pubchem.bio
Biologically Informed Metabolomic Libraries from 'PubChem'
Description
All 'PubChem' compounds are downloaded to a local computer, but for each compound, only partial records are used. The data are organized into small files referenced by 'PubChem' CID. This package also contains functions to parse the biologically relevant compounds from all 'PubChem' compounds, using biological database sources, pathway presence, and taxonomic relationships. Taxonomy is used to generate a lowest common ancestor taxonomy ID (NCBI) for each biological metabolite, which then enables creation of taxonomically specific metabolome databases for any taxon.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| r-oldrel-macos-x86_64 | ERROR |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | ERROR |
| r-release-macos-x86_64 | ERROR |
| r-release-windows-x86_64 | OK |
Check details (4 non-OK)
package dependencies
Packages required but not available: 'MetaboCoreUtils', 'CompoundDb' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘CompoundDb’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘CompoundDb’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'MetaboCoreUtils', 'CompoundDb' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
Check History
ERROR 6 OK · 0 NOTE · 0 WARNING · 8 ERROR · 0 FAILURE Mar 10, 2026
package dependencies
Packages required but not available: 'MetaboCoreUtils', 'CompoundDb' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘CompoundDb’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘CompoundDb’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘CompoundDb’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘CompoundDb’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'MetaboCoreUtils', 'CompoundDb' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'MetaboCoreUtils', 'CompoundDb' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘CompoundDb’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.