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
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
