Re: [PEAR-users] installation error

Tomas Flouri

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Mar 31, 2015, 5:51:40 AM3/31/15

to pedr...@gmail.com, pear-...@googlegroups.com

Hello Pedro,

most probably your system is outdated, and the zlib library installed is older than version 1.2.3.5. From version 1.2.3.5, zlib incorporates the gzoffset function which PEAR requires for compilation with zlib, and which seems to be missing from your system. You can check the version of zlib on your system by typing:

dpkg -l | grep zlib1g-dev

I also notice that you are using an older version of PEAR (0.9.6), probably downloaded by our website, which is 1 version behind. Please download the latest version (0.9.7) from the github at:

https://github.com/xflouris/PEAR

Using version 0.9.7, run the following:

./autogen.sh
./configure
make
sudo make install

It should automatically detect that your zlib version is inappropriate and will compile PEAR without it. Even if that fails, you can replace the command
./configure

with

./configure --disable-zlib

which will disable zlib compilation manually. But this option is only available in version 0.9.7 currently only on Github.
I will update the website to hold the latest version (0.9.7) but that might take a day.

Best regards,
Tomas

On 03/31/2015 01:19 AM, pedr...@gmail.com wrote:

Hi there guys,

I am having problems in installing successfully this tool.

I followed the "Building from source" instructions and everything seemed to be going great until > make command.

This is the command line output:

Making all in src

make[1]: Entering directory `/home/pedro/Soft/pear-0.9.6-src/src'

make all-am

make[2]: Entering directory `/home/pedro/Soft/pear-0.9.6-src/src'

gcc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -MT pear-pear-pt.o -MD -MP -MF .deps/pear-pear-pt.Tpo -c -o pear-pear-pt.o `test -f 'pear-pt.c' || echo './'`pear-pt.c

mv -f .deps/pear-pear-pt.Tpo .deps/pear-pear-pt.Po

gcc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -MT pear-args.o -MD -MP -MF .deps/pear-args.Tpo -c -o pear-args.o `test -f 'args.c' || echo './'`args.c

mv -f .deps/pear-args.Tpo .deps/pear-args.Po

gcc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -MT pear-statistics.o -MD -MP -MF .deps/pear-statistics.Tpo -c -o pear-statistics.o `test -f 'statistics.c' || echo './'`statistics.c

mv -f .deps/pear-statistics.Tpo .deps/pear-statistics.Po

gcc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -MT pear-reader.o -MD -MP -MF .deps/pear-reader.Tpo -c -o pear-reader.o `test -f 'reader.c' || echo './'`reader.c

reader.c: In function ‘db_read_fastq_block’:

reader.c:742:5: warning: implicit declaration of function ‘gzoffset’ [-Wimplicit-function-declaration]

reader.c:742:5: warning: nested extern declaration of ‘gzoffset’ [-Wnested-externs]

reader.c:758:15: warning: ‘nBytes’ may be used uninitialized in this function [-Wuninitialized]

mv -f .deps/pear-reader.Tpo .deps/pear-reader.Po

gcc -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -o pear pear-pear-pt.o pear-args.o pear-statistics.o pear-reader.o -lz -lbz2 -lpthread -lm

pear-reader.o: In function `db_read_fastq_block':

reader.c:(.text+0x15c5): undefined reference to `gzoffset'

reader.c:(.text+0x15d6): undefined reference to `gzoffset'

collect2: ld returned 1 exit status

make[2]: *** [pear] Error 1

make[2]: Leaving directory `/home/pedro/Soft/pear-0.9.6-src/src'

make[1]: *** [all] Error 2

make[1]: Leaving directory `/home/pedro/Soft/pear-0.9.6-src/src'

make: *** [all-recursive] Error 1

What might be causing this error?

Regards

Pedro Castro

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Brandi Kiel Reese

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Sep 7, 2015, 5:09:12 PM9/7/15

to pear-users

Tomas, I would like to follow up on this. I had success following your amendments to the installation directions and got as fare as the "make" command. However, I am having issues with "make install"

I do not have Administrative privileges, this is on a cluster running RedHat. Thank you for your help.

This is the output for both "make" and "make install"

[breese1@hpcm PEAR]$ make

Making all in src

make[1]: Entering directory `/home/breese1/pear/PEAR/src'

make all-am

make[2]: Entering directory `/home/breese1/pear/PEAR/src'

gcc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -MT pear-pear-pt.o -MD -MP -MF .deps/pear-pear-pt.Tpo -c -o pear-pear-pt.o `test -f 'pear-pt.c' || echo './'`pear-pt.c

mv -f .deps/pear-pear-pt.Tpo .deps/pear-pear-pt.Po

gcc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -MT pear-args.o -MD -MP -MF .deps/pear-args.Tpo -c -o pear-args.o `test -f 'args.c' || echo './'`args.c

mv -f .deps/pear-args.Tpo .deps/pear-args.Po

gcc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -MT pear-statistics.o -MD -MP -MF .deps/pear-statistics.Tpo -c -o pear-statistics.o `test -f 'statistics.c' || echo './'`statistics.c

mv -f .deps/pear-statistics.Tpo .deps/pear-statistics.Po

gcc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -MT pear-reader.o -MD -MP -MF .deps/pear-reader.Tpo -c -o pear-reader.o `test -f 'reader.c' || echo './'`reader.c

reader.c: In function ‘rewind_files’:

reader.c:213:33: warning: unused parameter ‘file1’ [-Wunused-parameter]

void rewind_files (const char * file1, const char * file2)

^

reader.c:213:53: warning: unused parameter ‘file2’ [-Wunused-parameter]

void rewind_files (const char * file1, const char * file2)

^

mv -f .deps/pear-reader.Tpo .deps/pear-reader.Po

gcc -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -O3 -o pear pear-pear-pt.o pear-args.o pear-statistics.o pear-reader.o -lbz2 -lpthread -lm

make[2]: Leaving directory `/home/breese1/pear/PEAR/src'

make[1]: Leaving directory `/home/breese1/pear/PEAR/src'

Making all in man

make[1]: Entering directory `/home/breese1/pear/PEAR/man'

make[1]: Nothing to be done for `all'.

make[1]: Leaving directory `/home/breese1/pear/PEAR/man'

make[1]: Entering directory `/home/breese1/pear/PEAR'

make[1]: Nothing to be done for `all-am'.

make[1]: Leaving directory `/home/breese1/pear/PEAR'

[breese1@hpcm PEAR]$ make install

Making install in src

make[1]: Entering directory `/home/breese1/pear/PEAR/src'

make[2]: Entering directory `/home/breese1/pear/PEAR/src'

test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"

/usr/bin/install -c pear '/usr/local/bin'

/usr/bin/install: cannot create regular file `/usr/local/bin/pear': Permission denied

make[2]: *** [install-binPROGRAMS] Error 1

make[2]: Leaving directory `/home/breese1/pear/PEAR/src'

make[1]: *** [install-am] Error 2

make[1]: Leaving directory `/home/breese1/pear/PEAR/src'

make: *** [install-recursive] Error 1

Message has been deleted

Tomas Flouri

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May 12, 2016, 7:45:03 PM5/12/16

to Sarah Hu, pear-users

Hello Sarah,

you have to run 'make install' as root, or as 'sudo make install'

the installation will copy the pear executable to a system-wide path.

Best regards,

Tomas

On 05/09/2016 11:23 PM, Sarah Hu wrote:

Was there a final solution to this issue?
I am experiencing the same problem.

I followed the instructions above to use: "./configure --disable-zlib"

And the make command went through without error.

This is the output from "make install"

/usr/local/bioinf/PEAR$ make install

Making install in src

make[1]: Entering directory `/usr/local/bioinf/PEAR/src'

make[2]: Entering directory `/usr/local/bioinf/PEAR/src'

test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"

/usr/bin/install -c pear '/usr/local/bin'

/usr/bin/install: cannot create regular file `/usr/local/bin/pear': Permission denied

make[2]: *** [install-binPROGRAMS] Error 1

make[2]: Leaving directory `/usr/local/bioinf/PEAR/src'

make[1]: *** [install-am] Error 2

make[1]: Leaving directory `/usr/local/bioinf/PEAR/src'

make: *** [install-recursive] Error 1

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