chromDraw 2.4.0
Jan Janecka
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/chromDraw | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | [ OK ] | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf chromDraw.buildbin-libdir && mkdir chromDraw.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chromDraw_2.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chromDraw.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=chromDraw.buildbin-libdir chromDraw_2.4.0.tar.gz'
>>>>>>>
* installing *source* package ‘chromDraw’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDraw.cpp -o chromDraw.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c libBoard/src/Board.cpp -o libBoard/src/Board.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c libBoard/src/Color.cpp -o libBoard/src/Color.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c libBoard/src/PSFonts.cpp -o libBoard/src/PSFonts.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c libBoard/src/Path.cpp -o libBoard/src/Path.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c libBoard/src/Rect.cpp -o libBoard/src/Rect.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c libBoard/src/ShapeList.cpp -o libBoard/src/ShapeList.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c libBoard/src/Shapes.cpp -o libBoard/src/Shapes.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c libBoard/src/Tools.cpp -o libBoard/src/Tools.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c libBoard/src/Transforms.cpp -o libBoard/src/Transforms.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/canvas.cpp -o chromDrawCPP/canvas.o
chromDrawCPP/canvas.cpp:362:8: warning: variable 'coordinate_y' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case canvas::LSouthTelomere:
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
chromDrawCPP/canvas.cpp:369:61: note: uninitialized use occurs here
sheet.drawRectangle(last_x-0.5*sizefactor*MARK_WIDTHSIZE1, coordinate_y+0.5*sizefactor*MARK_HEIGHTSIZE1, sizefactor*MARK_WIDTHSIZE1, sizefactor*MARK_HEIGHTSIZE1);
^˜˜˜˜˜˜˜˜˜˜˜
chromDrawCPP/canvas.cpp:320:20: note: initialize the variable 'coordinate_y' to silence this warning
float coordinate_y;
^
= 0.0
chromDrawCPP/canvas.cpp:438:8: warning: variable 'coordinate_y' is used uninitialized whenever switch case is taken [-Wsometimes-uninitialized]
case canvas::LSouthTelomere:
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
chromDrawCPP/canvas.cpp:446:27: note: uninitialized use occurs here
sheet.drawEllipse(last_x,coordinate_y, sizefactor*MARK_WIDTHSIZE1/2.0,sizefactor*MARK_HEIGHTSIZE1);
^˜˜˜˜˜˜˜˜˜˜˜
chromDrawCPP/canvas.cpp:396:20: note: initialize the variable 'coordinate_y' to silence this warning
float coordinate_y;
^
= 0.0
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/chBlock.cpp -o chromDrawCPP/chBlock.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/chCentromere.cpp -o chromDrawCPP/chCentromere.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/chromosome.cpp -o chromDrawCPP/chromosome.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/chromosomeElement.cpp -o chromDrawCPP/chromosomeElement.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/chromosomeMark.cpp -o chromDrawCPP/chromosomeMark.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/chromosomeSign.cpp -o chromDrawCPP/chromosomeSign.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/color.cpp -o chromDrawCPP/color.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/colorPalette.cpp -o chromDrawCPP/colorPalette.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/getOpts.cpp -o chromDrawCPP/getOpts.o
chromDrawCPP/getOpts.cpp:47:8: warning: unused variable 'x' [-Wunused-variable]
char x = argv[argcurent][1];
^
chromDrawCPP/getOpts.cpp:48:8: warning: unused variable 'y' [-Wunused-variable]
char y = argv[argcurent][2];
^
chromDrawCPP/getOpts.cpp:49:8: warning: unused variable 'o' [-Wunused-variable]
char o = optv[optcurent];
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/ideogram.cpp -o chromDrawCPP/ideogram.o
chromDrawCPP/ideogram.cpp:76:11: warning: variable 'retVal' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
else if (format.compare(BEDDATAFORMAT) == 0)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
chromDrawCPP/ideogram.cpp:80:5: note: uninitialized use occurs here
if(retVal != 0)
^˜˜˜˜˜
chromDrawCPP/ideogram.cpp:76:7: note: remove the 'if' if its condition is always true
else if (format.compare(BEDDATAFORMAT) == 0)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
chromDrawCPP/ideogram.cpp:70:12: note: initialize the variable 'retVal' to silence this warning
int retVal;
^
= 0
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/karyotype.cpp -o chromDrawCPP/karyotype.o
chromDrawCPP/karyotype.cpp:266:7: warning: delete called on 'chBlock' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
delete block;
^
chromDrawCPP/karyotype.cpp:274:6: warning: delete called on 'chBlock' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
delete block;
^
chromDrawCPP/karyotype.cpp:315:6: warning: delete called on 'chCentromere' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
delete centromere;
^
chromDrawCPP/karyotype.cpp:421:7: warning: delete called on 'markSign' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
delete mark;
^
chromDrawCPP/karyotype.cpp:429:6: warning: delete called on 'markSign' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
delete mark;
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/markSign.cpp -o chromDrawCPP/markSign.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c chromDrawCPP/parameters.cpp -o chromDrawCPP/parameters.o
chromDrawCPP/parameters.cpp:42:30: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *paramsExpanded[10] = {"--help",
^
chromDrawCPP/parameters.cpp:43:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"--outputpath",
^
chromDrawCPP/parameters.cpp:44:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"--colorinputpath",
^
chromDrawCPP/parameters.cpp:45:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"--datainputpath",
^
chromDrawCPP/parameters.cpp:46:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"--scale",
^
chromDrawCPP/parameters.cpp:47:9: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
"--format"};
^
chromDrawCPP/parameters.cpp:66:21: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
#ifdef _WIN32 || _WIN64
^
//
chromDrawCPP/parameters.cpp:147:15: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
#ifdef _WIN32 || _WIN64
^
//
chromDrawCPP/parameters.cpp:159:15: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
#ifdef _WIN32 || _WIN64
^
//
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -isystem ./libBoard/include -isystem ./chromDrawCPP -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c R_init_chromDraw.cpp -o R_init_chromDraw.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o chromDraw.so chromDraw.o RcppExports.o ./libBoard/src/Board.o ./libBoard/src/Color.o ./libBoard/src/PSFonts.o ./libBoard/src/Path.o ./libBoard/src/Rect.o ./libBoard/src/ShapeList.o ./libBoard/src/Shapes.o ./libBoard/src/Tools.o ./libBoard/src/Transforms.o ./chromDrawCPP/canvas.o ./chromDrawCPP/chBlock.o ./chromDrawCPP/chCentromere.o ./chromDrawCPP/chromosome.o ./chromDrawCPP/chromosomeElement.o ./chromDrawCPP/chromosomeMark.o ./chromDrawCPP/chromosomeSign.o ./chromDrawCPP/color.o ./chromDrawCPP/colorPalette.o ./chromDrawCPP/getOpts.o ./chromDrawCPP/ideogram.o ./chromDrawCPP/karyotype.o ./chromDrawCPP/markSign.o ./chromDrawCPP/parameters.o ./R_init_chromDraw.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/chromDraw.buildbin-libdir/chromDraw/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chromDraw)
>>>>>>>
>>>>>>> FIXING LINKS FOR chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "chromDraw.buildbin-libdir/chromDraw/libs//chromDraw.so"