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Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(scStability) > > test_check("scStability") see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts 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: Dner, Olfm1, Elmod1, Ogfrl1, Camk2b, Rph3a, D3Bwg0562e, Sema3c, Rgs7bp, Slc2a13 Nr2f1, Eef1a2, Syn2, Nfib, Shisa9, Nfix, Tspan5, Htr3a, Slc6a1, Spock1 Prkar2b, Chd3, Rab6a, Cpne7, Lrp12, Cxcl14, Atp2b2, Ptprm, Plcxd2, Cdk5r1 Negative: Rab3b, Zwint, Fth1, Ngfrap1, Sst, Gm6402, Lgals1, Rps15a-ps4, Rps20, 1500004A13Rik Gpx1, Crhbp, Gm15421, Plp1, Tmsb4x, OTTMUSG00000016609-loc3, Ptn, Csrp1, Prdx1, Schip1 Sepp1, Ndufab1, Cd9, mt-Tv, Gm14305, OTTMUSG00000016609-loc4, Fabp5, Cnp, Gm14436, Gatm PC_ 2 Positive: Mpped1, Lamp5, Adcy1, Bcl11a, Tsc22d1, Sema5a, Akap5, Itpr1, Hapln1, Tox3 Gabrd, Bcl11b, Nxph1, Crispld1, Rapgef4, Cap2, Grm5, Lin7a, Gda, Cpne8 Car4, Scube1, Gad2, Hlf, Caln1, Cacna2d1, Tnnt1, Enc1, Plk2, Rasl11a Negative: Npas1, Ddah1, Fxyd6, Gng4, Cplx2, Nrxn3, Rgs12, Trp53i11, Cnr1, Synpr Asic1, Vip, Npas3, Fstl5, Sncg, Wnt5a, Kazn, Enho, Galnt18, Htr3a Pcdh20, Cadps2, Marcks, Pde5a, Kctd12, Stk32c, Cpne2, Igf1, Fgf1, Cd63 PC_ 3 Positive: Cryab, Id2, Trf, Plp1, Gng11, Hapln2, Car14, Ermn, Mog, Gatm Apod, Mal, Tmem125, Mobp, Ugt8a, Elovl1, Car2, Aspa, Mag, Tmem63a Mbp, Cmtm5, Pdlim2, Sema3c, Cnp, Cldn11, Gsn, 2810468N07Rik, Csrp1, Enpp6 Negative: Grm1, Shisa6, Satb1, Elfn1, Kctd8, Trpc6, Slc24a2, Grin3a, Lphn2, Car10 Lmo4, Ephx4, Grik3, Cdh13, Kcnc2, Gria3, Lhx6, Tshz3, Vsnl1, Nppc Ppargc1a, Dpp10, Sst, Gria1, Runx1t1, Lypd6, Coch, Chst15, Timp3, Eya1 PC_ 4 Positive: Rgs16, Rgs10, Dlx6os1, Rgs8, Sparcl1, Cck, Pnoc, Ppp1r2, Dlx1os, Tsc22d1 Npy, Trp53i11, Nov, Ldhb, Frmd7, Dnajc15, Luzp2, Xist, Sp8, Mgll Car4, Ndufab1, Dhx32, Prss23, Frem1, Ociad2, Vip, Golm1, Htr1f, Gabrd Negative: Mag, Camk2n1, Dbndd2, Mog, Cmtm5, Mbp, Atp1a1, Elovl1, Mal, Apod Pou3f3, Gsn, Csrp1, Mobp, Hapln2, Cnp, Trf, Tmem88b, 2610017I09Rik, Ildr2 Car14, Tmem63a, Elovl7, Ugt8a, Ermn, Cd82, Cldn11, Pex5l, Gng12, Pcdh18 PC_ 5 Positive: Pthlh, Ptpre, Wnt5b, Caln1, Myl1, Grpr, Hpcal1, Pygm, Clstn2, Ano4 Ptprd, Sall1, Crispld2, Penk, Gpr176, Col24a1, Tiam1, Pde8b, Cadm2, Ppargc1a Pcdh10, Col26a1, Mybpc1, Btbd3, Vsnl1, Cbln2, Scgn, AI848285, Osbpl1a, Scn5a Negative: Neto1, Timp2, Pde1a, Gng2, Necab1, Cplx2, Ralyl, Gap43, Fxyd7, Reln Tnfaip8l3, Tmem91, Mmp17, Egln3, Ramp1, Zcchc12, Qpct, Serpina3n, Ptprm, Ildr2 Spock3, E130309F12Rik, Clu, Snca, Npas3, Col25a1, Rimkla, Fabp5, Celf6, Eps8 Mean of Mean NMI per Index: 1.0000 95 Percent CI of Mean NMI per Index: [1.0000, 1.0000] see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache Mean of Mean Correlation per Embedding: 0.9156 95 Percent CI of Mean Correlation per Embedding: [0.8880, 0.9321] Mean Correlation Range: Min = 0.8850 Max = 0.9324 see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts 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: Dner, Olfm1, Elmod1, Ogfrl1, Camk2b, Rph3a, D3Bwg0562e, Sema3c, Rgs7bp, Slc2a13 Nr2f1, Eef1a2, Syn2, Nfib, Shisa9, Nfix, Tspan5, Htr3a, Slc6a1, Spock1 Prkar2b, Chd3, Rab6a, Cpne7, Lrp12, Cxcl14, Atp2b2, Ptprm, Plcxd2, Cdk5r1 Negative: Rab3b, Zwint, Fth1, Ngfrap1, Sst, Gm6402, Lgals1, Rps15a-ps4, Rps20, 1500004A13Rik Gpx1, Crhbp, Gm15421, Plp1, Tmsb4x, OTTMUSG00000016609-loc3, Ptn, Csrp1, Prdx1, Schip1 Sepp1, Ndufab1, Cd9, mt-Tv, Gm14305, OTTMUSG00000016609-loc4, Fabp5, Cnp, Gm14436, Gatm PC_ 2 Positive: Mpped1, Lamp5, Adcy1, Bcl11a, Tsc22d1, Sema5a, Akap5, Itpr1, Hapln1, Tox3 Gabrd, Bcl11b, Nxph1, Crispld1, Rapgef4, Cap2, Grm5, Lin7a, Gda, Cpne8 Car4, Scube1, Gad2, Hlf, Caln1, Cacna2d1, Tnnt1, Enc1, Plk2, Rasl11a Negative: Npas1, Ddah1, Fxyd6, Gng4, Cplx2, Nrxn3, Rgs12, Trp53i11, Cnr1, Synpr Asic1, Vip, Npas3, Fstl5, Sncg, Wnt5a, Kazn, Enho, Galnt18, Htr3a Pcdh20, Cadps2, Marcks, Pde5a, Kctd12, Stk32c, Cpne2, Igf1, Fgf1, Cd63 PC_ 3 Positive: Cryab, Id2, Trf, Plp1, Gng11, Hapln2, Car14, Ermn, Mog, Gatm Apod, Mal, Tmem125, Mobp, Ugt8a, Elovl1, Car2, Aspa, Mag, Tmem63a Mbp, Cmtm5, Pdlim2, Sema3c, Cnp, Cldn11, Gsn, 2810468N07Rik, Csrp1, Enpp6 Negative: Grm1, Shisa6, Satb1, Elfn1, Kctd8, Trpc6, Slc24a2, Grin3a, Lphn2, Car10 Lmo4, Ephx4, Grik3, Cdh13, Kcnc2, Gria3, Lhx6, Tshz3, Vsnl1, Nppc Ppargc1a, Dpp10, Sst, Gria1, Runx1t1, Lypd6, Coch, Chst15, Timp3, Eya1 PC_ 4 Positive: Rgs16, Rgs10, Dlx6os1, Rgs8, Sparcl1, Cck, Pnoc, Ppp1r2, Dlx1os, Tsc22d1 Npy, Trp53i11, Nov, Ldhb, Frmd7, Dnajc15, Luzp2, Xist, Sp8, Mgll Car4, Ndufab1, Dhx32, Prss23, Frem1, Ociad2, Vip, Golm1, Htr1f, Gabrd Negative: Mag, Camk2n1, Dbndd2, Mog, Cmtm5, Mbp, Atp1a1, Elovl1, Mal, Apod Pou3f3, Gsn, Csrp1, Mobp, Hapln2, Cnp, Trf, Tmem88b, 2610017I09Rik, Ildr2 Car14, Tmem63a, Elovl7, Ugt8a, Ermn, Cd82, Cldn11, Pex5l, Gng12, Pcdh18 PC_ 5 Positive: Pthlh, Ptpre, Wnt5b, Caln1, Myl1, Grpr, Hpcal1, Pygm, Clstn2, Ano4 Ptprd, Sall1, Crispld2, Penk, Gpr176, Col24a1, Tiam1, Pde8b, Cadm2, Ppargc1a Pcdh10, Col26a1, Mybpc1, Btbd3, Vsnl1, Cbln2, Scgn, AI848285, Osbpl1a, Scn5a Negative: Neto1, Timp2, Pde1a, Gng2, Necab1, Cplx2, Ralyl, Gap43, Fxyd7, Reln Tnfaip8l3, Tmem91, Mmp17, Egln3, Ramp1, Zcchc12, Qpct, Serpina3n, Ptprm, Ildr2 Spock3, E130309F12Rik, Clu, Snca, Npas3, Col25a1, Rimkla, Fabp5, Celf6, Eps8 -----------------------Embedding Statistics----------------------------- Mean of Mean Correlation per Embedding: 0.8498 95 Percent CI of Mean Correlation per Embedding: [0.8042, 0.8736] Mean Correlation Range: Min = 0.8001 Max = 0.8740 ------------------------Cluster Statistics------------------------------ Mean of Mean NMI per Index: 1.0000 95 Percent CI of Mean NMI per Index: [1.0000, 1.0000] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 7 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 7 ] > > proc.time() user system elapsed 81.12 15.28 333.03