Installation error (using existing RepeatMasker and RepeatModeler installs)

[jaylward2]

I have a working conda installation of RepeatModeler and RepeatMasker, so I wanted to install EarlGrey in the same conda environment (called “earlGrey”), following the instructions under If you already have RepeatMasker and RepeatModeler.

I get the following error on the ./configure step:

ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_0'. Rolling back transaction: done class: LinkError message: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_0 location of failed script: /home/ldapusers/janneke.aylward/anaconda3/envs/earlGrey/bin/.bioconductor-genomeinfodbdata-post-link.sh ==> script messages <==

==> script output <== stdout: /home/ldapusers/janneke.aylward/anaconda3/envs/earlGrey/share/bioconductor-genomeinfodbdata-1.2.7-0/GenomeInfoDbData_1.2.7.tar.gz: FAILED /home/ldapusers/janneke.aylward/anaconda3/envs/earlGrey/share/bioconductor-genomeinfodbdata-1.2.7-0/GenomeInfoDbData_1.2.7.tar.gz: FAILED /home/ldapusers/janneke.aylward/anaconda3/envs/earlGrey/share/bioconductor-genomeinfodbdata-1.2.7-0/GenomeInfoDbData_1.2.7.tar.gz: FAILED ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 74c82f26111062a9ceb3c5331088cd56: https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.7.tar.gz https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.7_src_all.tar.gz stderr: % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 416 100 416 0 0 870 0 --:--:-- --:--:-- --:--:-- 870 md5sum: WARNING: 1 computed checksum did NOT match % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 153 100 153 0 0 135 0 0:00:01 0:00:01 --:--:-- 135 md5sum: WARNING: 1 computed checksum did NOT match % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 153 100 153 0 0 141 0 0:00:01 0:00:01 --:--:-- 142 md5sum: WARNING: 1 computed checksum did NOT match return code: 1 kwargs: {} Traceback (most recent call last): File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1082, in __call__ return func(*args, **kwargs) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call exit_code = getattr(module, func_name)(args, parser) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 142, in execute result[installer_type] = installer.install(prefix, pkg_specs, args, env) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda_env/installers/conda.py", line 59, in install unlink_link_transaction.execute() File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/core/link.py", line 281, in execute self._execute(tuple(concat(interleave(itervalues(self.prefix_action_groups))))) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/core/link.py", line 744, in _execute raise CondaMultiError(tuple(concatv( conda.CondaMultiErrorclass: LinkError message: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_0 location of failed script: /home/ldapusers/janneke.aylward/anaconda3/envs/earlGrey/bin/.bioconductor-genomeinfodbdata-post-link.sh ==> script messages <== ==> script output <== stdout: /home/ldapusers/janneke.aylward/anaconda3/envs/earlGrey/share/bioconductor-genomeinfodbdata-1.2.7-0/GenomeInfoDbData_1.2.7.tar.gz: FAILED /home/ldapusers/janneke.aylward/anaconda3/envs/earlGrey/share/bioconductor-genomeinfodbdata-1.2.7-0/GenomeInfoDbData_1.2.7.tar.gz: FAILED /home/ldapusers/janneke.aylward/anaconda3/envs/earlGrey/share/bioconductor-genomeinfodbdata-1.2.7-0/GenomeInfoDbData_1.2.7.tar.gz: FAILED ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 74c82f26111062a9ceb3c5331088cd56: https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.7.tar.gz https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.7_src_all.tar.gz stderr: % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 416 100 416 0 0 870 0 --:--:-- --:--:-- --:--:-- 870 md5sum: WARNING: 1 computed checksum did NOT match % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 153 100 153 0 0 135 0 0:00:01 0:00:01 --:--:-- 135 md5sum: WARNING: 1 computed checksum did NOT match % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 153 100 153 0 0 141 0 0:00:01 0:00:01 --:--:-- 142 md5sum: WARNING: 1 computed checksum did NOT match return code: 1 kwargs: {} : During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/ldapusers/janneke.aylward/anaconda3/bin/conda-env", line 7, in sys.exit(main()) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda_env/cli/main.py", line 91, in main return conda_exception_handler(do_call, args, parser) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1374, in conda_exception_handler return_value = exception_handler(func, *args, **kwargs) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1085, in __call__ return self.handle_exception(exc_val, exc_tb) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1116, in handle_exception return self.handle_application_exception(exc_val, exc_tb) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1132, in handle_application_exception self._print_conda_exception(exc_val, exc_tb) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1136, in _print_conda_exception print_conda_exception(exc_val, exc_tb) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1059, in print_conda_exception stderrlog.error("\n%r\n", exc_val) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/logging/__init__.py", line 1463, in error self._log(ERROR, msg, args, **kwargs) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/logging/__init__.py", line 1577, in _log self.handle(record) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/logging/__init__.py", line 1586, in handle if (not self.disabled) and self.filter(record): File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/logging/__init__.py", line 807, in filter result = f.filter(record) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/gateways/logging.py", line 61, in filter record.msg = record.msg % new_args File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/__init__.py", line 132, in __repr__ errs.append(e.__repr__()) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/__init__.py", line 71, in __repr__ return '%s: %s' % (self.__class__.__name__, text_type(self)) File "/home/ldapusers/janneke.aylward/anaconda3/lib/python3.8/site-packages/conda/__init__.py", line 90, in __str__ return text_type(self.message % self._kwargs) ValueError: unsupported format character 'T' (0x54) at index 1120 Setting path variables in script Path variables set Extracting zip archives Extracted required archives Remember to activate the earl grey conda environment before running earlGrey earlGrey is ready to use. To execute from any directory, add earlGrey to path by pasting the code (minus the square brackets) below... [export PATH=$PATH:$(realpath .)]

[katieemelianova]

I also have this exact error so would be good to hear if there is a solution!

[katieemelianova]

@jaylward2 not sure if it will work for you but I did:

conda install -c bioconda bioconductor-genomeinfodbdata

And that fixed it when I retried the configure it of earlgrey.

[TobyBaril]

This looks like an issue with trying to install into an existing conda environment, where there may be some conflicts. As mentioned above, try to reinstall the failed module separately and see if that works.

I would recommend NOT installing RepeatMasker and RepeatModeler2 using conda, as the source versions are better supported and easier to configure with new libraries, and there are quite a few issues users experience when trying to use the conda versions.