<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Caitlin<div><br></div><div>Yes the strategy works a lot of the time but not all the time sorry. Another Ensembl developer reminded me of this issue offline. The challenge is that the production name (and database names) are not meant to be 100% predictable even though they are composable from available metadata. I also believe your issue with the lack of finding ENSOARG00020024523 as this is in the ovis_aries_rambouillet database and not in ovis_aries.</div><div><br></div><div>If you look at http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Member.html you can see there is a method for retrieving the linked genome_db() which you can use to retrieve the underlying genome i.e. </div><div><br></div><div><div style="color: rgb(204, 204, 204); background-color: rgb(31, 31, 31); font-family: Menlo, Monaco, "Courier New", monospace; line-height: 18px; white-space: pre;"><div><span style="color: rgb(86, 156, 214);">my</span> <span style="color: rgb(156, 220, 254);">$members</span> = <span style="color: rgb(156, 220, 254);">$homology</span><span style="color: rgb(212, 212, 212);">-></span>get_all_GeneMembers();</div><div><span style="color: rgb(197, 134, 192);">foreach</span> <span style="color: rgb(86, 156, 214);">my</span> <span style="color: rgb(156, 220, 254);">$member</span> (@{<span style="color: rgb(156, 220, 254);">$members</span>}) {</div><div> <span style="color: rgb(86, 156, 214);">my</span> <span style="color: rgb(156, 220, 254);">$genome_db</span> = <span style="color: rgb(156, 220, 254);">$member</span><span style="color: rgb(212, 212, 212);">-></span>genome_db();</div><div> <span style="color: rgb(86, 156, 214);">my</span> <span style="color: rgb(156, 220, 254);">$core_dba</span> = <span style="color: rgb(156, 220, 254);">$genome_db</span><span style="color: rgb(212, 212, 212);">-></span>db_adaptor();</div><div> <span style="color: rgb(86, 156, 214);">my</span> <span style="color: rgb(156, 220, 254);">$slice_adaptor</span> = <span style="color: rgb(156, 220, 254);">$core_dba</span><span style="color: rgb(212, 212, 212);">-></span>get_SliceAdaptor();</div><div> <span style="color: rgb(106, 153, 85);"># Carrying on as you did before</span></div><div>}</div></div></div><div><br></div><div>I’ve not tested this code and it’s been quite a while since I was last in the APIs this deeply but I believe this should work.</div><div><br></div><div>Andy</div><div><br><div>
<meta charset="UTF-8"><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;">------------<br></div><div>I sometimes send emails out of hours; I do not expect a response outside of your working hours.</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;"><br></div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;">Andrew Yates - Genomics Technology Infrastructure Team Leader, Joint-PI Ensembl Project</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;">The European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Genome Campus<br>Hinxton, Cambridge<br>CB10 1SD, United Kingdom<br>Tel: +44-(0)1223-492538<br>Fax: +44-(0)1223-494468<br>Skype: andy.yates.ebi<br>https://www.ebi.ac.uk/<br>https://www.ensembl.org/</div></div></div></div></div></div></div></div></div></div></div></div>
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<div><br><blockquote type="cite"><div>On 10 Oct 2023, at 19:11, Caitlin Jagla (Affiliate) <cjagla@associates.sigsci.com> wrote:</div><br class="Apple-interchange-newline"><div><div>Hi Andy, <br><br>Thank you for the prompt reply and for your suggestions! I adopted the second strategy you mentioned, converting the species name to lowercase and replacing whitespace with underscores, and that resolved the majority of the issues. However, a couple databases remain unable to ping/access using both my code and the ping_ensembl.pl script:<br><br>neogale_vison <br>bos_indicus_x_bos_taurus <br>cricetulus_griseus <br>heterocephalus_glaber<br><br>Additionally, while I can ping the ovis_aries database, and my code is no longer returning an error, it's still not retrieving slices/sequences for the following genes: ENSOARG00020024523, ENSOARG00020024608<br><br>Do you have any suggestions for resolving these residual issues?<br><br>Also, could you please expand upon the first strategy you mentioned, about the GeneMember link to the GenomeDB object? I am new to the perl API and I couldn't find anything in the documentation that clarified your point for me any further.<br><br>Thank you,<br>Caitlin<br><br><br>--------------------------------------<br>Message: 1<br>Date: Fri, 6 Oct 2023 16:18:59 +0100<br>From: Andy Yates <ayates@ebi.ac.uk><br>To: Ensembl developers list <dev@ensembl.org><br>Subject: Re: [ensembl-dev] Unable to fetch slices from many species in<br> vertebrates database<br>Message-ID: <9E64635C-2A84-426F-AABA-19F06CAA3664@ebi.ac.uk><br>Content-Type: text/plain; charset="utf-8"<br><br>Hi Caitlin,<br><br>I believe the issue is actually at the Ensembl database end, as you?re using what we would call aliases to the registry to fetch your species of interest. If you run the ping script as such you?ll get hits for your two species:<br><br>% ./misc-scripts/ping_ensembl.pl --species "anolis_carolinensis"<br>Installation is good. Connection to Ensembl works and you can query the anolis_carolinensis core database % ./misc-scripts/ping_ensembl.pl --species "scophthalmus_maximus"<br>Installation is good. Connection to Ensembl works and you can query the scophthalmus_maximus core database<br><br>Ovis aries does work because that database has the aliases ?Ovis aries" and this is linked to the internal name ?ovis_aries?. We will flag internally the fact that aliases are missing from some databases.<br><br>The two ways to potentially mitigate this would be<br><br>1. GeneMember has a link to the GenomeDB object so you can access the db_adaptor() method. This is the same logic GeneMember::get_Gene() uses. That method fetches the gene linked to a GeneMember, which might be a better way to proceed than using an ID lookup<br><br>2. You can edit the species name by lowercasing the name & replacing spaces with underscores which should get you somewhere<br><br>HTH<br><br>Andy<br><br>------------<br>I sometimes send emails out of hours; I do not expect a response outside of your working hours.<br><br>Andrew Yates - Genomics Technology Infrastructure Team Leader, Joint-PI Ensembl Project The European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton, Cambridge<br>CB10 1SD, United Kingdom<br>Tel: +44-(0)1223-492538<br>Fax: +44-(0)1223-494468<br>Skype: andy.yates.ebi<br>https://www.ebi.ac.uk/<br>https://www.ensembl.org/<br><br><blockquote type="cite">On 6 Oct 2023, at 15:32, Caitlin Jagla (Affiliate) <cjagla@associates.sigsci.com> wrote:<br><br>Hello all,<br><br>I have installed the perl API and am using it to query Ensembl for orthologs across all species in the main/vertebrates database. I can get a list of Ensembl ids for all the orthologs using the HomologyAdaptor and GeneMemberAdaptor. However, when I go to use these Ensembl ids to retrieve the gene sequence using SliceAdaptor->fetch_by_gene_stable_id($gene), many species (116 out of 166) give an error message as seen below. I can retrieve gene sequences for the remainder of the species, and I can't see any pattern or systematic differences in the ones that work vs. those that don't.<br><br>```<br>-------------------- WARNING ----------------------<br>MSG: Scophthalmus maximus is not a valid species name (check DB and <br>API version)<br>FILE: Bio/EnsEMBL/Registry.pm LINE: 1334 CALLED BY: <br>Bio/EnsEMBL/Registry.pm LINE: 1109<br>Date (localtime) = Fri Oct 6 09:47:29 2023<br>Ensembl API version = 110<br>---------------------------------------------------<br>```<br><br>I tested a selection of these species with the ping_ensembl.pl script and some of them ping while others don?t:<br><br>```<br>[cjagla@mapp02 ~/homologuer]$ perl /data/users/cjagla/src/ensembl/misc-scripts/ping_ensembl.pl -species "Ovis aries"<br>Installation is good. Connection to Ensembl works and you can query <br>the Ovis aries core database<br>[cjagla@mapp02 ~/homologuer]$ perl <br>/data/users/cjagla/src/ensembl/misc-scripts/ping_ensembl.pl -species <br>"Ovis aries" -ue Installation is good. Connection to Ensembl works and <br>you can query the Ovis aries core database<br>[cjagla@mapp02 ~/homologuer]$ perl <br>/data/users/cjagla/src/ensembl/misc-scripts/ping_ensembl.pl -species <br>"Anolis carolinensis" -ue<br><br>-------------------- WARNING ----------------------<br>MSG: Anolis carolinensis is not a valid species name (check DB and API <br>version)<br>FILE: Bio/EnsEMBL/Registry.pm LINE: 1334 CALLED BY: <br>Bio/EnsEMBL/Registry.pm LINE: 636<br>Date (localtime) = Fri Oct 6 09:30:41 2023<br>Ensembl API version = 110<br>---------------------------------------------------<br>ERROR: Error detected when connecting to Ensembl!<br> Species was not found. You may have accidentally download the <br>HEAD API version (found API release 110 & public FTP release is 110). <br>Please consult <br>http://www.ensembl.org/info/docs/api/api_installation.html<br>======================================================================<br>========== If the problem persists please send the following error <br>message to helpdesk@ensembl.org <mailto:helpdesk@ensembl.org><br><br>-------------------- EXCEPTION --------------------<br>MSG: Can not find internal name for species 'Anolis carolinensis'<br>STACK Bio::EnsEMBL::Registry::get_DBAdaptor <br>/data/users/cjagla/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:640<br>STACK (eval) <br>/data/users/cjagla/src/ensembl/misc-scripts/ping_ensembl.pl:131 <http://ping_ensembl.pl:131/> STACK toplevel /data/users/cjagla/src/ensembl/misc-scripts/ping_ensembl.pl:114 <http://ping_ensembl.pl:114/><br>Date (localtime) = Fri Oct 6 09:30:41 2023<br>Ensembl API version = 110<br>---------------------------------------------------<br>======================================================================<br>==========<br>[cjagla@mapp02 ~/homologuer]$ perl /data/users/cjagla/src/ensembl/misc-scripts/ping_ensembl.pl -species "Scophthalmus maximus"<br><br>-------------------- WARNING ----------------------<br>MSG: Scophthalmus maximus is not a valid species name (check DB and <br>API version)<br>FILE: Bio/EnsEMBL/Registry.pm LINE: 1334 CALLED BY: <br>Bio/EnsEMBL/Registry.pm LINE: 636<br>Date (localtime) = Fri Oct 6 10:07:10 2023<br>Ensembl API version = 110<br>---------------------------------------------------<br>ERROR: Error detected when connecting to Ensembl!<br> Species was not found. You may have accidentally download the <br>HEAD API version (found API release 110 & public FTP release is 110). <br>Please consult <br>http://www.ensembl.org/info/docs/api/api_installation.html<br>======================================================================<br>========== If the problem persists please send the following error <br>message to helpdesk@ensembl.org <mailto:helpdesk@ensembl.org><br><br>-------------------- EXCEPTION --------------------<br>MSG: Can not find internal name for species 'Scophthalmus maximus'<br>STACK Bio::EnsEMBL::Registry::get_DBAdaptor <br>/data/users/cjagla/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:640<br>STACK (eval) <br>/data/users/cjagla/src/ensembl/misc-scripts/ping_ensembl.pl:131 <http://ping_ensembl.pl:131/> STACK toplevel /data/users/cjagla/src/ensembl/misc-scripts/ping_ensembl.pl:114 <http://ping_ensembl.pl:114/><br>Date (localtime) = Fri Oct 6 10:07:10 2023<br>Ensembl API version = 110<br>---------------------------------------------------<br>======================================================================<br>==========<br>```<br><br>I also loaded the registry using the -verbose option and found that all the core databases are being loaded with version 110 of their databases, and I am using v110 of the API:<br><br>```<br>...<br>Species 'anolis_carolinensis' loaded from database 'anolis_carolinensis_core_110_2'<br>Species 'ovis_aries' loaded from database 'ovis_aries_core_110_31'<br>Species 'scophthalmus_maximus' loaded from database 'scophthalmus_maximus_core_110_1'<br>...<br>ensembl_compara_110 loaded<br>ensembl_ancestral_110 loaded<br>ensembl_ontology_110 loaded<br>ncbi_taxonomy_110 loaded<br>ensembl_metadata_110 loaded<br>No production database or adaptor found<br>ensembl_stable_ids_110 loaded<br>```<br><br>I have tried uninstalling and reinstalling the Ensembl API using the GitHub method, which did not resolve the issue.<br><br>The only thing of note that I can see from the -verbose output is the second-to-last line, "No production database or adaptor found" - I'm not sure what that's referring to, but it looks like the load_registry_from_db method is looking for something and not finding it, so it could be relevant?<br><br>Does anyone have any suggestions to resolve this issue? It's a major roadblock and I can't move forward in my research until I fix it.<br><br>Thank you,<br>Caitlin Jagla<br>Bioinformatics Data Scientist<br>Signature Science<br>cjagla@associates.signaturescience.com <br><mailto:cjagla@associates.signaturescience.com><br><br><br><br><br>Output of requested commands from 'debugging ensembl API' page:<br><br>perl -V<br>```<br>Summary of my perl5 (revision 5 version 32 subversion 1) configuration:<br><br> Platform:<br> osname=linux<br> osvers=4.18.0-425.3.1.el8.x86_64<br> archname=x86_64-linux-thread-multi<br> uname='linux 70a103858837433dbfc3ed5de4202b9b 4.18.0-425.3.1.el8.x86_64 #1 smp tue nov 8 14:08:25 est 2022 x86_64 x86_64 x86_64 gnulinux '<br> config_args='-des -Doptimize=none -Dccflags=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Dldflags=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Dccdlflags=-Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Dlddlflags=-shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Dshrpdir=/usr/lib64 -DDEBUGGING=-g -Dversion=5.32.1 -Dmyhostname=localhost -Dperladmin=root@local<br></blockquote> host -Dcc=gcc -Dcf_by=Red Hat, Inc. -Dprefix=/usr -Dvendorprefix=/usr -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl5/5.32 -Dsitearch=/usr/local/lib64/perl5/5.32 -Dprivlib=/usr/share/perl5 -Dvendorlib=/usr/share/perl5/vendor_perl -Darchlib=/usr/lib64/perl5 -Dvendorarch=/usr/lib64/perl5/vendor_perl -Darchname=x86_64-linux-thread-multi -Dlibpth=/usr/local/lib64 /lib64 /usr/lib64 -Duseshrplib -Dusethreads -Duseithreads -Dusedtrace=/usr/bin/dtrace -Duselargefiles -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/less -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_sethostent_r_proto -Ud_endprotoent_r_proto -Ud_setprotoent_r_proto -Ud_endservent_r_proto -Ud_setservent_r_proto -Dscriptdir=/usr/bin -Dusesitecustomize -Duse64bitint'<br><blockquote type="cite"> hint=recommended<br> useposix=true<br> d_sigaction=define<br> useithreads=define<br> usemultiplicity=define<br> use64bitint=define<br> use64bitall=define<br> uselongdouble=undef<br> usemymalloc=n<br> default_inc_excludes_dot=define<br> bincompat5005=undef<br> Compiler:<br> cc='gcc'<br> ccflags ='-D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'<br> optimize=' -g'<br> cppflags='-D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include'<br> ccversion=''<br> gccversion='11.3.1 20221121 (Red Hat 11.3.1-4)'<br> gccosandvers=''<br> intsize=4<br> longsize=8<br> ptrsize=8<br> doublesize=8<br> byteorder=12345678<br> doublekind=3<br> d_longlong=define<br> longlongsize=8<br> d_longdbl=define<br> longdblsize=16<br> longdblkind=3<br> ivtype='long'<br> ivsize=8<br> nvtype='double'<br> nvsize=8<br> Off_t='off_t'<br> lseeksize=8<br> alignbytes=8<br> prototype=define<br> Linker and Libraries:<br> ld='gcc'<br> ldflags ='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fstack-protector-strong -L/usr/local/lib'<br> libpth=/usr/local/lib64 /lib64 /usr/lib64 /usr/local/lib /usr/lib /lib/../lib64 /usr/lib/../lib64 /lib<br> libs=-lpthread -lresolv -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc -lgdbm_compat<br> perllibs=-lpthread -lresolv -ldl -lm -lcrypt -lutil -lc<br> libc=/lib/../lib64/libc.so.6<br> so=so<br> useshrplib=true<br> libperl=libperl.so<br> gnulibc_version='2.34'<br> Dynamic Linking:<br> dlsrc=dl_dlopen.xs<br> dlext=so<br> d_dlsymun=undef<br> ccdlflags='-Wl,--enable-new-dtags -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 '<br> cccdlflags='-fPIC'<br> lddlflags='-lpthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -L/usr/local/lib -fstack-protector-strong'<br><br><br>Characteristics of this binary (from libperl):<br> Compile-time options:<br> HAS_TIMES<br> MULTIPLICITY<br> PERLIO_LAYERS<br> PERL_COPY_ON_WRITE<br> PERL_DONT_CREATE_GVSV<br> PERL_IMPLICIT_CONTEXT<br> PERL_MALLOC_WRAP<br> PERL_OP_PARENT<br> PERL_PRESERVE_IVUV<br> USE_64_BIT_ALL<br> USE_64_BIT_INT<br> USE_ITHREADS<br> USE_LARGE_FILES<br> USE_LOCALE<br> USE_LOCALE_COLLATE<br> USE_LOCALE_CTYPE<br> USE_LOCALE_NUMERIC<br> USE_LOCALE_TIME<br> USE_PERLIO<br> USE_PERL_ATOF<br> USE_REENTRANT_API<br> USE_SITECUSTOMIZE<br> USE_THREAD_SAFE_LOCALE<br> Locally applied patches:<br> Fedora Patch1: Removes date check, Fedora/RHEL specific<br> Fedora Patch2: support for libdir64<br> Fedora Patch3: use libresolv instead of libbind<br> Fedora Patch4: USE_MM_LD_RUN_PATH<br> Fedora Patch5: Provide MM::maybe_command independently (bug #1129443)<br> Fedora Patch6: Dont run one io test due to random builder failures<br> Fedora Patch8: Define SONAME for libperl.so<br> Fedora Patch9: Install libperl.so to -Dshrpdir value<br> Fedora Patch10: Make *DBM_File desctructors thread-safe (RT#61912)<br> Fedora Patch11: Replace EU::MakeMaker dependency with EU::MM::Utils in IPC::Cmd (bug #1129443)<br> Fedora Patch12: Link XS modules to pthread library to fix linking with -z defs<br> Fedora Patch13: Pass the correct CFLAGS to dtrace<br> Fedora Patch14: Do not use C compiler reserved identifiers<br> Fedora Patch15: Fix SvUV_nomg() macro definition<br> Fedora Patch16: Fix SvTRUE() documentation<br> Fedora Patch17: Fix ext/XS-APItest/t/utf8_warn_base.pl tests<br> Fedora Patch18: Fix IO::Handle::error() to report write errors (GH#6799)<br> Fedora Patch19: Fix IO::Handle::error() to report write errors (GH#6799)<br> Fedora Patch21: Fix setting a non-blocking mode in IO::Socket::UNIX (GH#17787)<br> Fedora Patch22: Fix running actions after stepping in a debugger (GH#17901)<br> Fedora Patch23: Fix running actions after stepping in a debugger (GH#17901)<br> Fedora Patch24: Fix running actions after stepping in a debugger (GH#17901)<br> Fedora Patch25: Fix a buffer size for asctime_r() and ctime_r() functions<br> Fedora Patch26: Prevent from an integer overflow in RenewDouble() macro<br> Fedora Patch28: Fix a number of arguments passed to a BOOT XS subroutine (GH#17755)<br> Fedora Patch29: Fix an IO::Handle spurious error reported for regular file handles (GH#18019)<br> Fedora Patch30: Fix inheritance resolution of lexial objects in a debugger (GH#17661)<br> Fedora Patch35: Fix sorting with a block that calls return (GH#18081)<br> Fedora Patch38: Fix sv_collxfrm macro to respect locale<br> Fedora Patch39: Fix an iterator signedness in handling an mro exception (GH#18155)<br> Fedora Patch40: Fix a code flow in Perl_sv_inc_nomg()<br> Fedora Patch41: Fix an undefined behavior in Perl_custom_op_get_field()<br> Fedora Patch42: Fix Config variable names in in t/op tests<br> Fedora Patch43: Fix fetching a magic on the stacked file test operators<br> Fedora Patch44: Fix a crash in optimizing split() (GH#18232)<br> Fedora Patch45: Fix a crash in optimizing split() (GH#18232)<br> Fedora Patch46: Fix a crash in optimizing split() (GH#18232)<br> Fedora Patch47: Fix a crash in optimizing split() (GH#18232)<br> Fedora Patch48: Make accessing environment by DynaLoader thread-safe<br> Fedora Patch49: Use duplocale() if available<br> Fedora Patch50: Fix fc() in Turkish locale<br> Fedora Patch51: Fix croaking on "my $_" when "use utf8" is in effect (GH#18449)<br> Fedora Patch52: Fix PERL_UNUSED_ARG() definition in XSUB.h<br> Fedora Patch53: Add missing entries to perldiag (GH#18276)<br> Fedora Patch54: Protect locale tests from LANGUAGE environment variable<br> Fedora Patch55: Prevent the number of buckets in a hash from getting too large<br> Fedora Patch56: Fix a memory leak when compiling a regular expression (GH#18604)<br> Fedora Patch57: Fix dumping a hash entry of PL_strtab type<br> Fedora Patch57: Fix an arithmetic left shift of a minimal integer value (GH#18639)<br> Fedora Patch200: Link XS modules to libperl.so with EU::CBuilder on Linux<br> Fedora Patch201: Link XS modules to libperl.so with EU::MM on Linux<br> Fedora Patch202: Add definition of OPTIMIZE to .ph files (bug #2159759)<br> Built under linux<br> Compiled at Jan 18 2023 00:00:00<br> %ENV:<br> PERL5LIB=":/data/users/cjagla/src/bioperl-1.6.924:/data/users/cjagla/src/ensembl/modules:/data/users/cjagla/src/ensembl-compara/modules:/data/users/cjagla/src/ensembl-variation/modules:/data/users/cjagla/src/ensembl-funcgen/modules:/data/users/cjagla/src/ensembl-metadata/modules:/data/users/cjagla/src/ensembl-taxonomy/modules"<br> @INC:<br> /data/users/cjagla/src/bioperl-1.6.924<br> /data/users/cjagla/src/ensembl/modules<br> /data/users/cjagla/src/ensembl-compara/modules<br> /data/users/cjagla/src/ensembl-variation/modules<br> /data/users/cjagla/src/ensembl-funcgen/modules<br> /data/users/cjagla/src/ensembl-metadata/modules<br> /data/users/cjagla/src/ensembl-taxonomy/modules<br> /usr/local/lib64/perl5/5.32<br> /usr/local/share/perl5/5.32<br> /usr/lib64/perl5/vendor_perl<br> /usr/share/perl5/vendor_perl<br> /usr/lib64/perl5<br> /usr/share/perl5<br>```<br><br><br>perl -MDBI -e 'warn $DBI::VERSION'<br>```<br>1.643 at -e line 1.<br>```<br><br>perl -MDBD::mysql -e 'warn $DBD::mysql::VERSION'<br>```<br>4.050 at -e line 1.<br>```<br>_______________________________________________<br>Dev mailing list Dev@ensembl.org <mailto:Dev@ensembl.org><br>Posting guidelines and subscribe/unsubscribe info: <br>https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org<br>Ensembl Blog: http://www.ensembl.info/<br></blockquote><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20231006/c94998ad/attachment.html><br><br>------------------------------<br><br>Subject: Digest Footer<br><br>_______________________________________________<br>Dev mailing list Dev@ensembl.org<br>Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org<br>Ensembl Blog: http://www.ensembl.info/<br><br><br>------------------------------<br><br>End of Dev Digest, Vol 54, Issue 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