* using log directory 'd:/Rcompile/CRANpkg/local/4.4/scStability.Rcheck' * using R version 4.4.3 (2025-02-28 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'scStability/DESCRIPTION' ... OK * this is package 'scStability' version '1.0.3' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'scStability' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [2s] OK * checking loading without being on the library search path ... [2s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [7s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... NONE * checking for unstated dependencies in 'tests' ... OK * checking tests ... [415s] ERROR Running 'spelling.R' [0s] Running 'testthat.R' [414s] Running the tests in 'tests/testthat.R' failed. Complete output: > # 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: 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 Negative: 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 Saving _problems/test-clustStable-14.R 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: 0.8930 95 Percent CI of Mean Correlation per Embedding: [0.8712, 0.9105] Mean Correlation Range: Min = 0.8693 Max = 0.9111 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: 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 Negative: 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 -----------------------Embedding Statistics----------------------------- Mean of Mean Correlation per Embedding: 0.8747 95 Percent CI of Mean Correlation per Embedding: [0.8616, 0.8837] Mean Correlation Range: Min = 0.8605 Max = 0.8838 ------------------------Cluster Statistics------------------------------ Mean of Mean NMI per Index: 1.0000 95 Percent CI of Mean NMI per Index: [1.0000, 1.0000] [ FAIL 1 | WARN 5 | SKIP 0 | PASS 5 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-clustStable.R:14:3'): Clusters were made correctly ───────────── Error: Future ('future_lapply-1') of class MultisessionFuture interrupted, while running on 'localhost' (pid 56400) Backtrace: ▆ 1. └─scStability::clustStable(n_runs = 10, seurat_obj, n_cores = 8) at test-clustStable.R:14:3 2. └─future.apply::future_lapply(...) 3. └─future.apply:::future_xapply(...) 4. └─base::tryCatch(...) 5. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 6. └─base (local) tryCatchOne(...) 7. └─value[[3L]](cond) 8. └─future.apply:::onError(e, futures = fs, debug = debug) [ FAIL 1 | WARN 5 | SKIP 0 | PASS 5 ] Error: ! Test failures. Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 4 (<-CRANWIN2.fb05.statistik.uni-dortmund.de:33664) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 14 (<-CRANWIN2.fb05.statistik.uni-dortmund.de:33664) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [185s] OK * checking PDF version of manual ... [16s] OK * checking HTML version of manual ... [1s] OK * DONE Status: 1 ERROR