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Error in Installing BSMAP-0.99 #1

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
Thank you!

Please reply to hmo@vcu.edu

What steps will reproduce the problem?
1. tar -xvvf bsmap-0.99.tgz
2. cd bsmap-0.99
3. make (fail even by root)

What is the expected output? What do you see instead?

What version of the product are you using? On what operating system?
$ uname -a
Linux vcu-genome-Koupe 2.6.28-15-generic #52-Ubuntu SMP Wed Sep 9 10:48:52
UTC 2009 x86_64 GNU/Linux

$ gcc -v
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu
4.3.3-5ubuntu4' --with-bugurl=file:///usr/share/doc/gcc-4.3/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared
--with-system-zlib --libexecdir=/usr/lib --without-included-gettext
--enable-threads=posix --enable-nls
--with-gxx-include-dir=/usr/include/c++/4.3 --program-suffix=-4.3
--enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc
--enable-mpfr --with-tune=generic --enable-checking=release
--build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.3.3 (Ubuntu 4.3.3-5ubuntu4)

Please provide any additional information below.

Error Message:
$ make                             
g++ -static -DMAXGAP=1 -DMAXHITS=1000 -DTHREAD -O3 -funroll-loops  
-DDB_CHR -DREAD_36 -c align.cpp -o align.a.o                              

align.cpp: In member function ‘void SingleAlign::s_OutHit(int, size_t,
bit8_t, Hit*, bool, RefSeq&, std::string&)’:                              

align.cpp:1847: warning: format ‘%d’ expects type ‘int’, but argument 3 
has
type ‘size_t’ 
align.cpp:1847: warning: format ‘%d’ expects type ‘int’, but argument 5 
has
type ‘size_t’ 
align.cpp: In member function ‘void SingleAlign::s_OutGapHit(int, size_t,
bit8_t, Hit*, RefSeq&, std::string&)’:                                    

align.cpp:1897: warning: format ‘%d’ expects type ‘int’, but argument 3 
has
type ‘size_t’ 
align.cpp:1897: warning: format ‘%d’ expects type ‘int’, but argument 5 
has
type ‘size_t’ 
align.cpp:1899: warning: format ‘%d’ expects type ‘int’, but argument 3 
has
type ‘size_t’ 
align.cpp:1899: warning: format ‘%d’ expects type ‘int’, but argument 5 
has
type ‘size_t’ 
align.cpp:1901: warning: format ‘%d’ expects type ‘int’, but argument 3 
has
type ‘size_t’ 
align.cpp:1901: warning: format ‘%d’ expects type ‘int’, but argument 5 
has
type ‘size_t’ 
g++ -static -DMAXGAP=1 -DMAXHITS=1000 -DTHREAD -O3 -funroll-loops  
-DDB_CHR -DREAD_36 -c dbseq.cpp -o dbseq.a.o                              

g++ -static -DMAXGAP=1 -DMAXHITS=1000 -DTHREAD -O3 -funroll-loops  
-DDB_CHR -DREAD_36 -c main.cpp -o main.a.o                                

In file included from main.cpp:11:                                        

align.h: In member function ‘void SingleAlign::Reverse_Seq()’:            

align.h:298: error: ‘reverse’ was not declared in this scope              

align.h: In member function ‘void SingleAlign::Reverse_Qual()’:           

align.h:306: error: ‘reverse’ was not declared in this scope              

main.cpp: In function ‘void usage()’:                                     

main.cpp:238: error: ‘exit’ was not declared in this scope                

main.cpp: In function ‘int mGetOptions(int, char**)’:                     

main.cpp:252: error: ‘atoi’ was not declared in this scope                

main.cpp: In function ‘void RunProcess()’:                                

main.cpp:293: error: ‘exit’ was not declared in this scope                

main.cpp:298: error: ‘exit’ was not declared in this scope                

main.cpp:303: error: ‘exit’ was not declared in this scope                

main.cpp:308: error: ‘exit’ was not declared in this scope                

main.cpp:330: error: ‘exit’ was not declared in this scope                

main.cpp:336: error: ‘exit’ was not declared in this scope                

main.cpp:343: error: ‘exit’ was not declared in this scope                

main.cpp: In function ‘int main(int, char**)’:                            

main.cpp:373: error: ‘exit’ was not declared in this scope                

make: *** [main.a.o] Error 1

Original issue reported on code.google.com by henry...@gmail.com on 20 Oct 2009 at 8:48

GoogleCodeExporter commented 8 years ago 
Could you check if STDLIB and STL are working on your system?  It looks like 
these two libraries were not found 
by the compiler.

The warning message will be corrected in BSMAP-1.0 (released today).

Thank you.

Original comment by xiyuanxin@gmail.com on 26 Oct 2009 at 3:09

GoogleCodeExporter commented 8 years ago 
I now successfully install it by downgrading gcc/cpp/g++ from 4.3 to 4.2.  
Thank you.

Original comment by henry...@gmail.com on 31 Oct 2009 at 11:13

GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
I have a similar problem in installing the bsmap program. info is attached 
below. please reply to xsun@zymoresearch.com 
Thanks!

What steps will reproduce the problem?
1. unzip the file
2. cd bsmap-1.07
3. make

What is the expected output? What do you see instead?
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -O3 -funroll-loops   -DDB_CHR -DREAD_80 
-c align.cpp -o align.a.o
align.cpp: In member function ‘void SingleAlign::s_OutHit(int, int, bit8_t, 
Hit*, int, RefSeq&, std::string&)’:
align.cpp:828: warning: format ‘%d’ expects type ‘int’, but argument 7 
has type ‘size_t’
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -O3 -funroll-loops   -DDB_CHR -DREAD_80 
-c dbseq.cpp -o dbseq.a.o
g++ -DMAXGAP=0 -DMAXHITS=1000 -DTHREAD -O3 -funroll-loops   -DDB_CHR -DREAD_80 
-c main.cpp -o main.a.o
In file included from main.cpp:11:
align.h: In member function ‘void SingleAlign::Reverse_Seq()’:
align.h:302: error: ‘reverse’ was not declared in this scope
align.h: In member function ‘void SingleAlign::Reverse_Qual()’:
align.h:310: error: ‘reverse’ was not declared in this scope
main.cpp: In function ‘void usage()’:
main.cpp:230: error: ‘exit’ was not declared in this scope
main.cpp: In function ‘int mGetOptions(int, char**)’:
main.cpp:244: error: ‘atoi’ was not declared in this scope
main.cpp: In function ‘void RunProcess()’:
main.cpp:287: error: ‘exit’ was not declared in this scope
main.cpp:292: error: ‘exit’ was not declared in this scope
main.cpp:297: error: ‘exit’ was not declared in this scope
main.cpp:311: error: ‘exit’ was not declared in this scope
main.cpp:334: error: ‘exit’ was not declared in this scope
main.cpp:340: error: ‘exit’ was not declared in this scope
main.cpp:347: error: ‘exit’ was not declared in this scope
main.cpp: In function ‘int main(int, char**)’:
main.cpp:386: error: ‘exit’ was not declared in this scope
make: *** [main.a.o] Error 1

What version of the product are you using? On what operating system?
Linux xueguang-NGS 2.6.32-24-generic #39-Ubuntu SMP Wed Jul 28 05:14:15 UTC 
2010 x86_64 GNU/Linux

gcc -v

Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.4.3-4ubuntu5' 
--with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs 
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared 
--enable-multiarch --enable-linker-build-id --with-system-zlib 
--libexecdir=/usr/lib --without-included-gettext --enable-threads=posix 
--with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls 
--enable-clocale=gnu --enable-libstdcxx-debug --enable-plugin --enable-objc-gc 
--disable-werror --with-arch-32=i486 --with-tune=generic 
--enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu 
--target=x86_64-linux-gnu
Thread model: posix
gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)

Original comment by sunx...@gmail.com on 22 Sep 2010 at 11:31