使用gdb运行R CMD安装来调试malloc错误

Question

我写了一些代码作为包。当我尝试发出A时R CMD install mypkg，会出现诸如以下错误

* installing to library ‘/Users/USERNAME/R/x86_64-apple-darwin11.0.0-library/2.14’
* installing *source* package ‘mypkg’ ...
** libs
*** arch - x86_64
make: Nothing to be done for `all'.
installing to /Users/USERNAME/R/x86_64-apple-darwin11.0.0-library/2.14/mypkg/libs/x86_64
** R
** preparing package for lazy loading
** help
Warning: /Users/USERNAME/temp/mypkg/man/mypkg-package.Rd:31: All text must be in a section
Warning: /Users/USERNAME/temp/mypkg/man/mypkg-package.Rd:32: All text must be in a section
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
R(57533) malloc: *** error for object 0x1110005e0: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
sh: line 1: 57533 Abort trap: 6           '/opt/local/lib/R/bin/R' --no-save --slave < /var/folders/2f/kxqs800n6rq09nrm8_t637g40000gr/T//Rtmp6McNDz/filee0b91bc7fa41
ERROR: loading failed
* removing ‘/Users/USERNAME/R/x86_64-apple-darwin11.0.0-library/2.14/mypkg’

为了解决这个问题，我尝试使用gdb运行R CMD，但无济于事

$ R -d gdb
GNU gdb 6.3.50-20050815 (Apple version gdb-1708) (Thu Nov  3 21:59:02 UTC 2011)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "x86_64-apple-darwin"...Reading symbols for shared libraries ...
(gdb) start CMD install mypkg
<-gdb intro ->
Breakpoint 1 at 0x100000ef4: file Rmain.c, line 30.
Starting program: /opt/local/lib/R/bin/exec/x86_64/R CMD install mypkg
Breakpoint 1, main (ac=4, av=0x7fff5fbff9a8) at Rmain.c:30
30      R_running_as_main_program = 1;
(gdb) c
Continuing.
ARGUMENT 'CMD' __ignored__

ARGUMENT 'install' __ignored__

ARGUMENT 'mypkg' __ignored__

Reading symbols for shared libraries . done

R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin11.0.0/x86_64 (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.

Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
> 

同样的，R -d gdb CMD install mypkg并且R CMD install mypkg -d gdb也不起作用。我的问题是：

1. 如何在gdb下运行R CMD安装？
2. 除了在gdb中，还有其他方法可以调试此错误吗？

Answer 1

该错误不会在INSTALL本身中发生，而是在加载程序包时发生，因此您可以简单地运行

R CMD INSTALL --no-test-load mypkg
R -d gdb
> library(mypkg)

至于调试，另一个解决内存问题的有用工具是valgrind。

但是请注意，您的包装很脏，因此应考虑清洁并R CMD build mypkg && R CMD INSTALL --no-test-load mypkg_x.y.tar.gz改用。