CRAN Package Check Results for Package scAnnotate

Last updated on 2022-10-30 07:55:23 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.0.4 ERROR
r-devel-linux-x86_64-debian-gcc 0.0.4 0.24 2.37 2.61 ERROR
r-devel-linux-x86_64-fedora-clang 0.0.4 13.96 ERROR
r-devel-linux-x86_64-fedora-gcc 0.0.4 13.82 ERROR
r-devel-windows-x86_64 0.0.4 43.00 344.00 387.00 ERROR
r-patched-linux-x86_64 0.0.4 0.31 3.01 3.32 ERROR
r-release-linux-x86_64 0.0.4 0.34 3.12 3.46 ERROR
r-release-macos-arm64 0.0.4 105.00 OK
r-release-macos-x86_64 0.0.4 160.00 OK
r-release-windows-x86_64 0.0.4 33.00 333.00 366.00 ERROR
r-oldrel-macos-arm64 0.0.4 98.00 OK
r-oldrel-macos-x86_64 0.0.4 155.00 OK
r-oldrel-windows-ix86+x86_64 0.0.4 59.00 345.00 404.00 ERROR

Check Details

Version: 0.0.4
Check: package dependencies
Result: ERROR
    Package required but not available: 'harmony'
    
    See section 'The DESCRIPTION file' in the 'Writing R Extensions'
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.0.4
Check: examples
Result: ERROR
    Running examples in 'scAnnotate-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: scAnnotate
    > ### Title: scAnnotate
    > ### Aliases: scAnnotate
    >
    > ### ** Examples
    >
    > data(pbmc1)
    > data(pbmc2)
    > predict_label=scAnnotate(train=pbmc1,
    + test=pbmc2[,-1],
    + distribution="normal",
    + correction ="harmony",
    + screening ="wilcox",
    + threshold=0,
    + lognormalized=TRUE)
    Calculating gene variances
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Calculating feature variances of standardized and clipped values
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Centering and scaling data matrix
    
     |
     | | 0%
     |
     |=================================== | 50%
     |
     |======================================================================| 100%
    PC_ 1
    Positive: COTL1, CST3, LST1, PSAP, CTSS, TYROBP, FCGR3A, IFITM3, SERPINA1, LYN
     FCER1G, AIF1, CEBPB, NEAT1, CDKN1C, MS4A7, FTL, MAFB, SPI1, CD68
     FTH1, PECAM1, S100A11, TNFRSF1B, LYZ, FCN1, SAT1, POU2F2, NPC2, HCK
    Negative: CCL5, IL32, ETS1, RPS6, TRBC2, RPS15A, CXCR4, RPS3, NKG7, CST7
     RPS21, AP000769.1, GZMA, GZMH, TRBC1, RPLP1, SIAE, SYNE2, RPS5, GNLY
     SLC25A37, RPS26, MS4A1, CD8A, JUN, FGFBP2, OGG1, ZNF302, GZMB, IGHM
    PC_ 2
    Positive: ZNF302, SLC25A37, ATP2A2, GMFB, DDX39B, GTF2I, OGG1, SMG1, SIAE, RP11.122M14.1
     RP11.382A20.3, RAB11A, PRKAA2, RP3.325F22.5, MALAT1, NCALD, TPM3, RP11.529K1.4, PAK2, SAT1
     S100A4, S100A6, GABRE, AIF1, NCL, GABRB1, EMC10, FOS, AP000769.1, LST1
    Negative: MT.ND3, CD74, CD37, CD79A, IGHM, HLA.DRA, IGKC, HLA.DRB1, HLA.DPA1, IGHD
     RPL36A, IGLC2, TCL1A, IGLC3, MS4A1, KLF2, HLA.DPB1, IGHG1, LTB, BANK1
     JUND, BTG1, RPS10, BIRC3, ZFP36L2, TNFRSF13C, IL4R, PABPN1, SEMA4B, CD52
    PC_ 3
    Positive: HLA.DRA, MS4A1, IGHM, CD79A, HLA.DPB1, CD74, BANK1, HLA.DPA1, HLA.DRB1, LTB
     IGKC, IGHD, RPS6, RPS21, SLC25A37, CD37, IGHG1, ZNF302, NAP1L1, IGLC2
     BIRC3, OGG1, TCL1A, RPLP1, RP11.382A20.3, RPS5, IGLC3, GMFB, ATP2A2, SIAE
    Negative: NKG7, CCL5, PFN1, CST7, PRF1, ARL4C, GNLY, FGFBP2, EFHD2, IL32
     GZMB, SRGN, GZMA, CD247, CALM1, IL2RB, RUNX3, CD8A, PTP4A2, GZMH
     TGFBR3, S100A4, TRBC1, ABCG1, FLNA, SSBP3, ZFP36L2, GZMM, TNFAIP3, IRF2BP2
    PC_ 4
    Positive: JUND, KLF6, NEAT1, GABRB1, DUSP1, ABCG1, NFKBIA, RPS4Y1, PAK2, RP3.325F22.5
     FOS, IGHM, HNRNPL, IFI44L, EIF5AL1, TNFRSF13C, ZNF326, METRNL, RP11.529K1.4, AC008914.1
     CD83, MYH11, PABPN1, ZBTB7A, CD79A, IRF2BP2, RP11.1143G9.4, SLC2A1.AS1, AC004069.2, IGKC
    Negative: RPLP1, RPS26, IFITM2, RPS3, RPS15A, MTRNR2L1, ACTG1, RPS6, CD52, RPS21
     FCER1G, S100A11, ITGB2, FCGR3A, S100A6, GZMA, RPS10, IL32, KLRB1, C1QA
     HCK, LINC01272, TYROBP, HLA.DPA1, HMOX1, CCL5, TRBC1, IL7R, RPS5, GZMH
    PC_ 5
    Positive: AC008914.1, RPS5, RPS15A, MS4A1, HLA.DPB1, LTB, MYH11, BANK1, SLC4A1, CD79A
     PFN1, RPS21, RPS26, DTWD1, CD52, KLF6, RP11.1143G9.4, FTH1, KLF2, SLC37A1
     RBM3, ARHGAP26, AP5B1, LEMD2, IGHM, IGHG1, JUN, ICOSLG, FTL, ZBTB7A
    Negative: RABL2A, CRY2, TANC2, SLC41A3, TSPAN33, FAM160B1, AC008079.10, PIP4K2B, EIF2AK3, C16orf52
     ZFYVE1, RP11.890B15.2, ARHGAP32, PAK4, EPHA4, MED14, GPRASP1, ACAD10, CTC.325J23.2, SEMA3C
     RP11.394O4.5, GDPGP1, ALDH16A1, SNX30, CTD.2620I22.3, AP000438.2, C1QTNF3.AMACR, TMEM57, COPS8, HELZ2
    Harmony 1/10
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Error in harmonyObj$cluster_cpp() :
     element-wise pow(): incompatible matrix dimensions: 41x2 and 2x1
    Calls: scAnnotate ... HarmonyMatrix -> harmonize -> cluster -> <Anonymous> -> .External
    Execution halted
Flavor: r-devel-windows-x86_64

Version: 0.0.4
Check: examples
Result: ERROR
    Running examples in 'scAnnotate-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: scAnnotate
    > ### Title: scAnnotate
    > ### Aliases: scAnnotate
    >
    > ### ** Examples
    >
    > data(pbmc1)
    > data(pbmc2)
    > predict_label=scAnnotate(train=pbmc1,
    + test=pbmc2[,-1],
    + distribution="normal",
    + correction ="harmony",
    + screening ="wilcox",
    + threshold=0,
    + lognormalized=TRUE)
    Calculating gene variances
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Calculating feature variances of standardized and clipped values
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Centering and scaling data matrix
    
     |
     | | 0%
     |
     |=================================== | 50%
     |
     |======================================================================| 100%
    PC_ 1
    Positive: COTL1, CST3, LST1, PSAP, CTSS, TYROBP, FCGR3A, IFITM3, SERPINA1, LYN
     FCER1G, AIF1, CEBPB, NEAT1, CDKN1C, MS4A7, FTL, MAFB, SPI1, CD68
     FTH1, PECAM1, S100A11, TNFRSF1B, LYZ, FCN1, SAT1, POU2F2, NPC2, HCK
    Negative: CCL5, IL32, ETS1, RPS6, TRBC2, RPS15A, CXCR4, RPS3, NKG7, CST7
     RPS21, AP000769.1, GZMA, GZMH, TRBC1, RPLP1, SIAE, SYNE2, RPS5, GNLY
     SLC25A37, RPS26, MS4A1, CD8A, JUN, FGFBP2, OGG1, ZNF302, GZMB, IGHM
    PC_ 2
    Positive: MT.ND3, CD74, CD37, CD79A, IGHM, HLA.DRA, IGKC, HLA.DRB1, HLA.DPA1, IGHD
     RPL36A, IGLC2, TCL1A, IGLC3, MS4A1, KLF2, HLA.DPB1, IGHG1, LTB, BANK1
     JUND, BTG1, RPS10, BIRC3, ZFP36L2, TNFRSF13C, IL4R, PABPN1, SEMA4B, CD52
    Negative: ZNF302, SLC25A37, ATP2A2, GMFB, DDX39B, GTF2I, OGG1, SMG1, SIAE, RP11.122M14.1
     RP11.382A20.3, RAB11A, PRKAA2, RP3.325F22.5, MALAT1, NCALD, TPM3, RP11.529K1.4, PAK2, SAT1
     S100A4, S100A6, GABRE, AIF1, NCL, GABRB1, EMC10, FOS, AP000769.1, LST1
    PC_ 3
    Positive: NKG7, CCL5, PFN1, CST7, PRF1, ARL4C, GNLY, FGFBP2, EFHD2, IL32
     GZMB, SRGN, GZMA, CD247, CALM1, IL2RB, RUNX3, CD8A, PTP4A2, GZMH
     TGFBR3, S100A4, TRBC1, ABCG1, FLNA, SSBP3, ZFP36L2, GZMM, TNFAIP3, IRF2BP2
    Negative: HLA.DRA, MS4A1, IGHM, CD79A, HLA.DPB1, CD74, BANK1, HLA.DPA1, HLA.DRB1, LTB
     IGKC, IGHD, RPS6, RPS21, SLC25A37, CD37, IGHG1, ZNF302, NAP1L1, IGLC2
     BIRC3, OGG1, TCL1A, RPLP1, RP11.382A20.3, RPS5, IGLC3, GMFB, ATP2A2, SIAE
    PC_ 4
    Positive: JUND, KLF6, NEAT1, GABRB1, DUSP1, ABCG1, NFKBIA, RPS4Y1, PAK2, RP3.325F22.5
     FOS, IGHM, HNRNPL, IFI44L, EIF5AL1, TNFRSF13C, ZNF326, METRNL, RP11.529K1.4, AC008914.1
     CD83, MYH11, PABPN1, ZBTB7A, CD79A, IRF2BP2, RP11.1143G9.4, SLC2A1.AS1, AC004069.2, IGKC
    Negative: RPLP1, RPS26, IFITM2, RPS3, RPS15A, MTRNR2L1, ACTG1, RPS6, CD52, RPS21
     FCER1G, S100A11, ITGB2, FCGR3A, S100A6, GZMA, RPS10, IL32, KLRB1, C1QA
     HCK, LINC01272, TYROBP, HLA.DPA1, HMOX1, CCL5, TRBC1, IL7R, RPS5, GZMH
    PC_ 5
    Positive: RABL2A, CRY2, TANC2, SLC41A3, TSPAN33, FAM160B1, AC008079.10, PIP4K2B, EIF2AK3, C16orf52
     ZFYVE1, RP11.890B15.2, ARHGAP32, PAK4, EPHA4, MED14, GPRASP1, ACAD10, CTC.325J23.2, SEMA3C
     RP11.394O4.5, GDPGP1, ALDH16A1, SNX30, AP000438.2, CTD.2620I22.3, C1QTNF3.AMACR, TMEM57, COPS8, HELZ2
    Negative: AC008914.1, RPS5, RPS15A, MS4A1, HLA.DPB1, LTB, MYH11, BANK1, SLC4A1, CD79A
     PFN1, RPS21, RPS26, DTWD1, CD52, KLF6, RP11.1143G9.4, FTH1, KLF2, SLC37A1
     RBM3, ARHGAP26, AP5B1, LEMD2, IGHM, IGHG1, JUN, ICOSLG, FTL, ZBTB7A
    Harmony 1/10
    0% 10 20 30 40 50 60 70 80 90 100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    Error in harmonyObj$cluster_cpp() :
     element-wise pow(): incompatible matrix dimensions: 41x2 and 2x1
    Calls: scAnnotate ... HarmonyMatrix -> harmonize -> cluster -> <Anonymous> -> .External
    Execution halted
Flavors: r-release-windows-x86_64, r-oldrel-windows-ix86+x86_64