• 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 See the install log for details.
• 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 ... [6s] 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 ... [410s] ERROR   Running 'spelling.R' [0s]   Running 'testthat.R' [410s] 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 ─────────────   <FutureInterruptError/FutureError/error/FutureCondition/condition>   Error: Future ('future_lapply-1') of class MultisessionFuture interrupted, while running on 'localhost' (pid 51192)   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:33261)   2: In .Internal(gc(verbose, reset, full)) :     closing unused connection 14 (<-CRANWIN2.fb05.statistik.uni-dortmund.de:33261)   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 ... [17s] OK
• checking HTML version of manual ... [1s] OK
• DONE

Status: 1 ERROR