Dear R-helpers, Christoph (author of phyloclim) and Luke (author of
tkrplot),

I would like to get your helps on installing of phyloclim in Ubuntu linux.
It seems a package named 'tkrplot' could not be installed at firstly, then
packages depends on it could not be installed latter.

As I have tested, installation of phyloclim works smoothly in Mac. I
attempted to install these packages in a Ubuntu server without root. I
guess if installation of tkrplot need a root priority.

It seems tkrplot is not so necessary for main functionalities of phyloclim,
so how to overcome the dependence of tkrplot, when installing phyloclim?

Could you please give any directions on my problem? Thanks in advance.

Please see details in the followings.

Best wishes,
Jian-Feng,

#####################################################################
# (1) my R version

R version 2.15.0 (2012-03-30)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
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.

  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.

#####################################################################
# (2) my session info
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.15.0

#####################################################################
# (3) my systems info
> Sys.info()
                               sysname
release
                               "Linux"
"2.6.37.6"
                               version
nodename
"#16 SMP Fri Jun 3 15:50:09 MEST 2011"
"upa"
                               machine
login
                              "x86_64"
"jmao"
                                  user
effective_user
                                "jmao"
"jmao"


#####################################################################
# (4) prompt from phyloclim installation

> install.packages("phyloclim")
Installing package(s) into ‘/ebio/abt6/jmao/R/Rpacks’
(as ‘lib’ is unspecified)
also installing the dependencies ‘gee’, ‘tkrplot’, ‘ape’, ‘adehabitat’

trying URL 'http://mirrors.softliste.de/cran/src/contrib/gee_4.13-18.tar.gz'
Content type 'application/x-gzip' length 57162 bytes (55 Kb)
opened URL
==================================================
downloaded 55 Kb

trying URL '
http://mirrors.softliste.de/cran/src/contrib/tkrplot_0.0-23.tar.gz'
Content type 'application/x-gzip' length 39037 bytes (38 Kb)
opened URL
==================================================
downloaded 38 Kb

trying URL 'http://mirrors.softliste.de/cran/src/contrib/ape_3.0-3.tar.gz'
Content type 'application/x-gzip' length 710889 bytes (694 Kb)
opened URL
==================================================
downloaded 694 Kb

trying URL '
http://mirrors.softliste.de/cran/src/contrib/adehabitat_1.8.10.tar.gz'
Content type 'application/x-gzip' length 2067806 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb

trying URL '
http://mirrors.softliste.de/cran/src/contrib/phyloclim_0.8.1.tar.gz'
Content type 'application/x-gzip' length 68133 bytes (66 Kb)
opened URL
==================================================
downloaded 66 Kb

* installing *source* package ‘gee’ ...
** package ‘gee’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -g -O2  -c dgedi.f -o dgedi.o
gfortran   -fpic  -g -O2  -c dgefa.f -o dgefa.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c ugee.c -o ugee.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o gee.so dgedi.o dgefa.o ugee.o
-L/ebio/abt6/jmao/R/R-2.15.0/lib -lRblas -lgfortran -lm -lgfortran -lm
installing to /ebio/abt6/jmao/R/Rpacks/gee/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (gee)
* installing *source* package ‘tkrplot’ ...
** package ‘tkrplot’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for tclConfig.sh... no
checking for tclConfig.sh in library (sub)directories... no
checking for tkConfig.sh... no
checking for tkConfig.sh in library (sub)directories... no
checking for tcl.h... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c tcltkimg.c -o tcltkimg.o
tcltkimg.c:2:16: error: tk.h: No such file or directory
tcltkimg.c:103: error: expected specifier-qualifier-list before ‘Tcl_Interp’
tcltkimg.c:114: error: expected specifier-qualifier-list before ‘Tk_Window’
tcltkimg.c: In function ‘GetRplotImage’:
tcltkimg.c:164: error: ‘TCL_ERROR’ undeclared (first use in this function)
tcltkimg.c:164: error: (Each undeclared identifier is reported only once
tcltkimg.c:164: error: for each function it appears in.)
tcltkimg.c:168: error: ‘TCL_OK’ undeclared (first use in this function)
tcltkimg.c: In function ‘CreateRplot’:
tcltkimg.c:193: error: expected declaration specifiers before ‘Tcl_Interp’
tcltkimg.c:196: error: expected declaration specifiers before ‘Tcl_Obj’
tcltkimg.c:198: error: expected declaration specifiers before ‘Tk_ImageType’
tcltkimg.c:199: error: expected declaration specifiers before
‘Tk_ImageMaster’
tcltkimg.c:200: error: expected declaration specifiers before ‘ClientData’
tcltkimg.c:192: warning: type of ‘interp’ defaults to ‘int’
tcltkimg.c:192: warning: type of ‘objv’ defaults to ‘int’
tcltkimg.c:192: warning: type of ‘typePtr’ defaults to ‘int’
tcltkimg.c:192: warning: type of ‘master’ defaults to ‘int’
tcltkimg.c:192: warning: type of ‘clientDataPtr’ defaults to ‘int’
tcltkimg.c:206: warning: implicit declaration of function ‘Tcl_AppendResult’
tcltkimg.c:207: error: ‘TCL_ERROR’ undeclared (first use in this function)
tcltkimg.c:215: error: ‘RplotMaster’ has no member named ‘Rdevice’
tcltkimg.c:218: error: ‘RplotMaster’ has no member named ‘Rdevice’
tcltkimg.c:218: error: ‘RplotMaster’ has no member named ‘image’
tcltkimg.c:219: error: ‘RplotMaster’ has no member named ‘width’
tcltkimg.c:219: error: ‘RplotMaster’ has no member named ‘height’
tcltkimg.c:219: error: ‘TCL_OK’ undeclared (first use in this function)
tcltkimg.c:225: warning: implicit declaration of function ‘ckalloc’
tcltkimg.c:225: warning: cast to pointer from integer of different size
tcltkimg.c:226: error: ‘RplotMaster’ has no member named ‘interp’
tcltkimg.c:227: error: ‘RplotMaster’ has no member named ‘Rdevice’
tcltkimg.c:227: error: ‘RplotMaster’ has no member named ‘Rdevice’
tcltkimg.c:228: error: ‘RplotMaster’ has no member named ‘haveImage’
tcltkimg.c:229: error: ‘RplotMaster’ has no member named ‘image’
tcltkimg.c:229: error: ‘RplotMaster’ has no member named ‘image’
tcltkimg.c:230: error: ‘RplotMaster’ has no member named ‘width’
tcltkimg.c:230: error: ‘RplotMaster’ has no member named ‘width’
tcltkimg.c:231: error: ‘RplotMaster’ has no member named ‘height’
tcltkimg.c:231: error: ‘RplotMaster’ has no member named ‘height’
tcltkimg.c:232: error: ‘RplotMaster’ has no member named ‘instanceCount’
tcltkimg.c:233: error: ‘RplotMaster’ has no member named ‘master’
tcltkimg.c:234: error: invalid type argument of ‘unary *’ (have ‘int’)
tcltkimg.c:234: error: ‘ClientData’ undeclared (first use in this function)
tcltkimg.c:234: error: expected ‘;’ before ‘prpm’
tcltkimg.c: At top level:
tcltkimg.c:257: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘GetRplot’
tcltkimg.c:259: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘masterData’
tcltkimg.c:260: error: expected identifier or ‘(’ before ‘{’ token
tcltkimg.c: In function ‘DisplayRplot’:
tcltkimg.c:300: error: expected declaration specifiers before ‘ClientData’
tcltkimg.c:298: warning: type of ‘clientData’ defaults to ‘int’
tcltkimg.c:308: warning: cast to pointer from integer of different size
tcltkimg.c:320: warning: implicit declaration of function ‘Tk_Depth’
tcltkimg.c:320: error: ‘RplotInstance’ has no member named ‘tkwin’
tcltkimg.c:326: warning: implicit declaration of function ‘Tk_GetPixmap’
tcltkimg.c:326: warning: implicit declaration of function ‘Tk_WindowId’
tcltkimg.c:326: error: ‘RplotInstance’ has no member named ‘tkwin’
tcltkimg.c:328: warning: implicit declaration of function ‘Tk_GetGC’
tcltkimg.c:328: error: ‘RplotInstance’ has no member named ‘tkwin’
tcltkimg.c:329: error: ‘RplotMaster’ has no member named ‘image’
tcltkimg.c:330: warning: implicit declaration of function ‘Tk_FreeGC’
tcltkimg.c:334: error: ‘RplotInstance’ has no member named ‘tkwin’
tcltkimg.c:342: warning: implicit declaration of function ‘Tk_FreePixmap’
tcltkimg.c: In function ‘FreeRplot’:
tcltkimg.c:365: error: expected declaration specifiers before ‘ClientData’
tcltkimg.c:364: warning: type of ‘clientData’ defaults to ‘int’
tcltkimg.c:368: warning: cast to pointer from integer of different size
tcltkimg.c:371: error: ‘RplotMaster’ has no member named ‘instanceCount’
tcltkimg.c:372: warning: implicit declaration of function ‘ckfree’
tcltkimg.c: In function ‘DeleteRplot’:
tcltkimg.c:394: error: expected declaration specifiers before ‘ClientData’
tcltkimg.c:393: warning: type of ‘masterData’ defaults to ‘int’
tcltkimg.c:396: warning: cast to pointer from integer of different size
tcltkimg.c:398: error: ‘RplotMaster’ has no member named ‘instanceCount’
tcltkimg.c:399: warning: implicit declaration of function ‘panic’
tcltkimg.c:401: error: ‘RplotMaster’ has no member named ‘haveImage’
tcltkimg.c:405: error: ‘RplotMaster’ has no member named ‘image’
tcltkimg.c:405: error: ‘RplotMaster’ has no member named ‘image’
tcltkimg.c: At top level:
tcltkimg.c:440: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘RplotImageType’
tcltkimg.c: In function ‘Rplot_Init’:
tcltkimg.c:451: error: expected declaration specifiers before ‘Tcl_Interp’
tcltkimg.c:450: warning: type of ‘interp’ defaults to ‘int’
tcltkimg.c:454: error: ‘CONST’ undeclared (first use in this function)
tcltkimg.c:454: error: expected ‘;’ before ‘char’
tcltkimg.c:456: error: ‘version’ undeclared (first use in this function)
tcltkimg.c:456: warning: implicit declaration of function ‘Tcl_PkgRequire’
tcltkimg.c:456: error: ‘TCL_VERSION’ undeclared (first use in this function)
tcltkimg.c:457: error: ‘TCL_ERROR’ undeclared (first use in this function)
tcltkimg.c:458: error: ‘TK_VERSION’ undeclared (first use in this function)
tcltkimg.c:463: warning: implicit declaration of function
‘Tk_CreateImageType’
tcltkimg.c:463: error: ‘RplotImageType’ undeclared (first use in this
function)
tcltkimg.c:465: warning: implicit declaration of function ‘Tcl_PkgProvide’
tcltkimg.c: In function ‘Rplot_SafeInit’:
tcltkimg.c:469: error: expected declaration specifiers before ‘Tcl_Interp’
tcltkimg.c:468: warning: type of ‘interp’ defaults to ‘int’
make: *** [tcltkimg.o] Error 1
ERROR: compilation failed for package ‘tkrplot’
* removing ‘/ebio/abt6/jmao/R/Rpacks/tkrplot’
* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c BIONJ.c -o BIONJ.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c NNI.c -o NNI.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c SPR.c -o SPR.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c TBR.c -o TBR.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c additive.c -o additive.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c ape.c -o ape.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c bNNI.c -o bNNI.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c bionjs.c -o bionjs.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c bipartition.c -o bipartition.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c delta_plot.c -o delta_plot.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c dist_dna.c -o dist_dna.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c heap.c -o heap.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c mat_expo.c -o mat_expo.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c me.c -o me.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c me_balanced.c -o me_balanced.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c me_ols.c -o me_ols.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c mvr.c -o mvr.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c mvrs.c -o mvrs.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c newick.c -o newick.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c nj.c -o nj.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c njs.c -o njs.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c pic.c -o pic.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c plot_phylo.c -o plot_phylo.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c rTrait.c -o rTrait.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c reorder_phylo.c -o reorder_phylo.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c treePop.c -o treePop.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c tree_build.c -o tree_build.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c tree_phylo.c -o tree_phylo.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c triangMtd.c -o triangMtd.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c triangMtds.c -o triangMtds.o
gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG
-I/usr/local/include    -fpic  -g -O2  -c ultrametric.c -o ultrametric.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ape.so BIONJ.o NNI.o SPR.o
TBR.o additive.o ape.o bNNI.o bionjs.o bipartition.o delta_plot.o
dist_dna.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o
newick.o nj.o njs.o pic.o plot_phylo.o rTrait.o reorder_phylo.o treePop.o
tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o
-L/ebio/abt6/jmao/R/R-2.15.0/lib -lRlapack -L/ebio/abt6/jmao/R/R-2.15.0/lib
-lRblas -lgfortran -lm
installing to /ebio/abt6/jmao/R/Rpacks/ape/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘MoranI.Rnw’
** testing if installed package can be loaded

* DONE (ape)
ERROR: dependency ‘tkrplot’ is not available for package ‘adehabitat’
* removing ‘/ebio/abt6/jmao/R/Rpacks/adehabitat’
ERROR: dependency ‘adehabitat’ is not available for package ‘phyloclim’
* removing ‘/ebio/abt6/jmao/R/Rpacks/phyloclim’

The downloaded source packages are in
    ‘/tmp/Rtmpv9GXTB/downloaded_packages’
Warning messages:
1: In install.packages("phyloclim") :
  installation of package ‘tkrplot’ had non-zero exit status
2: In install.packages("phyloclim") :
  installation of package ‘adehabitat’ had non-zero exit status
3: In install.packages("phyloclim") :
  installation of package ‘phyloclim’ had non-zero exit status

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