[BioC] problem with tkrplot installation

[James W. MacDonald]

Hi Yulandi,

A Yulandi wrote:
> Dear All,
> 
> I am  a new BioConductor user, I am success  install limmaGUI in my
> machine (openSUSE 11), but i have some probelem with tkrplot
> installation, when i try to install tkrplot use this command
> 
> # R CMD INSTALL tkrplot_0.0-18.tar.gz
> 
> and i have this error ..
> 
> * Installing to library '/usr/lib/R/library'
> * Installing *source* package 'tkrplot' ...
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/lib/R/include -I/usr/include -I/usr/include
> -I/usr/local/include    -fpic  -g -O2 -c tcltkimg.c -o tcltkimg.o
> In file included from tcltkimg.c:2:
> /usr/include/tk.h:78:23: error: X11/Xlib.h: No such file or directory

I think this is the important error. It appears you don't have the X11 
header files which if I am not mistaken come with X11-devel. Try 
installing X11-devel using Yast or YUM and then try installing tkrplot.

I would also recommend using the installation functions that come with R 
rather than downloading and installing by hand, as you can automatically 
get all required dependencies. Something like 
install.packages("tkrplot", dependencies = TRUE)

Best,

Jim


> In file included from tcltkimg.c:2:
> /usr/include/tk.h:549: error: expected declaration specifiers or ‘...’
> before ‘Window’
> /usr/include/tk.h:549: error: ‘Window’ declared as function returning a
> function
> /usr/include/tk.h:552: error: expected declaration specifiers or ‘...’
> before ‘XEvent’
> /usr/include/tk.h:561: error: expected specifier-qualifier-list before
> ‘Tk_ClassCreateProc’
> /usr/include/tk.h:657: error: expected specifier-qualifier-list before
> ‘Bool’
> /usr/include/tk.h:679: error: expected specifier-qualifier-list before
> ‘Bool’
> /usr/include/tk.h:756: error: expected specifier-qualifier-list before
> ‘Display’
> /usr/include/tk.h:899: error: expected declaration specifiers or ‘...’
> before ‘XPoint’
> /usr/include/tk.h:993: error: expected declaration specifiers or ‘...’
> before ‘Display’
> /usr/include/tk.h:995: error: expected declaration specifiers or ‘...’
> before ‘Display’
> /usr/include/tk.h:995: error: expected declaration specifiers or ‘...’
> before ‘Drawable’
> /usr/include/tk.h:1096: error: expected specifier-qualifier-list before
> ‘XColor’
> /usr/include/tk.h:1159: error: expected specifier-qualifier-list before
> ‘GC’
> /usr/include/tk.h:1201: error: expected declaration specifiers or ‘...’
> before ‘Display’
> /usr/include/tk.h:1201: error: expected declaration specifiers or ‘...’
> before ‘Drawable’
> /usr/include/tk.h:1204: error: expected declaration specifiers or ‘...’
> before ‘Display’
> /usr/include/tk.h:1400: error: expected declaration specifiers or ‘...’
> before ‘Drawable’
> /usr/include/tk.h:1510: error: expected declaration specifiers or ‘...’
> before ‘XErrorEvent’
> /usr/include/tk.h:1512: error: expected declaration specifiers or ‘...’
> before ‘XEvent’
> /usr/include/tk.h:1514: error: expected declaration specifiers or ‘...’
> before ‘XEvent’
> /usr/include/tk.h:1516: error: expected declaration specifiers or ‘...’
> before ‘XEvent’
> /usr/include/tk.h:1521: error: expected declaration specifiers or ‘...’
> before ‘XEvent’
> In file included from /usr/include/tk.h:1534,
>                  from tcltkimg.c:2:
> /usr/include/tkDecls.h:42: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘*’ token
> /usr/include/tkDecls.h:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_3DBorderGC’
> /usr/include/tkDecls.h:54: error: expected declaration specifiers or
> ‘...’ before ‘Drawable’
> /usr/include/tkDecls.h:62: error: expected declaration specifiers or
> ‘...’ before ‘Drawable’
> /usr/include/tkDecls.h:76: error: expected declaration specifiers or
> ‘...’ before ‘XEvent’
> /usr/include/tkDecls.h:108: error: expected declaration specifiers or
> ‘...’ before ‘Pixmap’
> /usr/include/tkDecls.h:115: error: expected declaration specifiers or
> ‘...’ before ‘XColor’
> /usr/include/tkDecls.h:134: error: expected declaration specifiers or
> ‘...’ before ‘Pixmap’
> /usr/include/tkDecls.h:144: error: expected declaration specifiers or
> ‘...’ before ‘GC’
> /usr/include/tkDecls.h:178: error: expected declaration specifiers or
> ‘...’ before ‘XSetWindowAttributes’
> /usr/include/tkDecls.h:190: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:196: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:196: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:234: error: expected declaration specifiers or
> ‘...’ before ‘XWindowChanges’
> /usr/include/tkDecls.h:266: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:303: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:304: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:305: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:378: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:379: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:400: error: expected declaration specifiers or
> ‘...’ before ‘Drawable’
> /usr/include/tkDecls.h:401: error: expected declaration specifiers or
> ‘...’ before ‘XPoint’
> /usr/include/tkDecls.h:409: error: expected declaration specifiers or
> ‘...’ before ‘Drawable’
> /usr/include/tkDecls.h:416: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:423: error: expected declaration specifiers or
> ‘...’ before ‘GC’
> /usr/include/tkDecls.h:424: error: expected declaration specifiers or
> ‘...’ before ‘Drawable’
> /usr/include/tkDecls.h:429: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:437: error: expected declaration specifiers or
> ‘...’ before ‘Drawable’
> /usr/include/tkDecls.h:438: error: expected declaration specifiers or
> ‘...’ before ‘XPoint’
> /usr/include/tkDecls.h:446: error: expected declaration specifiers or
> ‘...’ before ‘Drawable’
> /usr/include/tkDecls.h:459: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_FontId’
> /usr/include/tkDecls.h:469: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:474: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:479: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:485: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:495: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:506: error: expected declaration specifiers or
> ‘...’ before ‘Display’
> /usr/include/tkDecls.h:512: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:522: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:527: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_GCForColor’
> /usr/include/tkDecls.h:557: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:569: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_GetBitmap’
> /usr/include/tkDecls.h:575: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_GetBitmapFromData’
> /usr/include/tkDecls.h:588: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘*’ token
> /usr/include/tkDecls.h:594: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘*’ token
> /usr/include/tkDecls.h:600: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_GetColormap’
> /usr/include/tkDecls.h:637: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_GetGC’
> /usr/include/tkDecls.h:692: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_GetPixmap’
> /usr/include/tkDecls.h:724: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:724: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:735: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘*’ token
> /usr/include/tkDecls.h:754: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:759: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:776: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_InternAtom’
> /usr/include/tkDecls.h:849: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:860: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:865: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:902: error: expected declaration specifiers or
> ‘...’ before ‘Atom’
> /usr/include/tkDecls.h:971: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:977: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:985: error: expected declaration specifiers or
> ‘...’ before ‘Drawable’
> /usr/include/tkDecls.h:1048: error: expected declaration specifiers or
> ‘...’ before ‘Pixmap’
> /usr/include/tkDecls.h:1065: error: expected declaration specifiers or
> ‘...’ before ‘Pixmap’
> /usr/include/tkDecls.h:1071: error: expected declaration specifiers or
> ‘...’ before ‘Colormap’
> /usr/include/tkDecls.h:1076: error: expected declaration specifiers or
> ‘...’ before ‘Visual’
> /usr/include/tkDecls.h:1077: error: expected declaration specifiers or
> ‘...’ before ‘Colormap’
> /usr/include/tkDecls.h:1082: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:1116: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:1124: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:1159: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_AllocBitmapFromObj’
> /usr/include/tkDecls.h:1171: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘*’ token
> /usr/include/tkDecls.h:1253: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘Tk_GetBitmapFromObj’
> /usr/include/tkDecls.h:1259: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
> ‘__attribute__’ before ‘*’ token
> /usr/include/tkDecls.h:1374: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:1380: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:1405: error: expected declaration specifiers or
> ‘...’ before ‘GC’
> /usr/include/tkDecls.h:1417: error: expected declaration specifiers or
> ‘...’ before ‘GC’
> /usr/include/tkDecls.h:1431: error: expected declaration specifiers or
> ‘...’ before ‘Pixmap’
> /usr/include/tkDecls.h:1438: error: expected declaration specifiers or
> ‘...’ before ‘XColor’
> /usr/include/tkDecls.h:1466: error: expected declaration specifiers or
> ‘...’ before ‘Pixmap’
> /usr/include/tkDecls.h:1542: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:1639: error: expected declaration specifiers or
> ‘...’ before ‘Drawable’
> /usr/include/tkDecls.h:1674: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:1679: error: expected ‘)’ before ‘*’ token
> /usr/include/tkDecls.h:1710: error: expected specifier-qualifier-list
> before ‘XColor’
> tcltkimg.c:97:23: error: X11/Xutil.h: No such file or directory
> tcltkimg.c:98: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘*’ token
> tcltkimg.c:106: error: expected specifier-qualifier-list before
> ‘RplotImage’
> tcltkimg.c:135: error: expected declaration specifiers or ‘...’ before
> ‘RplotImage’
> tcltkimg.c: In function ‘GetRplotImage’:
> tcltkimg.c:166: error: ‘pximage’ undeclared (first use in this function)
> tcltkimg.c:166: error: (Each undeclared identifier is reported only once
> tcltkimg.c:166: error: for each function it appears in.)
> tcltkimg.c: In function ‘CreateRplot’:
> 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: too many arguments to function ‘GetRplotImage’
> 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: In function ‘GetRplot’:
> tcltkimg.c:267: error: ‘RplotMaster’ has no member named ‘instanceCount’
> tcltkimg.c:272: error: ‘RplotMaster’ has no member named ‘instanceCount’
> tcltkimg.c:273: error: ‘RplotMaster’ has no member named ‘width’
> tcltkimg.c:274: error: ‘RplotMaster’ has no member named ‘height’
> tcltkimg.c:275: error: ‘RplotMaster’ has no member named ‘master’
> tcltkimg.c: In function ‘DisplayRplot’:
> tcltkimg.c:301: error: expected declaration specifiers before ‘Display’
> tcltkimg.c:302: error: expected declaration specifiers before ‘Drawable’
> tcltkimg.c:307: warning: type of ‘display’ defaults to ‘int’
> tcltkimg.c:307: warning: type of ‘drawable’ defaults to ‘int’
> tcltkimg.c:320: error: ‘Tk_FakeWin’ has no member named ‘depth’
> tcltkimg.c:322: error: ‘XGCValues’ undeclared (first use in this
> function)
> tcltkimg.c:322: error: expected ‘;’ before ‘gcValues’
> tcltkimg.c:323: error: ‘Pixmap’ undeclared (first use in this function)
> tcltkimg.c:323: error: expected ‘;’ before ‘pixmap’
> tcltkimg.c:324: error: ‘GC’ undeclared (first use in this function)
> tcltkimg.c:324: error: expected ‘;’ before ‘gc’
> tcltkimg.c:326: error: ‘pixmap’ undeclared (first use in this function)
> tcltkimg.c:326: warning: implicit declaration of function ‘Tk_GetPixmap’
> tcltkimg.c:326: error: ‘Tk_FakeWin’ has no member named ‘window’
> tcltkimg.c:328: error: ‘gc’ undeclared (first use in this function)
> tcltkimg.c:328: warning: implicit declaration of function ‘Tk_GetGC’
> tcltkimg.c:329: warning: implicit declaration of function ‘XPutImage’
> tcltkimg.c:329: error: ‘RplotMaster’ has no member named ‘image’
> tcltkimg.c:330: warning: implicit declaration of function ‘Tk_FreeGC’
> tcltkimg.c:332: error: ‘GCGraphicsExposures’ undeclared (first use in
> this function)
> tcltkimg.c:333: error: ‘gcValues’ undeclared (first use in this
> function)
> tcltkimg.c:333: error: ‘False’ undeclared (first use in this function)
> tcltkimg.c:336: warning: implicit declaration of function
> ‘XSetClipOrigin’
> tcltkimg.c:337: warning: implicit declaration of function ‘XCopyArea’
> tcltkimg.c:342: warning: implicit declaration of function
> ‘Tk_FreePixmap’
> tcltkimg.c: In function ‘FreeRplot’:
> tcltkimg.c:366: error: expected declaration specifiers before ‘Display’
> tcltkimg.c:367: warning: type of ‘display’ defaults to ‘int’
> tcltkimg.c:371: error: ‘RplotMaster’ has no member named ‘instanceCount’
> tcltkimg.c: In function ‘DeleteRplot’:
> tcltkimg.c:398: error: ‘RplotMaster’ has no member named ‘instanceCount’
> tcltkimg.c:405: warning: implicit declaration of function
> ‘XDestroyImage’
> tcltkimg.c:405: error: ‘RplotMaster’ has no member named ‘image’
> make: *** [tcltkimg.o] Error 1
> chmod: cannot access `/usr/lib/R/library/tkrplot/libs/*': No such file
> or directory
> ERROR: compilation failed for package 'tkrplot'
> ** Removing '/usr/lib/R/library/tkrplot'
> 
> 
> Have you got an answer to your question? Have you found a solution?
> 
> thanks in advance 
> 
> 
> Yulandi
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662