Re: [galaxy-dev] mirDeep2 install error
Now it worked! I had to purge the old squid version 1.9g version because it still recognised the old one to be not correctly installed... Thanks Jochen On 22.03.2016 11:26, Bjoern Gruening wrote: > Can you remove and reinstall > > package_randfold_2_0 > > Hopefully this solves your problem, > Cheers, > Bjoern > > > On 22.03.2016 11:21, Jochen Bick wrote: >> Hej Björn, >> >> so it did work in the development galaxy but not in our production >> galaxy. Here I get the following error in package_randfold_2_0 after >> successfully installing squid version 1.9g : >> >> randfold.c:24:18: error: squid.h: No such file or directory >> randfold.c:26:23: error: sre_random.h: No such file or directory >> randfold.c: In function 'main': >> randfold.c:30: error: 'SQFILE' undeclared (first use in this function) >> randfold.c:30: error: (Each undeclared identifier is reported only once >> randfold.c:30: error: for each function it appears in.) >> randfold.c:30: error: 'sqfp' undeclared (first use in this function) >> randfold.c:38: error: 'SQINFO' undeclared (first use in this function) >> randfold.c:38: error: expected ';' before 'sqinfo' >> randfold.c:89: warning: incompatible implicit declaration of built-in >> function 'strcpy' >> randfold.c:96: error: 'SQFILE_FASTA' undeclared (first use in this >> function) >> randfold.c:100: error: 'sqinfo' undeclared (first use in this function) >> randfold.c:103: warning: incompatible implicit declaration of built-in >> function 'malloc' >> randfold.c:103: warning: incompatible implicit declaration of built-in >> function 'strlen' >> randfold.c:136: warning: incompatible implicit declaration of built-in >> function 'fabs' >> randfold.c:158: warning: incompatible implicit declaration of built-in >> function 'free' >> make: *** [randfold] Error 1 >> >> Cheer Jochen >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] mirDeep2 install error
Hej Björn, so it did work in the development galaxy but not in our production galaxy. Here I get the following error in package_randfold_2_0 after successfully installing squid version 1.9g : randfold.c:24:18: error: squid.h: No such file or directory randfold.c:26:23: error: sre_random.h: No such file or directory randfold.c: In function 'main': randfold.c:30: error: 'SQFILE' undeclared (first use in this function) randfold.c:30: error: (Each undeclared identifier is reported only once randfold.c:30: error: for each function it appears in.) randfold.c:30: error: 'sqfp' undeclared (first use in this function) randfold.c:38: error: 'SQINFO' undeclared (first use in this function) randfold.c:38: error: expected ';' before 'sqinfo' randfold.c:89: warning: incompatible implicit declaration of built-in function 'strcpy' randfold.c:96: error: 'SQFILE_FASTA' undeclared (first use in this function) randfold.c:100: error: 'sqinfo' undeclared (first use in this function) randfold.c:103: warning: incompatible implicit declaration of built-in function 'malloc' randfold.c:103: warning: incompatible implicit declaration of built-in function 'strlen' randfold.c:136: warning: incompatible implicit declaration of built-in function 'fabs' randfold.c:158: warning: incompatible implicit declaration of built-in function 'free' make: *** [randfold] Error 1 Cheer Jochen ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] mirDeep2 install error
Thanks Björn, looks good! Cheers Jochen On 22.03.2016 10:46, Bjoern Gruening wrote: > Hi Jochen, > > can you please try again I updated the recipes. > > Sorry for the inconvenience, > Bjoern > > On 22.03.2016 10:24, Jochen Bick wrote: >> Hi, >> >> I tried to install suite_mirdeep_2_0. There is an error in the >> dependencies of package_squid_1_9g the download link has change to >> http://eddylab.org/software/squid/squid.tar.gz >> >> Cheers Jochen >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] mirDeep2 install error
Hi Jochen, can you please try again I updated the recipes. Sorry for the inconvenience, Bjoern On 22.03.2016 10:24, Jochen Bick wrote: Hi, I tried to install suite_mirdeep_2_0. There is an error in the dependencies of package_squid_1_9g the download link has change to http://eddylab.org/software/squid/squid.tar.gz Cheers Jochen ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
