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I am having some issues installing Bio-DB-HTS (https://github.com/Ensembl/Bio-DB-HTS) requried to run a perl script from a cloned git repository.
System & Perl information
I am on Mac OSx High Sierra v.10.13.6 and using perl 5, version 18, subversion 2 (v5.18.2). I have added this information in my original question now.
Background information
When trying to perform a local installation, according to README instructions, i receive the error...
git clone https://github.com/Ensembl/Bio-DB-HTS.git
cd Bio-DB-HTS-2.10
perl INSTALL.pl
lzma.h library header not found in /usr/include
I tried to install the LZMA library but found that it actually was installed and that the lzma.h header file was simply missing from the path /usr/include. As LZMA is deprecated and replaced with XZ I installed the XZ library
brew install xz
After a quick search i found the lzma.h header in...
/usr/local/Cellar/xz/5.2.4/include/lzma.h
Main Issue
Now this is where I am not sure of how to proceed and if I have messed up something while trying to get around this. Since /usr/include has a directory with restricted access I added a line in the INSTALL.pl script to check existence for the file in both locations (which could probably disrupt something downstream in the analysis as I didn't change anything else except the if condition. However, when running the install this time i ran into a new problem.
perl INSTALL.pl
BioPerl does not seem to be installed. Please install it and try again.
On Debian/Ubuntu systems you can do this with the command:
apt-get install bioperl
On other systems use the CPAN shell:
perl -MCPAN -e 'install Bio::Perl'
And this is where my main issues reside. When trying to install Bio:Perl using cpan tests fail at various stage and I'm not sure which ones are the essential ones. The last lines from the output are
Result: FAIL
Failed 3/325 test programs. 16/19945 subtests failed.
CJFIELDS/BioPerl-1.007002.tar.gz
./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module,
try:
reports CJFIELDS/BioPerl-1.007002.tar.gz
Running Build install
make test had returned bad status, won't install without force
I reconfigured cpan to install dependancies automatically as mentioned here How do I tell CPAN to install all dependencies?.
perl -MCPAN -Mlocal::lib=~/perl5 -e 'my $c = "CPAN::HandleConfig"; $c->load(doit => 1, autoconfig => 1); $c->edit(prerequisites_policy => "follow"); $c->edit(build_requires_install_policy => "yes"); $c->commit'
And tried installing again forcing installation...
perl -f -MCPAN -e 'install Bio::Perl'
But I just get the same error
Result: FAIL
Failed 3/325 test programs. 16/19945 subtests failed.
CJFIELDS/BioPerl-1.007002.tar.gz
./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module,
try:
reports CJFIELDS/BioPerl-1.007002.tar.gz
Running Build install
make test had returned bad status, won't install without force
When I look at what modules have been installed using...
cpan -l
Bio::DB::HTS 2.11
Bio::DB::HTS::ReadIterator 2.11
Bio::DB::HTS::VCF 2.11
Bio::DB::HTS::Faidx 2.11
Bio::DB::HTS::PileupWrapper 2.11
Bio::DB::HTS::Alignment 2.11
Bio::DB::HTS::ConfigData undef
.
.
.
Bio::DB::HTS::VCF::Iterator 2.11
Bio::DB::HTS::VCF::Row 2.11
I can see that many of the ones I need from the Bio-DB-HTS package are there (assuming that they were one of the succesful installations when isntalling Bio::Perl) but now it prompts the error
Can't locate Bio/SeqFeature/Lite.pm in #INC
However, I never manage to actually get Bio:Seq nor Bio::Perl installed. I do have some perl knowledge but mostly work on python so I am feeling a bit lost of how to proceed.
Extra information
My cpan installs modules to
/usr/local/perl
And I have added the path to my environment variable
export PERL5LIB=/usr/local/perl
Edited information (failed tests & errors) as response to Shawn
#Shawn, Its a long list of errors, test failures and recommended installations. I I can post some examples of the first couple of errors. I am not really sure what to look neither.
Recommended installations
Checking prerequisites...
recommends:
* Algorithm::Munkres is not installed
* Array::Compare is not installed
* Bio::Phylo is not installed
* Convert::Binary::C is not installed
* GD is not installed
* Graph is not installed
* GraphViz is not installed
* HTML::TableExtract is not installed
* Inline::C (0.53) is installed, but we prefer to have 0.67
* PostScript::TextBlock is not installed
* SVG is not installed
* SVG::Graph is not installed
* Set::Scalar is not installed
* Sort::Naturally is not installed
* Spreadsheet::ParseExcel is not installed
* XML::DOM is not installed
* XML::DOM::XPath is not installed
* XML::Parser::PerlSAX is not installed
* XML::SAX::Writer is not installed
* XML::Twig is not installed
* YAML is not installed
Checking optional features...
EntrezGene............disabled
requires:
! Bio::ASN1::EntrezGene is not installed
MySQL Tests...........disabled
requires:
! DBD::mysql is not installed
Pg Tests..............disabled
requires:
! DBD::Pg is not installed
Here is the test summary report. I did not print the entire list of failed tests as it is extremely long. But What I cans see is that /LocalDB/SeqFeature_BDB.t is a part of the majority of the failed tests when looking at the verbose output.
Test Summary Report
-------------------
t/LocalDB/Fasta.t (Wstat: 1024 Tests: 109 Failed: 4)
Failed tests: 73, 91, 95, 101
Non-zero exit status: 4
t/LocalDB/Index/Index.t (Wstat: 20224 Tests: 36 Failed: 6)
Failed tests: 12-17
Non-zero exit status: 79
Parse errors: Bad plan. You planned 73 tests but ran 36.
t/LocalDB/Qual.t (Wstat: 1536 Tests: 56 Failed: 6)
Failed tests: 7-9, 49-50, 52
Non-zero exit status: 6
t/LocalDB/SeqFeature_BDB.t (Wstat: 0 Tests: 38 Failed: 4)
Failed tests: 17-19, 24
Parse errors: Bad plan. You planned 116 tests but ran 38.
t/Perl.t (Wstat: 512 Tests: 47 Failed: 16)
Failed tests: 28, 28, 28, 28-29, 29, 29, 29-30, 30, 30
30-31, 31, 31, 31
Non-zero exit status: 2
Parse errors: Tests out of sequence. Found (24) but expected (26)
Tests out of sequence. Found (25) but expected (27)
Tests out of sequence. Found (26) but expected (28)
Tests out of sequence. Found (26) but expected (29)
Tests out of sequence. Found (27) but expected (30)
Displayed the first 5 of 23 TAP syntax errors.
Re-run prove with the -p option to see them all.
t/RemoteDB/BioFetch.t (Wstat: 0 Tests: 83 Failed: 47)
Failed tests: 20-21, 21-22, 22-23, 23-24, 24-25, 25-26
26-27, 27-28, 28-29, 29-30, 30, 30, 30-31
31, 31, 31-32, 32, 32, 32-33, 33, 33, 33-34
34, 34, 34-35, 35, 35, 35-36, 36, 36, 36
Parse errors: Tests out of sequence. Found (4) but expected (6)
Tests out of sequence. Found (6) but expected (7)
Tests out of sequence. Found (7) but expected (8)
Tests out of sequence. Found (5) but expected (9)
Tests out of sequence. Found (6) but expected (10)
Displayed the first 5 of 79 TAP syntax errors.
Re-run prove with the -p option to see them all.
t/RemoteDB/GenBank.t (Wstat: 0 Tests: 658 Failed: 614)
Failed tests: 10-11, 11, 11-12, 12, 12-13, 13, 13-14
14, 14-15, 15, 15-16, 16, 16-17, 17, 17-18
18, 18-19, 19, 19, 19, 19, 19, 19-20, 20
20, 20, 20, 20, 20-21, 21, 21, 21, 21, 21
21-22, 22, 22, 22, 22, 22, 22-23, 23, 23
Thanks to everyone that helped out, I managed to figure it out in the end. I will explain the process here from beginning to end incase anyone else has the same issue.
The question I posted was to solve how to install Bio::Perl using CPAN as I was having issues with tests failing. Although I had some issues installing Bio-DB-HTS (which I solved before posting) and I will explain how I managed to install that as well in case anyone comes across the same issue.
It seems that Mac users tend to have an issue with the lzma.h header missing. In the case of installing Bio-DB-HTS. I had to modify a line in the Bio-DB-HTS/INSTALL.pl file that checked for the existence of the lzma.h file. See "Installing Bio-DB-HTS on Mac OSx" below for instructions.
Solving installation of Bio::Perl
Essentially I solved it by reinstalling/reconfiguring my CPAN installation. Although I believe the issue in the end was due to some environment variables that I had not set as I chose to manual sort out my CPAN directory structure, I recommend letting CPAN do this for you using the local:lib option as it will set or tell you how to set the environment variables at the end of the installation.
I had only set one of the environment variables below (PERL5LIB) which was probably the reason for my error. NOTE! that the paths you see below are specific for my system.
PATH="/Users/sjamal/perl5/bin${PATH:+:${PATH}}"; export PATH;
PERL5LIB="/Users/sjamal/perl5/lib/perl5${PERL5LIB:+:${PERL5LIB}}"; export PERL5LIB;
PERL_LOCAL_LIB_ROOT="/Users/sjamal/perl5${PERL_LOCAL_LIB_ROOT:+:${PERL_LOCAL_LIB_ROOT}}"; export PERL_LOCAL_LIB_ROOT;
PERL_MB_OPT="--install_base \"/Users/sjamal/perl5\""; export PERL_MB_OPT;
PERL_MM_OPT="INSTALL_BASE=/Users/sjamal/perl5"; export PERL_MM_OPT;
If you have already it configured like me but what to start from a clean slate you will need to remove the CPAN folder created on the user that you installed cpan on.
/Users/<USERNAME>/.cpan
rm -rf /Users/<USERNAME>/.cpan
Now you should be able to run the cpan command as done at the first instance and get prompted with lots of questions of how you want to set up the installation and this is where you will be able to chose 'local:lib' (if you are able to access sudo you can choose the 'sudo' option as well). I installed cpanm based on multiple recommendations and also since it prompts less question apparently and then installed Bio::Perl. Although I should mention that the installation did failed a test and refused to install so I had to run the force command for it to build Bio::Perl.
cpan -i App:cpanminus
cpanm --force Bio::Perl
You should now have Bio::Perl installed.
Installing Bio-DB-HTS on Mac OSx
The lzma library is deprecated on Mac OSx but has been replaced with the XZ library so if you are missing the file as well you can install XZ using brew. If you don't have brew installed you can find how to install it here https://brew.sh/
brew install xz
You will now have a lzma.h header file in the location where XZ was installed using brew, in my case /usr/local/Cellar/xz/5.2.4/include/lzma.h.
git clone https://github.com/Ensembl/Bio-DB-HTS.git
cd Bio-DB-HTS-2.10
vim Bio-DB-HTS/INSTALL.pl
So, I changed the line using vim...
-e '/usr/include/lzma.h' or die <<END;
to
-e '/usr/include/lzma.h' **|| '/usr/local/Cellar/xz/5.2.4/include/lzma.h'** or die <<END;
NOTE! You have to change '/usr/local/Cellar/xz/5.2.4/include/lzma.h' path to where you have the lzma.h in XZ package just installed using brew. However, I want to clarify that this does not solve anything other than telling the script that the file does exist. The Install script won't be able to make use of the file (if that is what it needs to do) as nothing else has been changed in the installation script.
You should now be able to install Bio-DB-HTS by simply running the perl script as below
cd Bio-DB-HTS-2.10
perl INSTALL.pl
Hope that helps!
Sabri
I'm trying to run a Yocto Raspberry Pi 2 build on qemu-system-arm.
I got this far:
$ qemu-system-arm -version
QEMU emulator version 2.10.1(Debian 1:2.10+dfsg-0ubuntu3.5)
Copyright (c) 2003-2017 Fabrice Bellard and the QEMU Project developers
$ qemu-system-arm \
-M raspi2 \
-cpu arm1176 \
-dtb ./tmp/deploy/images/raspberrypi2/bcm2709-rpi-2-b.dtb \
-sd ./tmp/deploy/images/raspberrypi2/berrynux-image-raspberrypi2.rootfs.rpi-sdimg \
-m 1G \
-smp 1 \
-nographic \
-kernel ./kernel-qemu \
-append "rw earlyprintk loglevel=8 console=ttyS0 dwc_otg.lpm_enable=0 root=/dev/mmcblk0p2" \
-serial mon:stdio
Execution hangs with:
WARNING:
Image format was not specified for
'./tmp/deploy/images/raspberrypi2/berrynux-image-raspberrypi2.rootfs.rpi-sdimg' and probing guessed raw.
Automatically detecting the format is dangerous for
raw images, write operations on block 0 will be restricted.
Specify the 'raw' format explicitly to remove the restrictions.
The kernel produced by meta-raspberrypi (kernel7.img) immediately breaks qemu with:
qemu-system-arm: Trying to execute code outside RAM or ROM at 0xe0833006
so i'm using kernel-qemu-4.4.34-jessie instead (tried stretch and wheezy, same result - hang)
Not ever sure where to start debugging here, is this even attempting to boot? Can i hammer it to give me some useful output? Do i need a specially baked kernel, and if so, where do i get it from?
strace didn't get me anywhere (or i don't know how to interpret the output):
...
openat(AT_FDCWD, "./kernel-qemu-4.4.34-jessie", O_RDONLY) = 11
lseek(11, 0, SEEK_END) = 3024048
mmap(NULL, 3026944, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f4ed8106000
lseek(11, 0, SEEK_SET) = 0
read(11, "\0\0\240\341\0\0\240\341\0\0\240\341\0\0\240\341\0\0\240\341\0\0\240\341\0\0\240\341\0\0\240\341"..., 3024048) = 3024048
close(11) = 0
access("./tmp/deploy/images/raspberrypi2/bcm2709-rpi-2-b.dtb", R_OK) = 0
openat(AT_FDCWD, "./tmp/deploy/images/raspberrypi2/bcm2709-rpi-2-b.dtb", O_RDONLY) = 11
lseek(11, 0, SEEK_END) = 16693
close(11) = 0
openat(AT_FDCWD, "./tmp/deploy/images/raspberrypi2/bcm2709-rpi-2-b.dtb", O_RDONLY) = 11
lseek(11, 0, SEEK_END) = 16693
lseek(11, 0, SEEK_SET) = 0
read(11, "\320\r\376\355\0\0A5\0\0\0H\0\0;0\0\0\0(\0\0\0\21\0\0\0\20\0\0\0\0"..., 16693) = 16693
close(11) = 0
futex(0x563f38608c3c, FUTEX_WAKE_PRIVATE, 2147483647) = 1
futex(0x563f383d040c, FUTEX_WAKE_PRIVATE, 2147483647) = 1
futex(0x563f384305cc, FUTEX_WAKE_PRIVATE, 2147483647) = 1
ppoll([{fd=0, events=POLLIN}, {fd=3, events=POLLIN}, {fd=5, events=POLLIN}, {fd=7, events=POLLIN}, {fd=8, events=POLLIN}], 5, {tv_sec=0, tv_nsec=0}, NULL, 8) = 0 (Timeout)
futex(0x563f372cac00, FUTEX_WAKE_PRIVATE, 1) = 1
ppoll([{fd=0, events=POLLIN}, {fd=3, events=POLLIN}, {fd=5, events=POLLIN}, {fd=7, events=POLLIN}, {fd=8, events=POLLIN}], 5, {tv_sec=1, tv_nsec=0}, NULL, 8) = 0 (Timeout)
ppoll([{fd=0, events=POLLIN}, {fd=3, events=POLLIN}, {fd=5, events=POLLIN}, {fd=7, events=POLLIN}, {fd=8, events=POLLIN}], 5, {tv_sec=1, tv_nsec=0}, NULL, 8) = 0 (Timeout)
The POLLIN event repeats indefinitely every second.
The SD card image boots just fine on real hardware Pi2.
EDIT
I copied over kernel7.img and bcm2709-rpi-2-b.dtb from the latest Raspbian Stretch image and i'm stil getting the same exact hang. I'm starting to think there's something screwy with my QEMU build - it's the stock Ubuntu 17.10 .deb package.
EDIT #2
Compiled qemu-2.12.0-rc2 from source, same deal. I must be doing something terribly wrong.
"Nothing happens" and "tried to execute from a bogus address" are often the result of either:
misconfigured kernel (is this kernel definitely intended to boot on the raspi2 board, and not on something else?)
something goes wrong in early boot before the kernel manages to produce output (though usually this causes a hang rather than a bad-address output)
For the latter, assuming this really is a raspi2 kernel, you might try using
earlycon=pl011,0x3f201000
in your kernel append arguments. (The Linux kernel can produce earlycon output for the PL011 UART, but not for the raspi-specific 'mini UART'.)
I would suggest also dropping "-nographic" and "-serial mon:stdio" for the moment. Then you can use the graphical UI to check both UART outputs. (You can do this without using the GUI by redirecting them both correctly using two lots of -serial command line options, but then you have to figure out sensible places to send them; the GUI's simpler.) The first serial port will be the PL011, and the second the mini-UART, so if you only tell QEMU where to send the first serial port output and the guest is writing to the second, you'll never see it.
When it comes to QEMU on arm Yocto is tested for versatilepb machine. Therefore, there might be issues for other configs. It is recommended to look into runqemu script for all the options on how qemu is configured to run.
The fzn2smt tool allows one to solve flatzinc formulas via Yices.
When I try to run it, the solver answers with UNKNOWN to every formula I test. e.g.:
~$ java -Xmx4096M fzn2smt -ce "./yices-2.5.2/bin/yices -f" -i 2DPacking.fzn
Time1:170
=====UNKNOWN=====
However, on the given example, it seems to correctly create the 2DPacking.fzn.smt instance in the same directory of the 2DPacking.fzn file:
~$ ls
2DPacking.fzn.smt 2DPacking.fzn 2DPacking.mzn 2DPacking.ozn
If I manually run Yices over the smt formula, I get a positive result:
~$ yices-smt -f 2DPacking.fzn.smt
sat
(= x____00002_6_ 0)
...
IMPLICANT:
(>= x____00003_4_ 0)
...
Q: Does anyone else have experience with fzn2smt and know how to fix this issue?
Just to be sure that the issue I am experiencing is not due to the installation part, I will share it here:
main_dir
main_dir/fzn2smt-2-0-02 # unpacked fzn2smt files
main_dir/antlr # unpacked antlr-runtime-3.5 files
main_dir/yices-2.5.2 # unpacked yices files
I also modified the environment variables as requested by the tool instructions:
PATH=${main_dir}/yices-2.5.2/bin/:${PATH}
PATH=${main_dir}/fzn2smt-2-0-02/:${PATH}
CLASSPATH=${main_dir}:${CLASSPATH}
CLASSPATH=${main_dir}/antlr:${CLASSPATH}
CLASSPATH=${main_dir}/fzn2smt-2-0-02:${CLASSPATH}
As #Dekker suggested in the comments, the issue is due to fzn2smt seemingly not being updated in a while.
After some trials and errors, I found out that the most recent version of Yices that appears to be compatible with fzn2smt is version 2.2.1.
It can be executed as follows:
~$ java -Xmx4096M fzn2smt -ce "./yices-2.2.1/bin/yices-smt -f" -i 2DPacking.fzn
Time1:162
Time: 207
Pos: 0
item = array2d(1..2, 1..4, [0, 0, 0, 0, 1, 1, 1, 1]);
obj = 1;
----------
Time: 223
Pos: 0
item = array2d(1..2, 1..4, [0, 0, 0, 0, 1, 1, 1, 1]);
obj = 1;
----------
==========
Time2:228
Originally, fzn2smt was coupled with version 2 of Yices presented at the SMT-COMP 2009. To use that version, the command-line instruction to use the tool is slightly different:
~$ java -Xmx4096M fzn2smt -ce "./yices2smt09/bin/yices -f" -i 2DPacking.fzn
Time1:160
Time: 208
Pos: 0
item = array2d(1..2, 1..4, [0, 0, 0, 0, 1, 1, 1, 1]);
obj = 1;
----------
==========
Time2:223
Notice that
the executable is named yices here, rather than yices-smt
the output is slightly different, for some reasons the solution is printed more than once when using the newer version of the tool
Old versions of Yices can be downloaded from here.
I have installed Canopy 1.7.4.3348 (64 bit). My OS is Windows 10 (64 bit). I have the most updated Canopy and Windows 10.
When I tried to update and install any packages in Package Manager, the "Status" would turn out to be "Error", and I got the message:
IOError: [Errno 10038] An operation was attempted on something that is not a socket.
I looked up the Error code on microsoft.com (https://msdn.microsoft.com/en-us/library/windows/desktop/ms740668(v=vs.85).aspx) and found Microsoft's definition of socket error 10038:
WSAENOTSOCK 10038
Socket operation on nonsocket.
An operation was attempted on something that is not a socket.
Either the socket handle parameter did not reference a valid socket,
or for select, a member of an fd_set was not valid.
I think this error from Canopy may only exist in Windows but not in other OS like Linux. Could anyone please kindly help with this issue? Really appreciate it!!
The detailed messages are as below:
Warming up...
Traceback (most recent call last):
File "build\bdist.win-amd64\egg\canopy_dashboard\packman\package_action_worker.py", line 54, in run
File "build\bdist.win-amd64\egg\canopy_dashboard\packman\package_action.py", line 193, in execute
File "build\bdist.win-amd64\egg\canopy_dashboard\packman\packman.py", line 346, in <lambda>
File "build\bdist.win-amd64\egg\canopy_dashboard\packman\packman.py", line 893, in _install
File "build\bdist.win-amd64\egg\canopy_platform\cpython_packages_manager.py", line 98, in install_package
File "build\bdist.win-amd64\egg\canopy_platform\enpkg_api.py", line 102, in install_package
File "build\bdist.win-amd64\egg\canopy_platform\enpkg_api.py", line 177, in _execute_in_subprocess
File "build\bdist.win-amd64\egg\canopy_platform\enpkg_api.py", line 212, in _propagate_progress_events
IOError: [Errno 10038] An operation was attempted on something that is not a socket
Please file a bug report from the Canopy help menu for Enthought tech support records (and please refer to this SO question in your report).
I don't know what causes this rare error, but it should disappear in Canopy 2.0, which uses a different package manager backend, based on the Enthought Deployment Manager (EDM).
Meanwhile, you can avoid the error by using the command-line package installer, enpkg, from a Canopy Command Prompt. Please see this Knowledge Base article for details: https://support.enthought.com/entries/22415022-Using-enpkg-to-update-Canopy-EPD-packages.
I am new to this, or better rusted (being 62).
Trying to develop on Beaglebone Black running Debian over IP using Eclipse Luna CDT and linaro tools.
I succeed in running and debugging standard helloworld.c.
Need to control GPIO fast (to connect to uncommon peripheral) but
all attempts to read or write to memory mapped registers fail.
Instruction
i = (*((volatile unsigned int *)(0x4804c130)))
which should read GPIO status register results in
Child terminated with signal = 0xb (SIGSEGV)
GDBserver exiting
logout
This is the source (hellobone.c) I compile without errors:
int main(void)
{
unsigned int i = 1;
i = (*((volatile unsigned int *)(0x4804c130))) ;
}
(I tried all variations on this pointer arithmetic)
Makefile trace: (ignore includes)
---COMPILE--- C:/hellobone/source/hellobone.c
"C:\gcc-linaro\bin\arm-linux-gnueabihf-gcc.exe" -c -o C:/hellobone/object/hellobone.o C:/hellobone/source/hellobone.c -marm -O0 -g -I. -IC:/hellobone/include
.
---LINK---
"C:\gcc-linaro\bin\arm-linux-gnueabihf-gcc.exe" -o hellobone C:/hellobone/object/hellobone.o C:/hellobone/object/tools.o C:/hellobone/object/gpio_v2.o -marm -O0 -g -I. -IC:/hellobone/include
.
The binary also crashes running as root from TTY:
root#beaglebone:~# ./hellobone
Segmentation fault
I installed Eclipse on the BBB Debian and read and write to memory works just fine. Just too slow compiling, and unstable, to be practical.
Reading memory should be doable. What am I doing wrong?
I suspect
GNU gdbserver (GDB) 7.4.1-debian
This gdbserver was configured as "arm-linux-gnueabihf"
But maybe I am missing something obvious, have not seen any post on this problem...
Really stuck. Being working on this for months now. Setting up toolchain very frustrating, nothing works as in YouTube videos..
Any help would be really appreciated
Marco
You need to mmap /dev/mem to access memory mapped peripherals through physical addresses. Easiest example / code I know does this goes by the name devmem2.
Thank you a lot, that certainly helped.
I compiled the program you gave me and it worked perfect in run mode in Eclipse, and in terminal on the remote machine.
Curiously, when running the Eclipse debugger, it crashes executing:
if((fd = open("/dev/mem", O_RDWR | O_SYNC)) == -1) FATAL;
I get this error message from gdbserver
Remote debugging from host 192.168.1.2
/root/hellobone: relocation error: /root/hellobone: symbol �pen, version GLIBC_2.4 not defined in file libc.so.6 with link time reference
Child exited with status 127
GDBserver exiting
Have been trying to use fopen but that gives a segmentation fault. Anyhow, I think that is a toolchain issue and not a programming issue.