Re: [spctools-discuss] Installing TPP 5.1.0 on RHEL 7 gives error
I believe you need to have libgd2 (or libgd2-dev) installed.
J
On Tuesday, February 20, 2018 at 12:26:57 PM UTC-5, Monica HPC wrote:
>
> Hi Mike,
>
> Thanks for your response. This error is gone after the sprintf change you
> suggested but I now get the following error and couple of warnings when I
> run `make install`.
>
> *Error:*
>
>
> *TPP/5.1.0/TPP_5.1.0-src/src/Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cpp:47:16:*
> *fatal
> error: *gd.h: No such file or directory
>
> #include "gd.h"
>
> *^*
>
> compilation terminated.
>
>
> *Warnings:*
>
> warning: "BOOST_NO_CXX11_SCOPED_ENUMS" redefined [enabled by default]
>
>
> and
>
>
> TPP/5.1.0/TPP_5.1.0-src/src/Parsers/mzIMLTools/mzIMLDemo/PepXMLParser3.cpp:363:43:
>
> warning: deprecated conversion from string constant to ‘char*’
> [-Wwrite-strings]
>
> mod.massStd=calcMonoMass("E",false)-18.0105633;
>
>
> Regards,
>
> Monica
>
> On Wednesday, February 14, 2018 at 6:04:12 PM UTC-5, Michael Hoopmann
> wrote:
>>
>> Hi Monica,
>>
>> Thanks for reporting the bug. I have a fix for the source tree, but
>> sourceforge is having problems right now. You can add the fix manually,
>> though, by going into CProteinAmbiguityGroup.cpp and changing:
>>
>>
>>
>> sprintf(dbid, "%s_%d", baseRef, proteinDetectionHypothesis->size());
>>
>>
>>
>>
>>
>> to
>>
>>
>>
>> sprintf(dbid, "%s_%d", [0], proteinDetectionHypothesis->size());
>>
>>
>>
>>
>>
>> Cheers,
>>
>> Mike
>>
>>
>>
>> *From:* spctools...@googlegroups.com [mailto:spctools...@googlegroups.com]
>> *On Behalf Of *Monica HPC
>> *Sent:* Wednesday, February 14, 2018 10:04 AM
>> *To:* spctools-discuss
>> *Subject:* [spctools-discuss] Installing TPP 5.1.0 on RHEL 7 gives error
>>
>>
>>
>> Hi there!
>>
>>
>>
>> I am trying to install the newer version of TPP 5.1.0 on RedHat
>> Enterprise Linux 7 server and I am getting the following error and warning
>> after running `make install`.
>>
>>
>>
>> I have installed all the prerequite libraries mentioned in the
>> BUILD_LINUX documentation:
>>
>> *libgd2*
>>
>> *libpng*
>>
>> *zlib*
>>
>> *libbz2*
>>
>>
>>
>> *WARNING:*
>>
>> TPP/5.1.0/TPP_5.1.0-src/build/linux-x86_64/include/boost/config/compiler/gcc.hpp:205:0:
>>
>> warning: "BOOST_NO_CXX11_SCOPED_ENUMS" redefined [enabled by default]
>>
>> # define BOOST_NO_CXX11_SCOPED_ENUMS
>>
>> ^
>>
>>
>>
>> *ERROR:*
>>
>> TPP/5.1.0/TPP_5.1.0-src/src/Parsers/mzIMLTools/CProteinAmbiguityGroup.cpp:106:69:
>>
>> error: cannot pass objects of non-trivially-copyable type ‘std::string {aka
>> class std::basic_string}’ through ‘...’
>>
>>sprintf(dbid, "%s_%d", baseRef, proteinDetectionHypothesis->size());
>>
>>
>>
>> Am I missing something or is it a bug in the code?
>>
>>
>>
>> Please do let me know if there is any workaround to fix this issue.
>>
>>
>>
>> Thanks,
>>
>> Monica
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to spctools-discu...@googlegroups.com.
>> To post to this group, send email to spctools...@googlegroups.com.
>> Visit this group at https://groups.google.com/group/spctools-discuss.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to spctools-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to spctools-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
Re: [spctools-discuss] Installing TPP 5.1.0 on RHEL 7 gives error
Hi Mike,
Thanks for your response. This error is gone after the sprintf change you
suggested but I now get the following error and couple of warnings when I
run `make install`.
*Error:*
*TPP/5.1.0/TPP_5.1.0-src/src/Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cpp:47:16:*
*fatal
error: *gd.h: No such file or directory
#include "gd.h"
*^*
compilation terminated.
*Warnings:*
warning: "BOOST_NO_CXX11_SCOPED_ENUMS" redefined [enabled by default]
and
TPP/5.1.0/TPP_5.1.0-src/src/Parsers/mzIMLTools/mzIMLDemo/PepXMLParser3.cpp:363:43:
warning: deprecated conversion from string constant to ‘char*’
[-Wwrite-strings]
mod.massStd=calcMonoMass("E",false)-18.0105633;
Regards,
Monica
On Wednesday, February 14, 2018 at 6:04:12 PM UTC-5, Michael Hoopmann wrote:
>
> Hi Monica,
>
> Thanks for reporting the bug. I have a fix for the source tree, but
> sourceforge is having problems right now. You can add the fix manually,
> though, by going into CProteinAmbiguityGroup.cpp and changing:
>
>
>
> sprintf(dbid, "%s_%d", baseRef, proteinDetectionHypothesis->size());
>
>
>
>
>
> to
>
>
>
> sprintf(dbid, "%s_%d", [0], proteinDetectionHypothesis->size());
>
>
>
>
>
> Cheers,
>
> Mike
>
>
>
> *From:* spctools...@googlegroups.com [mailto:
> spctools...@googlegroups.com ] *On Behalf Of *Monica HPC
> *Sent:* Wednesday, February 14, 2018 10:04 AM
> *To:* spctools-discuss
> *Subject:* [spctools-discuss] Installing TPP 5.1.0 on RHEL 7 gives error
>
>
>
> Hi there!
>
>
>
> I am trying to install the newer version of TPP 5.1.0 on RedHat Enterprise
> Linux 7 server and I am getting the following error and warning after
> running `make install`.
>
>
>
> I have installed all the prerequite libraries mentioned in the BUILD_LINUX
> documentation:
>
> *libgd2*
>
> *libpng*
>
> *zlib*
>
> *libbz2*
>
>
>
> *WARNING:*
>
> TPP/5.1.0/TPP_5.1.0-src/build/linux-x86_64/include/boost/config/compiler/gcc.hpp:205:0:
>
> warning: "BOOST_NO_CXX11_SCOPED_ENUMS" redefined [enabled by default]
>
> # define BOOST_NO_CXX11_SCOPED_ENUMS
>
> ^
>
>
>
> *ERROR:*
>
> TPP/5.1.0/TPP_5.1.0-src/src/Parsers/mzIMLTools/CProteinAmbiguityGroup.cpp:106:69:
>
> error: cannot pass objects of non-trivially-copyable type ‘std::string {aka
> class std::basic_string}’ through ‘...’
>
>sprintf(dbid, "%s_%d", baseRef, proteinDetectionHypothesis->size());
>
>
>
> Am I missing something or is it a bug in the code?
>
>
>
> Please do let me know if there is any workaround to fix this issue.
>
>
>
> Thanks,
>
> Monica
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discu...@googlegroups.com .
> To post to this group, send email to spctools...@googlegroups.com
> .
> Visit this group at https://groups.google.com/group/spctools-discuss.
> For more options, visit https://groups.google.com/d/optout.
>
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to spctools-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to spctools-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
RE: [spctools-discuss] Installing TPP 5.1.0 on RHEL 7 gives error
Hi Monica,
Thanks for reporting the bug. I have a fix for the source tree, but sourceforge
is having problems right now. You can add the fix manually, though, by going
into CProteinAmbiguityGroup.cpp and changing:
sprintf(dbid, "%s_%d", baseRef, proteinDetectionHypothesis->size());
to
sprintf(dbid, "%s_%d", [0], proteinDetectionHypothesis->size());
Cheers,
Mike
From: spctools-discuss@googlegroups.com
[mailto:spctools-discuss@googlegroups.com] On Behalf Of Monica HPC
Sent: Wednesday, February 14, 2018 10:04 AM
To: spctools-discuss
Subject: [spctools-discuss] Installing TPP 5.1.0 on RHEL 7 gives error
Hi there!
I am trying to install the newer version of TPP 5.1.0 on RedHat Enterprise
Linux 7 server and I am getting the following error and warning after running
`make install`.
I have installed all the prerequite libraries mentioned in the BUILD_LINUX
documentation:
libgd2
libpng
zlib
libbz2
WARNING:
TPP/5.1.0/TPP_5.1.0-src/build/linux-x86_64/include/boost/config/compiler/gcc.hpp:205:0:
warning: "BOOST_NO_CXX11_SCOPED_ENUMS" redefined [enabled by default]
# define BOOST_NO_CXX11_SCOPED_ENUMS
^
ERROR:
TPP/5.1.0/TPP_5.1.0-src/src/Parsers/mzIMLTools/CProteinAmbiguityGroup.cpp:106:69:
error: cannot pass objects of non-trivially-copyable type ‘std::string {aka
class std::basic_string}’ through ‘...’
sprintf(dbid, "%s_%d", baseRef, proteinDetectionHypothesis->size());
Am I missing something or is it a bug in the code?
Please do let me know if there is any workaround to fix this issue.
Thanks,
Monica
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to spctools-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to spctools-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to spctools-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to spctools-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
