CRAN Package Check Results for Package BioMedR

Last updated on 2021-10-16 22:52:46 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.1 29.44 323.98 353.42 OK
r-devel-linux-x86_64-debian-gcc 1.2.1 26.31 239.80 266.11 OK
r-devel-linux-x86_64-fedora-clang 1.2.1 404.62 ERROR
r-devel-linux-x86_64-fedora-gcc 1.2.1 370.41 ERROR
r-devel-windows-x86_64 1.2.1 10.00 7.00 17.00 ERROR
r-devel-windows-x86_64-gcc10-UCRT 1.2.1 OK
r-patched-linux-x86_64 1.2.1 41.27 305.45 346.72 OK
r-release-linux-x86_64 1.2.1 28.83 309.23 338.06 OK
r-release-macos-arm64 1.2.1 OK
r-release-macos-x86_64 1.2.1 ERROR
r-release-windows-ix86+x86_64 1.2.1 53.00 394.00 447.00 OK
r-oldrel-macos-x86_64 1.2.1 ERROR
r-oldrel-windows-ix86+x86_64 1.2.1 77.00 398.00 475.00 OK

Check Details

Version: 1.2.1
Check: examples
Result: ERROR
    Running examples in ‘BioMedR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: Constitutional
    > ### Title: Calculates the Number of Amino Acids Descriptor
    > ### Aliases: Constitutional extrDrugAminoAcidCount
    > ### extrDrugAromaticAtomsCount extrDrugAromaticBondsCount
    > ### extrDrugAtomCount extrDrugBondCount extrDrugLargestChain
    > ### extrDrugLargestPiSystem extrDrugLongestAliphaticChain
    > ### extrDrugRotatableBondsCount
    > ### Keywords: Acid Aliphatic Amino Aromatic Atom Atoms Bond Bonds Chain
    > ### Count Largest Longest Pi Rotatable extrDrugAminoAcidCount
    > ### extrDrugAromaticAtomsCount extrDrugAromaticBondsCount
    > ### extrDrugAtomCount extrDrugBondCount extrDrugLargestChain
    > ### extrDrugLargestPiSystem extrDrugLongestAliphaticChain
    > ### extrDrugRotatableBondsCount
    >
    > ### ** Examples
    >
    > # Calculates the Number of Amino Acids Descriptor
    > smi = system.file('vignettedata/test.smi', package = 'BioMedR')
    > mol = readMolFromSmi(smi, type = 'mol')
    > dat = extrDrugAminoAcidCount(mol)
    org.openscience.cdk.io.cml.CMLHandler WARN: Detected unknown convention: cdk:substructureList
    > head(dat)
     nA nR nN nD nC nF nQ nE
    c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 0 0 0 0 0 0 0 0
    c1(ccc(cc1)O)NC(=O)C 0 0 0 0 0 0 0 0
    c1ccccc1NC(=O)C 0 0 0 0 0 0 0 0
     nG nH nI nP nL nK nM nS
    c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 0 0 0 0 0 0 0 0
    c1(ccc(cc1)O)NC(=O)C 0 0 0 0 0 0 0 0
    c1ccccc1NC(=O)C 0 0 0 0 0 0 0 0
     nT nY nV nW
    c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 0 0 0 0
    c1(ccc(cc1)O)NC(=O)C 0 0 0 0
    c1ccccc1NC(=O)C 0 0 0 0
    >
    > # Calculates the Number of Aromatic Atoms Descriptor
    > smi = system.file('vignettedata/test.smi', package = 'BioMedR')
    > mol = readMolFromSmi(smi, type = 'mol')
    > dat = extrDrugAromaticAtomsCount(mol)
    > head(dat)
     naAromAtom
    c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 16
    c1(ccc(cc1)O)NC(=O)C 6
    c1ccccc1NC(=O)C 6
    >
    > # Calculates the Number of Aromatic Bonds Descriptor
    > smi = system.file('vignettedata/test.smi', package = 'BioMedR')
    > mol = readMolFromSmi(smi, type = 'mol')
    > dat = extrDrugAromaticBondsCount(mol)
    > head(dat)
     nAromBond
    c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 17
    c1(ccc(cc1)O)NC(=O)C 6
    c1ccccc1NC(=O)C 6
    >
    > # Calculates the Number of Atom Descriptor
    > smi = system.file('vignettedata/test.smi', package = 'BioMedR')
    > mol = readMolFromSmi(smi, type = 'mol')
    > dat = extrDrugAtomCount(mol)
    > head(dat)
     nAtom
    c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 41
    c1(ccc(cc1)O)NC(=O)C 20
    c1ccccc1NC(=O)C 19
    >
    > # Calculates the Descriptor Based on the Number of Bonds of a
    > # Certain Bond Order
    > smi = system.file('vignettedata/test.smi', package = 'BioMedR')
    > mol = readMolFromSmi(smi, type = 'mol')
    > dat = extrDrugBondCount(mol)
    > head(dat)
     nB
    c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 28
    c1(ccc(cc1)O)NC(=O)C 11
    c1ccccc1NC(=O)C 10
    >
    > # Descriptor that Calculates the Number of Atoms in the Largest Chain
    > smi = system.file('vignettedata/test.smi', package = 'BioMedR')
    > mol = readMolFromSmi(smi, type = 'mol')
    > dat = extrDrugLargestChain(mol)
    > head(dat)
     nAtomLC
    c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 13
    c1(ccc(cc1)O)NC(=O)C 8
    c1ccccc1NC(=O)C 7
    >
    > # Descriptor that Calculates the Number of Atoms in the Largest Pi Chain
    > smi = system.file('vignettedata/test.smi', package = 'BioMedR')
    > mol = readMolFromSmi(smi, type = 'mol')
    > dat = extrDrugLargestPiSystem(mol)
    > head(dat)
     nAtomP
    c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 12
    c1(ccc(cc1)O)NC(=O)C 10
    c1ccccc1NC(=O)C 9
    >
    > # Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain
    > smi = system.file('vignettedata/test.smi', package = 'BioMedR')
    > mol = readMolFromSmi(smi, type = 'mol')
    > dat = extrDrugLongestAliphaticChain(mol)
    Error: segfault from C stack overflow
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.2.1
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-devel-windows-x86_64

Version: 1.2.1
Check: package dependencies
Result: ERROR
    Packages required but not available: 'ChemmineR', 'fmcsR', 'org.Hs.eg.db'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-macos-x86_64

Version: 1.2.1
Check: package dependencies
Result: ERROR
    Packages required but not available: 'ChemmineR', 'fmcsR'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-oldrel-macos-x86_64