL_STUBS /home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic/ttk/ttkStubLib.c
In file included from /home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic/tkPort.h:21:0,
                 from /home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic/tkInt.h:19,
                 from /home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic/tkStubLib.c:14:
/home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic/tk.h:96:25: fatal error: X11/Xlib.h: No such file or directory
 #   include <X11/Xlib.h>
                         ^
compilation terminated.
In file included from /home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic/ttk/ttkStubLib.c:9:0:
/home/vagrant/.local/easybuild/build/Tk/8.6.4/foss-2016a-no-X11/tk8.6.4/unix/../generic/tk.h:96:25: fatal error: X11/Xlib.h: No such file or directory
 #   include <X11/Xlib.h>
                         ^
compilation terminated.
Makefile:1165: recipe for target 'tkStubLib.o' failed
make: *** [tkStubLib.o] Error 1
make: *** Waiting for unfinished jobs....
Makefile:1429: recipe for target 'ttkStubLib.o' failed
make: *** [ttkStubLib.o] Error 1

verdurin · 2016-03-14T23:09:34Z

I haven't installed anything in this VM other than what was requested by EB.

boegel · 2016-03-15T08:02:39Z

Now a duplicate of #1845?

Also, how did you resolve the ISL issue? How is it related to RPM groups, since ISL is provided by EB itself when building GCC?

boegel · 2016-03-15T08:04:08Z

Also duplicate of #2261, which has more info.

verdurin · 2016-03-15T08:55:52Z

On the latter point, I had installed the development-tools group, but now it appears you need c-development too. After doing that, the ISL error disappeared.

verdurin · 2016-03-15T08:58:29Z

Happy to close this and #1845 in favour of #2261 if you prefer.

boegel · 2016-09-19T12:57:04Z

let's follow up in #2261

This may help though: easybuilders/easybuild-easyblocks#995

boegel added this to the v2.2.1 milestone Aug 17, 2015

boegel modified the milestones: v2.4.0, v2.3.0 Aug 27, 2015

boegel removed this from the v2.5.0 milestone Dec 14, 2015

boegel modified the milestones: v2.6.0, v2.7.0 Jan 23, 2016

boegel modified the milestones: v2.8.0, v2.7.0 Mar 11, 2016

boegel modified the milestones: v2.8.0, v2.9.0 May 10, 2016

boegel mentioned this issue May 19, 2016

Adding updated easyconfigs for R 3.3 foss and intel 2016a, along with… #3079

Closed

boegel closed this as completed Sep 19, 2016

tcltk package failure with Bioconductor #1863

tcltk package failure with Bioconductor #1863

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