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A further complication is that R depends on system libraries. New versions of packages, or of R, may include dependencies on additional library for whihc the development versions must be instaklled. These are routinely added to the env/Makefile targets for each operating system for new users.

To keep the R installation updated, daily tests would be ideal to catch new dependencies, ideally for each supported operrating system as some will have libraries loaded by default.

In-house extensions

In the pharmaceutical industry the practice has been to develop their own extensions to tranSMART. At Sanofi the Browse tab study metadata and a series of new data types were developed, but they continued to maintain their own transmart code including support for additional large files in MongoDB, an ETL package (ICE) and alternative authentication mechanisms. At Pfizer extensions to handle GWAS results were added. In both cases the native code only supported Oracle and needed to be ported to Postgres. Some ETL issues remain to be resolved. The Hyve developed new analysis methods and support for aCGH data for the TraIT projects in the Netherlands but Oracle support for these extensions has gaps (e.g. data loading).

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