R Under development (unstable) (2024-02-13 r85898 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(scAnnotate)
> 
> test_check("scAnnotate")

 !!! 
 Switch to Harmony batch effect removal, Seurat batch effect removal
         is tempoarily disabled due to conflict introduced by its version 5 upgrade 
 !!! 
`vst.flavor` is set to 'v2' but could not find glmGamPoi installed.
Please install the glmGamPoi package for much faster estimation.
--------------------------------------------
install.packages('BiocManager')
BiocManager::install('glmGamPoi')
--------------------------------------------
Falling back to native (slower) implementation.

PC_ 1 
Positive:  COTL1, PSAP, LST1, CST3, FCGR3A, CTSS, TYROBP, AIF1, IFITM3, FCER1G 
	   NEAT1, LYN, CDKN1C, CEBPB, SERPINA1, LYZ, FTL, MAFB, FTH1, SAT1 
	   MS4A7, PECAM1, SPI1, CD68, TNFRSF1B, DUSP1, S100A11, PTP4A2, FCN1, LINC01272 
Negative:  RPS6, RPLP1, CCL5, RPS15A, RPS3, SLC25A37, MALAT1, RPS21, RPS26, ZNF302 
	   RPS5, SIAE, IL32, CXCR4, ETS1, MS4A1, TRBC2, AP000769.1, NKG7, IGHM 
	   GMFB, SMG1, ATP2A2, GNLY, OGG1, IGKC, CD52, RP11.382A20.3, CD79A, GZMH 
PC_ 2 
Positive:  CCL5, SLC25A37, ZNF302, NKG7, S100A4, GNLY, ATP2A2, GMFB, SIAE, DDX39B 
	   GTF2I, RP11.122M14.1, SMG1, IL32, GZMH, RP3.325F22.5, PRKAA2, OGG1, PAK2, CST7 
	   RP11.382A20.3, RAB11A, FGFBP2, GZMB, RP11.529K1.4, TPM3, NCALD, CALM1, GZMA, MALAT1 
Negative:  CD74, HLA.DRA, IGKC, CD79A, MT.ND3, IGHM, CD37, HLA.DRB1, HLA.DPA1, HLA.DPB1 
	   IGHD, MS4A1, IGLC2, IGLC3, TCL1A, LTB, BANK1, IGHG1, RPL36A, RPS26 
	   RPLP1, BIRC3, RPS5, RPS10, MTRNR2L1, RPS15A, RPS21, RPS3, CD52, IL4R 
PC_ 3 
Positive:  SLC25A37, ZNF302, ATP2A2, GMFB, SIAE, OGG1, SMG1, RP11.382A20.3, SAT1, RAB11A 
	   NCALD, GTF2I, DDX39B, TPM3, MALAT1, AIF1, RP11.122M14.1, FTH1, LST1, NAP1L1 
	   HLA.DRA, FTL, RPS6, RP3.325F22.5, PRKAA2, MS4A1, RP11.529K1.4, PSAP, BANK1, CTSS 
Negative:  PFN1, MT.ND3, NKG7, CCL5, GNLY, ARL4C, PRF1, ZFP36L2, BTG1, IL2RB 
	   KLF2, CST7, CD247, RUNX3, FGFBP2, EFHD2, FLNA, SSBP3, GZMB, CALM1 
	   IRF2BP2, JUND, PTP4A2, MYH9, PABPN1, ABCG1, IL32, CD8A, ETS1, DNMT3A 
PC_ 4 
Positive:  RPS26, RPLP1, RPS6, RPS3, ACTG1, IFITM2, RPS15A, MTRNR2L1, RPS21, FTL 
	   FCGR3A, FCER1G, FTH1, KLRB1, S100A6, CD52, IL32, CCL5, GZMA, IL7R 
	   TYROBP, ITGB2, LINC01272, CST3, S100A11, RPS10, MT.ND3, TRDC, TRBC1, C1QA 
Negative:  JUND, KLF6, BTG1, DUSP1, IGKC, NFKBIA, IGHM, NEAT1, MALAT1, IRF2BP2 
	   PAK2, RPS4Y1, ABCG1, IGHD, PABPN1, CD83, CD79A, HNRNPL, CXCR4, GABRB1 
	   KLF2, SLC2A1.AS1, TNFRSF13C, FOS, AC004069.2, BIRC3, RBM3, ZNF326, DNMT3A, PTP4A2 
PC_ 5 
Positive:  PIP4K2B, COPS8, SNX30, CRY2, ALDH16A1, TMEM57, HELZ2, MED14, FAM160B1, C16orf52 
	   RABL2A, FOXO1, SLC41A3, EIF2AK3, TANC2, TSPAN33, AC008079.10, SEMA3C, CD8B, ARHGAP32 
	   ZFYVE1, CTC.325J23.2, EPHA4, RP11.890B15.2, GPRASP1, ACAD10, RP11.394O4.5, PAK4, GDPGP1, PAPD4 
Negative:  GNLY, IGLC3, IGLC2, GZMB, FTH1, PFN1, NKG7, CD79A, FTL, KLF2 
	   IGHG1, HLA.DPB1, FGFBP2, GZMH, RBM3, HLA.DRA, C1orf21, IGHM, SRGN, HLA.DPA1 
	   EIF5AL1, PRF1, KLF6, IFITM2, ITGB1, AC004069.2, CST7, HNRNPL, MS4A1, PTGDS 
Transposing data matrix
Initializing state using k-means centroids initialization
Harmony 1/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 2/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 3/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 4/10
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony converged after 4 iterations
[ FAIL 0 | WARN 82518 | SKIP 0 | PASS 3 ]

[ FAIL 0 | WARN 82518 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
1313.21  171.15 1489.21