Re: [ccp4bb] Building static libs.
Yes that was it, I had built it previously & forgot. Forcing it fixes it. Thanks! Cheers -- Ian On 14 March 2015 at 18:00, Marcin Wojdyr wrote: > Dear Ian, > > Hard to tell without more details. What options are passed to the > configure scripts in mmdb2 and libccp4? (you can find it in the output) > The options include either "--disable-shared --enable-static" or the > other way around. > > Maybe you built it before setting BUILD_STATIC, and then when you > tried to build it again you got message: > *** Skipping [module] (package and dependencies not updated) *** > In such case either remove the install directory or do: > > ./build --force libccp4 > > Cheers > Marcin > > On Sat, Mar 14, 2015 at 12:17:16PM +, Ian Tickle wrote: > > Hello All > > > > I want to build static libs (libccp4.a etc.), basically to avoid hassle > > when deploying executables of my own programs to other machines that are > > not on my LAN and don't have up-to-date compilers or system libraries. > > > > I downloaded the CCP4 sources & followed instructions in the README, > > basically AFAICS just 'setenv BUILD_STATIC 1' (tcsh) and './build libccp4 > > etc.' which claimed to be successful. But I can't find libccp4*.a > > anywhere. In fact 'find' says that the only .a files are in the > > cmake-3.0.2 directory and are called 'libtest*.a'. I found > > 'libccp4c.so.0.0.0' in builddir/libccp4/ccp4/.libs so it seems to be > > building the dynamic libs. I also tried 'setenv STATIC 1' but got the > same > > result. > > > > What am I doing wrong? > > > > Cheers > > > > -- Ian > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >
Re: [ccp4bb] Building static libs.
Dear Ian, Hard to tell without more details. What options are passed to the configure scripts in mmdb2 and libccp4? (you can find it in the output) The options include either "--disable-shared --enable-static" or the other way around. Maybe you built it before setting BUILD_STATIC, and then when you tried to build it again you got message: *** Skipping [module] (package and dependencies not updated) *** In such case either remove the install directory or do: ./build --force libccp4 Cheers Marcin On Sat, Mar 14, 2015 at 12:17:16PM +, Ian Tickle wrote: > Hello All > > I want to build static libs (libccp4.a etc.), basically to avoid hassle > when deploying executables of my own programs to other machines that are > not on my LAN and don't have up-to-date compilers or system libraries. > > I downloaded the CCP4 sources & followed instructions in the README, > basically AFAICS just 'setenv BUILD_STATIC 1' (tcsh) and './build libccp4 > etc.' which claimed to be successful. But I can't find libccp4*.a > anywhere. In fact 'find' says that the only .a files are in the > cmake-3.0.2 directory and are called 'libtest*.a'. I found > 'libccp4c.so.0.0.0' in builddir/libccp4/ccp4/.libs so it seems to be > building the dynamic libs. I also tried 'setenv STATIC 1' but got the same > result. > > What am I doing wrong? > > Cheers > > -- Ian -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Building static libs.
Weird. I did my best to follow the instructions and - [andrew-mac-3:~/ccp4-6.5.0/ccp4-src-6.5-gfortran-4.5.0] harry% find . -name "libccp4f.a" ./builddir/libccp4/fortran/.libs/libccp4f.a ./ccp4-6.4.9/lib/libccp4f.a I *might* have changed shell to bash when I did the build (I can't remember). On 14 Mar 2015, at 17:39, Alastair Fyfe wrote: > Having struggled through similar build problems, I'd like to suggest > augmenting the existing source and binary distributions with a distribution > that includes header files and static libraries. > thanks, > Alastair Fyfe > UCSC > > On 03/14/2015 05:17 AM, Ian Tickle wrote: >> Hello All >> >> I want to build static libs (libccp4.a etc.), basically to avoid hassle >> when deploying executables of my own programs to other machines that are >> not on my LAN and don't have up-to-date compilers or system libraries. >> >> I downloaded the CCP4 sources & followed instructions in the README, >> basically AFAICS just 'setenv BUILD_STATIC 1' (tcsh) and './build libccp4 >> etc.' which claimed to be successful. But I can't find libccp4*.a >> anywhere. In fact 'find' says that the only .a files are in the >> cmake-3.0.2 directory and are called 'libtest*.a'. I found >> 'libccp4c.so.0.0.0' in builddir/libccp4/ccp4/.libs so it seems to be >> building the dynamic libs. I also tried 'setenv STATIC 1' but got the same >> result. >> >> What am I doing wrong? >> >> Cheers >> >> -- Ian >> Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] Building static libs.
Having struggled through similar build problems, I'd like to suggest augmenting the existing source and binary distributions with a distribution that includes header files and static libraries. thanks, Alastair Fyfe UCSC On 03/14/2015 05:17 AM, Ian Tickle wrote: Hello All I want to build static libs (libccp4.a etc.), basically to avoid hassle when deploying executables of my own programs to other machines that are not on my LAN and don't have up-to-date compilers or system libraries. I downloaded the CCP4 sources & followed instructions in the README, basically AFAICS just 'setenv BUILD_STATIC 1' (tcsh) and './build libccp4 etc.' which claimed to be successful. But I can't find libccp4*.a anywhere. In fact 'find' says that the only .a files are in the cmake-3.0.2 directory and are called 'libtest*.a'. I found 'libccp4c.so.0.0.0' in builddir/libccp4/ccp4/.libs so it seems to be building the dynamic libs. I also tried 'setenv STATIC 1' but got the same result. What am I doing wrong? Cheers -- Ian
[ccp4bb] Problem running DMMULTI in CCP4
Hi all, Recently I am working on a protein and the phase could be obtained from low resolution datasets (~6A) of native and heavy atom derivative. Later a relatively higher native dataset with ~4A was obtained , but it is somewhat non-isomorphous to the previous datasets used for phasing, making it not suitable for SIR phasing with previous 6A heavy atom dataset. After reading some literature, I realized that DMMULTI might work in my case to extend the phase to the higher resolution non-isomorphous dataset. However, I was not able to run the program successfully. Briefly, I provided the MTZ file of the initial low-resolution map then MTZ file of high-resolution native dataset, inputting the required field like solvent content, leaving other parameters as default. According to the log file, the program was able to go through the initial map MTZ file, however, when the program try to open MTZ file of the high resolution dataset, it gave me error message "CCP4 library signal library_file:Cannot open file". What is the possible reason for this? Do I need more inputs other than the high-resolution dataset and initial map? Thanks in advance,
[ccp4bb] Building static libs.
Hello All I want to build static libs (libccp4.a etc.), basically to avoid hassle when deploying executables of my own programs to other machines that are not on my LAN and don't have up-to-date compilers or system libraries. I downloaded the CCP4 sources & followed instructions in the README, basically AFAICS just 'setenv BUILD_STATIC 1' (tcsh) and './build libccp4 etc.' which claimed to be successful. But I can't find libccp4*.a anywhere. In fact 'find' says that the only .a files are in the cmake-3.0.2 directory and are called 'libtest*.a'. I found 'libccp4c.so.0.0.0' in builddir/libccp4/ccp4/.libs so it seems to be building the dynamic libs. I also tried 'setenv STATIC 1' but got the same result. What am I doing wrong? Cheers -- Ian
[ccp4bb] CCP4-6.5 Update 006
Dear CCP4 Users An update for the CCP4-6.5 series has just been released, consisting of the following changes * ccp4-progs - areaimol - bug fixes - r500 - update= - standard_geometry.cif - update * imosflm/mosflm - update to 7.1.3 * Molrep - fix for bug in multi-copy search * aimless - 0.5.7, bug fixes * privateer - extended support for disaccharides - added support for external validation strings * prosmart - minor update to h-bond restaint generation * mmdb2 - update to rwbrook interface * ccp4i' - updated autoSHARP interface Please report any bugs to c...@stfc.ac.uk. Many thanks for using CCP4. The CCP4 Core Team
Re: [ccp4bb] CCP4 PATH variable
Dear Petr Moving CCP4 to the end of the PATH could cause some problems, for example on Linux CCP4 truncate would be shadowed by relatively new truncate from GNU coreutils. We've been aware that having tclsh, wish, etc in $CCP4/bin could cause conflicts, but since no one complained it was a low-priority issue. We'll try to do something with it for the next release. Marcin On Thu, Mar 12, 2015 at 07:49:15PM +, Petr Leiman wrote: > Dear Community, > > What is the reason of placing the CCP4 PATH and other path-related variables > in front of existing variables? This forces a linux system to use > CCP4-distributed wish in all applications by default. Note that the ccp4i > script calls CCP4 distributed wish explicitly with its full path. > > This might be trivial, and the fix is also trivial, but trivial things like > that cause a lot of lost time and head scratching when tcl/tk programs > compile without errors and perform some operations correctly but segfault on > others - all due to a mixup of libraries and wish executables caused by CCP4 > wish. > > Would it be possible to append CCP4 path variables by default instead of > rather rudely jumping in front of the queue? > > Thank you, > > Petr > > -- > Petr Leiman > EPFL > BSP 415 > CH-1015 Lausanne > Switzerland > Office: +41 21 69 30 441 > Mobile: +41 79 538 7647 > Fax: +41 21 69 30 422 > http://lbbs.epfl.ch -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
