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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% | |======================================================================| 100% PC_ 1 Positive: Mdh1, Th, Rbp4, Zwint, Crhbp, Sst, Cort, Ndufa13, Gm14305, Ndufa5 Atp5f1, BC002163-loc2, OTTMUSG00000016609-loc4, Atp5j, Rab3b, Klhdc9, OTTMUSG00000016609-loc3, Sod1, Tac1, Ngfrap1 Cox4i1, Prmt2, Hspe1, Acadm, Gm15421, Acot7, Nxph2, Ndufa8, Ndufab1, Gabarapl2 Negative: Eef1a2, Dner, Slc6a1, Tspan7, Rab6b, 6430548M08Rik, Plcxd2, Klc1, Vdac1, Clip3 Nmnat2, Rph3a, Gad1, Dynll2, Pten, Lmo2, Prkar2b, Slc32a1, Rab3a, Ptprm Kif1a, Purb, Ogfrl1, Kcnc1, Pebp1, Gad2, Lrp12, Nr2f1, Stxbp1, Cntnap2 PC_ 2 Positive: Npas1, Nrxn3, Rgs12, Ddah1, Fxyd6, Cnr1, Npas3, Marcks, Asic1, Htr3a Synpr, Gng4, Gng2, Nap1l5, Qpct, Cxcl14, Wnt5a, Celf6, Igf1, Sncg Galnt14, Slc35f1, Egln3, Sorcs1, Btbd11, Nr2f2, Htr2c, Enho, Fgf12, Acot7 Negative: Sema5a, Nxph1, Tox3, Hapln1, Crispld1, Ndufa4, Alk, Gad2, Tnnt1, Npy Kcns3, Slc6a1, Frmpd4, Sv2c, Fgf9, Gad1, Fam46a, Slc35d3, Serpini1, Mpdz Ptprm, Mafb, Cadps, Lrp8, Ptchd4, Mctp1, Gabrb2, Asph, Sox1, Irs1 PC_ 3 Positive: Sema3c, Shisa9, Necab1, Jam2, Slc25a4, Cxcl14, Dner, Sub1, Tnfaip8l3, Ogfrl1 Tmem132e, Sumo1, Cnr1, Htr3a, Nrip3, Gpx4, Bex4, Deptor, Adarb2, 6030419C18Rik Nr2f2, Egln3, A830018L16Rik, Prkar2b, Sorcs1, Apbb1ip, Uqcrh, Ndufa11, Pdhb, Cox4i1 Negative: Lhx6, Elfn1, Cdh7, Trpc6, Sst, Kctd8, Rab3b, Cacna2d2, Nppc, Dynll2 Oprk1, Mkx, Sox6, Lypd6, Crhbp, Vamp1, Cdh13, Stac2, Mafb, Gnas Srcin1, Syngr1, Kcnmb2, Scn1a, Unc13c, Bfsp1, Akr1c18, Kcnc2, Zfp385a, Pappa PC_ 4 Positive: Wnt5b, Cbln2, Osbpl3, Grpr, Mybpc1, Cntn6, Col24a1, Pacsin2, Ap1s2, Penk Col26a1, Tac2, Myl1, Slc18a3, Glra2, Stac2, Scg2, Slc5a7, Magi1, Sorbs1 Cenpa, Scgn, Scn5a, Snurf, Rgs8, Gpr176, Kcnab3, Scn7a, Rgs16, Gjd2 Negative: Neto1, Uchl1, Reln, Celf4, Spock1, Tuba1a, Stmn2, Ndn, Gng2, Rimkla Syt1, Ptprm, Cpne5, Tubb2a, Hdgfrp3, Mfn2, 1500011B03Rik, AI504432, Necab1, Unc5d Tnfaip8l3, Zcchc12, Npas3, B230216G23Rik, Atp6v0d1, Qpct, Syngr3, Grip1, Ogfrl1, Gad2 PC_ 5 Positive: Phyhipl, Rgs10, Rasgrf2, Dlx6os1, Ppp1r2, Wnt5a, Sp8, Atp6v0d1, Clrn1, Rcan2 Rgs8, Rgs16, Arl4c, Mtss1, Scn1a, Ubash3b, Maf, Pebp1, Pnoc, BC002163-loc2 Cpne4, Sfxn1, Ube2e1, Ndufa13, Bag2, Gnas, Hspa8, Slc2a13, Stxbp1, Abat Negative: Pcdh18, Ptprt, Reln, Tmem91, 2310042E22Rik, Zmat4, Apbb1ip, Kcna6, Deptor, Tspan7 Spock3, Kcnc2, Sst, Frem2, Klhl13, Cdh13, Asic4, Sgk1, Chrna4, Grik1 Scg2, Rxfp1, A030009H04Rik, Ndnf, Tubb2a, Crhbp, Nr2e1, Rbp4, Rnf152, Fam19a2 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: 0.8988 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% | |======================================================================| 100% PC_ 1 Positive: Mdh1, Th, Rbp4, Zwint, Crhbp, Sst, Cort, Ndufa13, Gm14305, Ndufa5 Atp5f1, BC002163-loc2, OTTMUSG00000016609-loc4, Atp5j, Rab3b, Klhdc9, OTTMUSG00000016609-loc3, Sod1, Tac1, Ngfrap1 Cox4i1, Prmt2, Hspe1, Acadm, Gm15421, Acot7, Nxph2, Ndufa8, Ndufab1, Gabarapl2 Negative: Eef1a2, Dner, Slc6a1, Tspan7, Rab6b, 6430548M08Rik, Plcxd2, Klc1, Vdac1, Clip3 Nmnat2, Rph3a, Gad1, Dynll2, Pten, Lmo2, Prkar2b, Slc32a1, Rab3a, Ptprm Kif1a, Purb, Ogfrl1, Kcnc1, Pebp1, Gad2, Lrp12, Nr2f1, Stxbp1, Cntnap2 PC_ 2 Positive: Npas1, Nrxn3, Rgs12, Ddah1, Fxyd6, Cnr1, Npas3, Marcks, Asic1, Htr3a Synpr, Gng4, Gng2, Nap1l5, Qpct, Cxcl14, Wnt5a, Celf6, Igf1, Sncg Galnt14, Slc35f1, Egln3, Sorcs1, Btbd11, Nr2f2, Htr2c, Enho, Fgf12, Acot7 Negative: Sema5a, Nxph1, Tox3, Hapln1, Crispld1, Ndufa4, Alk, Gad2, Tnnt1, Npy Kcns3, Slc6a1, Frmpd4, Sv2c, Fgf9, Gad1, Fam46a, Slc35d3, Serpini1, Mpdz Ptprm, Mafb, Cadps, Lrp8, Ptchd4, Mctp1, Gabrb2, Asph, Sox1, Irs1 PC_ 3 Positive: Sema3c, Shisa9, Necab1, Jam2, Slc25a4, Cxcl14, Dner, Sub1, Tnfaip8l3, Ogfrl1 Tmem132e, Sumo1, Cnr1, Htr3a, Nrip3, Gpx4, Bex4, Deptor, Adarb2, 6030419C18Rik Nr2f2, Egln3, A830018L16Rik, Prkar2b, Sorcs1, Apbb1ip, Uqcrh, Ndufa11, Pdhb, Cox4i1 Negative: Lhx6, Elfn1, Cdh7, Trpc6, Sst, Kctd8, Rab3b, Cacna2d2, Nppc, Dynll2 Oprk1, Mkx, Sox6, Lypd6, Crhbp, Vamp1, Cdh13, Stac2, Mafb, Gnas Srcin1, Syngr1, Kcnmb2, Scn1a, Unc13c, Bfsp1, Akr1c18, Kcnc2, Zfp385a, Pappa PC_ 4 Positive: Wnt5b, Cbln2, Osbpl3, Grpr, Mybpc1, Cntn6, Col24a1, Pacsin2, Ap1s2, Penk Col26a1, Tac2, Myl1, Slc18a3, Glra2, Stac2, Scg2, Slc5a7, Magi1, Sorbs1 Cenpa, Scgn, Scn5a, Snurf, Rgs8, Gpr176, Kcnab3, Scn7a, Rgs16, Gjd2 Negative: Neto1, Uchl1, Reln, Celf4, Spock1, Tuba1a, Stmn2, Ndn, Gng2, Rimkla Syt1, Ptprm, Cpne5, Tubb2a, Hdgfrp3, Mfn2, 1500011B03Rik, AI504432, Necab1, Unc5d Tnfaip8l3, Zcchc12, Npas3, B230216G23Rik, Atp6v0d1, Qpct, Syngr3, Grip1, Ogfrl1, Gad2 PC_ 5 Positive: Phyhipl, Rgs10, Rasgrf2, Dlx6os1, Ppp1r2, Wnt5a, Sp8, Atp6v0d1, Clrn1, Rcan2 Rgs8, Rgs16, Arl4c, Mtss1, Scn1a, Ubash3b, Maf, Pebp1, Pnoc, BC002163-loc2 Cpne4, Sfxn1, Ube2e1, Ndufa13, Bag2, Gnas, Hspa8, Slc2a13, Stxbp1, Abat Negative: Pcdh18, Ptprt, Reln, Tmem91, 2310042E22Rik, Zmat4, Apbb1ip, Kcna6, Deptor, Tspan7 Spock3, Kcnc2, Sst, Frem2, Klhl13, Cdh13, Asic4, Sgk1, Chrna4, Grik1 Scg2, Rxfp1, A030009H04Rik, Ndnf, Tubb2a, Crhbp, Nr2e1, Rbp4, Rnf152, Fam19a2 Finished creating embeddings -----------------------Embedding Statistics----------------------------- Mean of Mean Correlation per Embedding: 0.7041 95 Percent CI of Mean Correlation per Embedding: [0.5940, 0.7488] Mean Correlation Range: Min = 0.5850 Max = 0.7489 ------------------------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 4 | SKIP 0 | PASS 7 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 7 ] > > proc.time() user system elapsed 214.10 9.07 359.53