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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, Atp2a2, Rgs7bp, Ogfrl1, Elmod1, Camk2b, Nfib, Nfix, Eef1a2 Slc6a1, Plcxd2, Atp2b2, Bcl11b, Lrp12, D3Bwg0562e, Rab6a, Gabrb2, Rph3a, Nr2f1 Chd3, Celf2, Ptprm, Tspan5, Slc2a13, Tspan7, Kit, Nt5dc3, Mef2c, Gnao1 Negative: Zwint, Ngfrap1, Fth1, Gm6402, Rps15a-ps4, Rab3b, Ndufab1, OTTMUSG00000016609-loc3, 1500004A13Rik, Tmsb4x Gm14305, OTTMUSG00000016609-loc4, Fabp5, Trappc2, Ndfip1, Zfp931, Glrx, Gm14436, Plp1, Gpx4 Sst, Csrp1, Lgals1, Schip1, Cd81, Cnp, Car2, Sepp1, Ptn, Cd9 PC_ 2 Positive: Cnr1, Trp53i11, Cplx2, Cadps2, Npas1, Gng2, Nrxn3, Cck, Sncg, Adarb2 Eps8, Kctd12, Fxyd6, Necab1, Rgs12, Igf1, Syt6, Gng4, Celf6, Col25a1 Pde5a, Necab2, Wnt5a, Fstl5, Lix1, Npas3, Stk32c, Cntnap2, Dlx6os1, Ddah1 Negative: Adcy1, Mpped1, Bcl11a, Akap5, Nxph1, Cacna1a, Prkacb, Lamp5, Gda, Ncald Rgs17, Gabrd, Mafb, Tox3, Grm5, Rbfox1, Sema5a, Hapln1, Cyp46a1, Sst Cap2, Grin3a, Tspan7, Gria3, Celf2, Srgap3, Car4, Fam46a, Bcl11b, Rapgef4 PC_ 3 Positive: Grm1, Shisa6, Kctd8, Satb1, Trpc6, Elfn1, Kcnc2, Cdh13, Gria1, Lphn2 Grin3a, Gria3, Ephx4, Lmo4, Runx1t1, Vsnl1, Coch, Sst, Car10, Nppc Cbln4, Grik3, Cdh8, Slc24a2, Cacna2d2, Ntm, Lhx6, Rab3b, Dgkg, Eya1 Negative: Cryab, Trf, Mal, Plp1, Car14, Mog, Apod, Ugt8a, Mobp, Hapln2 Cmtm5, Ermn, Elovl1, Tmem63a, Tmem125, Gsn, Cldn11, Gatm, Gng11, Mbp Aspa, Cnp, Mag, Pdlim2, Id2, Elovl7, Phgdh, Enpp6, Gjc3, Csrp1 PC_ 4 Positive: Elfn1, Camk2n1, Cadm2, Satb1, Asic1, Lgi3, Chrna4, Htra1, Aldoc, Timp2 Vgf, Marcks, Grpr, Glra2, Penk, Cacna1h, Cacna2d3, Igsf3, Crh, Tmem229b 2610017I09Rik, Adra1b, Ppargc1a, Asic4, Ptpn5, Ano4, Gpd1, Lynx1, Pthlh, Ndrg2 Negative: Tsc22d1, Id2, Cpne8, Lamp5, Tgfb2, Ldha, Ndst3, Vwa5a, Itpr1, Sema5a Crispld1, Gabra5, Rgs10, Gm14305, Wif1, Mpped1, Cpne6, Gpr158, Plch2, Enc1 Ddn, 9930013L23Rik, Pls3, Cacna2d1, Ociad2, Dkk3, Wls, Scube1, Slc35d3, Sv2c PC_ 5 Positive: Baiap2, Neurod2, Fam19a1, Atp2b1, Itpka, Pde1a, Ppp3ca, Rgs14, Prkcb, Neurod6 Lpl, Rprml, Crym, Nrgn, Sv2b, 2010300C02Rik, Ildr2, Crim1, Cpne6, Camk2a 6330403A02Rik, Fam131a, Miat, Slc17a7, Hpca, Klk8, Ptk2b, Nrn1, Lingo1, Ddn Negative: Sparcl1, Rgs8, Mgll, Rgs16, Ankrd29, Rgs10, Cox6a2, Kcnc1, Gabrd, Ptpre Npy, Ppargc1a, Ncald, Pthlh, Fryl, Slc24a2, mt-Ty, Dlx1os, Abat, Pacsin2 Slc2a13, Pygm, Ptprd, Gpr176, Maf, Rab6a, Wnt5b, Kcng4, Pid1, Osbpl3 Mean of Mean NMI per Index: 0.9863 95 Percent CI of Mean NMI per Index: [0.9772, 0.9902] 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: 0.8988 95 Percent CI of Mean Correlation per Embedding: [0.8752, 0.9140] Mean Correlation Range: Min = 0.8730 Max = 0.9145 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, Atp2a2, Rgs7bp, Ogfrl1, Elmod1, Camk2b, Nfib, Nfix, Eef1a2 Slc6a1, Plcxd2, Atp2b2, Bcl11b, Lrp12, D3Bwg0562e, Rab6a, Gabrb2, Rph3a, Nr2f1 Chd3, Celf2, Ptprm, Tspan5, Slc2a13, Tspan7, Kit, Nt5dc3, Mef2c, Gnao1 Negative: Zwint, Ngfrap1, Fth1, Gm6402, Rps15a-ps4, Rab3b, Ndufab1, OTTMUSG00000016609-loc3, 1500004A13Rik, Tmsb4x Gm14305, OTTMUSG00000016609-loc4, Fabp5, Trappc2, Ndfip1, Zfp931, Glrx, Gm14436, Plp1, Gpx4 Sst, Csrp1, Lgals1, Schip1, Cd81, Cnp, Car2, Sepp1, Ptn, Cd9 PC_ 2 Positive: Cnr1, Trp53i11, Cplx2, Cadps2, Npas1, Gng2, Nrxn3, Cck, Sncg, Adarb2 Eps8, Kctd12, Fxyd6, Necab1, Rgs12, Igf1, Syt6, Gng4, Celf6, Col25a1 Pde5a, Necab2, Wnt5a, Fstl5, Lix1, Npas3, Stk32c, Cntnap2, Dlx6os1, Ddah1 Negative: Adcy1, Mpped1, Bcl11a, Akap5, Nxph1, Cacna1a, Prkacb, Lamp5, Gda, Ncald Rgs17, Gabrd, Mafb, Tox3, Grm5, Rbfox1, Sema5a, Hapln1, Cyp46a1, Sst Cap2, Grin3a, Tspan7, Gria3, Celf2, Srgap3, Car4, Fam46a, Bcl11b, Rapgef4 PC_ 3 Positive: Grm1, Shisa6, Kctd8, Satb1, Trpc6, Elfn1, Kcnc2, Cdh13, Gria1, Lphn2 Grin3a, Gria3, Ephx4, Lmo4, Runx1t1, Vsnl1, Coch, Sst, Car10, Nppc Cbln4, Grik3, Cdh8, Slc24a2, Cacna2d2, Ntm, Lhx6, Rab3b, Dgkg, Eya1 Negative: Cryab, Trf, Mal, Plp1, Car14, Mog, Apod, Ugt8a, Mobp, Hapln2 Cmtm5, Ermn, Elovl1, Tmem63a, Tmem125, Gsn, Cldn11, Gatm, Gng11, Mbp Aspa, Cnp, Mag, Pdlim2, Id2, Elovl7, Phgdh, Enpp6, Gjc3, Csrp1 PC_ 4 Positive: Elfn1, Camk2n1, Cadm2, Satb1, Asic1, Lgi3, Chrna4, Htra1, Aldoc, Timp2 Vgf, Marcks, Grpr, Glra2, Penk, Cacna1h, Cacna2d3, Igsf3, Crh, Tmem229b 2610017I09Rik, Adra1b, Ppargc1a, Asic4, Ptpn5, Ano4, Gpd1, Lynx1, Pthlh, Ndrg2 Negative: Tsc22d1, Id2, Cpne8, Lamp5, Tgfb2, Ldha, Ndst3, Vwa5a, Itpr1, Sema5a Crispld1, Gabra5, Rgs10, Gm14305, Wif1, Mpped1, Cpne6, Gpr158, Plch2, Enc1 Ddn, 9930013L23Rik, Pls3, Cacna2d1, Ociad2, Dkk3, Wls, Scube1, Slc35d3, Sv2c PC_ 5 Positive: Baiap2, Neurod2, Fam19a1, Atp2b1, Itpka, Pde1a, Ppp3ca, Rgs14, Prkcb, Neurod6 Lpl, Rprml, Crym, Nrgn, Sv2b, 2010300C02Rik, Ildr2, Crim1, Cpne6, Camk2a 6330403A02Rik, Fam131a, Miat, Slc17a7, Hpca, Klk8, Ptk2b, Nrn1, Lingo1, Ddn Negative: Sparcl1, Rgs8, Mgll, Rgs16, Ankrd29, Rgs10, Cox6a2, Kcnc1, Gabrd, Ptpre Npy, Ppargc1a, Ncald, Pthlh, Fryl, Slc24a2, mt-Ty, Dlx1os, Abat, Pacsin2 Slc2a13, Pygm, Ptprd, Gpr176, Maf, Rab6a, Wnt5b, Kcng4, Pid1, Osbpl3 Finished creating embeddings -----------------------Embedding Statistics----------------------------- Mean of Mean Correlation per Embedding: 0.8251 95 Percent CI of Mean Correlation per Embedding: [0.7675, 0.8533] Mean Correlation Range: Min = 0.7562 Max = 0.8545 ------------------------Cluster Statistics------------------------------ Mean of Mean NMI per Index: 0.9863 95 Percent CI of Mean NMI per Index: [0.9772, 0.9902] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 7 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 7 ] > > proc.time() user system elapsed 84.28 16.32 371.06