[maker-devel] Does Conda Maker actually work?

Wed Feb 13 07:51:44 MST 2019

The conda recipe was produced by another group. I do not currently recommend using it because I have seen a number of issues pop up on the list based on people attempting to install MAKER via conda.  I know there is at least an issue with the conda RepeatMasker install, and there may be others. The specific failure you show is from Bio::DB::IndexedBase trying to compile an Inline::C function. It may be that conda is installing an older BioPerl where this issue still exists —> https://github.com/bioperl/bioperl-live/issues/215 <https://github.com/bioperl/bioperl-live/issues/215>

Or it may be that there is a new related issue (I’ve seen a handful of other examples that seem to relate back to Bio::DB::IndexedBase) —> https://github.com/bioperl/bioperl-live/issues/305 <https://github.com/bioperl/bioperl-live/issues/305>

Try installing MAKER without conda (make sure to remove any components that are in conda first to avoid conflicts).

—Carson

> On Feb 13, 2019, at 5:20 AM, SARIGOEL, FATIH <fatih.sarigoel at durham.ac.uk> wrote:
> 
> Greetings,
> I notice that you never mention conda installation on your website, so I am curious if the conda version is actually supposed to be working fine or not; as for me it didn't.
> I created a new conda environment and installed Maker (tried this with both installation options)
> When I run the example files, I get this error:
> 
> "make: *** [Makefile:330: IndexedBase_14e0.o] Error 127
> A problem was encountered while attempting to compile and install your Inline
> C code. The command that failed was:
>   "make > out.make 2>&1" with error code 2"
> 
> My conda environment is here
> /fast_new/work/users/fsarigo_m/miniconda3
> I don't understand why the program is trying to look here:
> /home/conda
> which does not exist
> 
> Also begins with a "possible precedence issue"
> 
> Thanks for your help in advance!
> Fatih
> 
> +++++
> 
> Here is the full log until the end of the contig:
> 
> (MakerX) [fsarigo_m at med0223 MAKER]$ maker
> Possible precedence issue with control flow operator at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 845.
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> A data structure will be created for you at:
> /fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_datastore
> 
> To access files for individual sequences use the datastore index:
> /fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/dpp_contig.maker.output/dpp_contig_master_datastore_index.log
> 
> STATUS: Now running MAKER...
> examining contents of the fasta file and run log
> 
> 
> 
> --Next Contig--
> 
> Processing run.log file...
> #---------------------------------------------------------------------
> Now starting the contig!!
> SeqID: contig-dpp-500-500
> Length: 32156
> #---------------------------------------------------------------------
> 
> 
> Running Mkbootstrap for IndexedBase_14e0 ()
> chmod 644 "IndexedBase_14e0.bs"
> "/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- IndexedBase_14e0.bs blib/arch/auto/Bio/DB/IndexedBase_14e0/IndexedBase_14e0.bs 644
> "/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/perl" "/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/ExtUtils/xsubpp"  -typemap "/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/5.26.2/ExtUtils/typemap"   IndexedBase_14e0.xs > IndexedBase_14e0.xsc
> mv IndexedBase_14e0.xsc IndexedBase_14e0.c
> /home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc -c  -I"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin" -D_REENTRANT -D_GNU_SOURCE --sysroot=/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/x86_64-conda_cos6-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2   -DVERSION=\"0.00\" -DXS_VERSION=\"0.00\" -fPIC --sysroot=/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/x86_64-conda_cos6-linux-gnu/sysroot "-I/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/5.26.2/x86_64-linux-thread-multi/CORE"   IndexedBase_14e0.c
> /bin/sh: /home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc: No such file or directory
> make: *** [Makefile:330: IndexedBase_14e0.o] Error 127
> 
> A problem was encountered while attempting to compile and install your Inline
> C code. The command that failed was:
>   "make > out.make 2>&1" with error code 2
> 
> The build directory was:
> /fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0
> 
> To debug the problem, cd to the build directory, and inspect the output files.
> 
> Environment PATH = '/fast/users/fsarigo_m/miniconda3/envs/MakerX/bin:/fast/users/fsarigo_m/miniconda3/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/fast/users/fsarigo_m/.local/bin:/fast/users/fsarigo_m/bin'
>  at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
> --> rank=NA, hostname=med0223
> ...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
> --> rank=NA, hostname=med0223
>  at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 38.
> Error::_throw_Error_Simple(HASH(0x564b40c78870)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 306
> Error::subs::run_clauses(HASH(0x564b40688970), "Running Mkbootstrap for IndexedBase_14e0 ()\x{a}chmod 644 \"Indexe"..., undef, ARRAY(0x564b40673ad0)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Error.pm line 426
> Error::subs::try(CODE(0x564b406899b8), HASH(0x564b40688970)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/FastaSeq.pm line 95
> FastaSeq::seq(FastaSeq=HASH(0x564b4068a7f0)) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm line 478
> Process::MpiChunk::_go(Process::MpiChunk=HASH(0x564b40673c08), "run", HASH(0x564b40673c80), 0, 0) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm line 341
> Process::MpiChunk::run(Process::MpiChunk=HASH(0x564b40673c08), 0) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiChunk.pm line 357
> Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x564b40673c08), 0) called at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/../lib/Process/MpiTiers.pm line 287
> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x564b4053f9f0), 0) called at /fast/users/fsarigo_m/miniconda3/envs/MakerX/bin/maker line 683
> Running Mkbootstrap for IndexedBase_14e0 ()
> chmod 644 "IndexedBase_14e0.bs"
> "/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- IndexedBase_14e0.bs blib/arch/auto/Bio/DB/IndexedBase_14e0/IndexedBase_14e0.bs 644
> "/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin/perl" "/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/ExtUtils/xsubpp"  -typemap "/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/5.26.2/ExtUtils/typemap"   IndexedBase_14e0.xs > IndexedBase_14e0.xsc
> mv IndexedBase_14e0.xsc IndexedBase_14e0.c
> /home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc -c  -I"/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/bin" -D_REENTRANT -D_GNU_SOURCE --sysroot=/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/x86_64-conda_cos6-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2   -DVERSION=\"0.00\" -DXS_VERSION=\"0.00\" -fPIC --sysroot=/home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/x86_64-conda_cos6-linux-gnu/sysroot "-I/fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/5.26.2/x86_64-linux-thread-multi/CORE"   IndexedBase_14e0.c
> /bin/sh: /home/conda/feedstock_root/build_artifacts/perl_1548813468557/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc: No such file or directory
> make: *** [Makefile:330: IndexedBase_14e0.o] Error 127
> 
> A problem was encountered while attempting to compile and install your Inline
> C code. The command that failed was:
>   "make > out.make 2>&1" with error code 2
> 
> The build directory was:
> /fast_new/work/users/fsarigo_m/scratch/tmp/urchin_holder/SeaUrchins/MAKER/_Inline/build/Bio/DB/IndexedBase_14e0
> 
> To debug the problem, cd to the build directory, and inspect the output files.
> 
> Environment PATH = '/fast/users/fsarigo_m/miniconda3/envs/MakerX/bin:/fast/users/fsarigo_m/miniconda3/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/fast/users/fsarigo_m/.local/bin:/fast/users/fsarigo_m/bin'
>  at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 275.
> --> rank=NA, hostname=med0223
> ...propagated at /fast_new/work/users/fsarigo_m/miniconda3/envs/MakerX/lib/site_perl/5.26.2/Inline/C.pm line 869.
> --> rank=NA, hostname=med0223
> --> rank=NA, hostname=med0223
> --> rank=NA, hostname=med0223
> ERROR: Failed while examining contents of the fasta file and run log
> ERROR: Chunk failed at level:0, tier_type:0
> FAILED CONTIG:contig-dpp-500-500
> 
> examining contents of the fasta file and run log
> 
> 
> 
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