• using R version 4.5.0 beta (2025-03-27 r88067 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 14.2.0     GNU Fortran (GCC) 14.2.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• checking for file 'rliger/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'rliger' version '2.1.0'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: 'DoubletFinder'
• 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 'rliger' can be installed ... OK See the install log for details.
• used C++ compiler: 'g++.exe (GCC) 14.2.0'
• 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 ... [3s] OK
• checking whether the package can be loaded with stated dependencies ... [3s] OK
• checking whether the package can be unloaded cleanly ... [3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s] OK
• checking loading without being on the library search path ... [3s] OK
• checking whether startup messages can be suppressed ... [3s] 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 ... [28s] OK
• checking Rd files ... [3s] 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 contents of 'data' directory ... OK
• checking data for non-ASCII characters ... [3s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compiled code ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [77s] ERROR Running examples in 'rliger-Ex.R' failed The error most likely occurred in: > ### Name: optimizeNewLambda > ### Title: Perform factorization for new lambda value > ### Aliases: optimizeNewLambda > > ### ** Examples > > pbmc <- normalize(pbmc) ℹ Normalizing datasets "ctrl" ℹ Normalizing datasets "stim" ✔ Normalizing datasets "stim" ... done ℹ Normalizing datasets "ctrl" ✔ Normalizing datasets "ctrl" ... done > pbmc <- selectGenes(pbmc) ℹ Selecting variable features for dataset "ctrl" ✔ ... 168 features selected out of 249 shared features. ℹ Selecting variable features for dataset "stim" ✔ ... 166 features selected out of 249 shared features. ✔ Finally 173 shared variable features are selected. > pbmc <- scaleNotCenter(pbmc) ℹ Scaling dataset "ctrl" ✔ Scaling dataset "ctrl" ... done ℹ Scaling dataset "stim" ✔ Scaling dataset "stim" ... done > if (requireNamespace("RcppPlanc", quietly = TRUE)) { + # Only running a few iterations for fast examples + pbmc <- runINMF(pbmc, k = 20, nIteration = 2) + pbmc <- optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2) + } INMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 43773 Error: Must provide 2 V matrices Execution halted
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [12m] ERROR   Running 'testthat.R' [12m] Running the tests in 'tests/testthat.R' failed. Complete output:   > library(testthat)   > library(rliger)   Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.      We recommand you backup your old analysis before overwriting any existing result.      `readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.   >   > test_check("rliger")   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 37129   **|   Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck      Reading input file...      Number of nodes: 600   Number of edges: 16900      Running Louvain algorithm...   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|      Modularity: 0.7596   Number of communities: 9   Elapsed time: 0 seconds   Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck      Reading input file...      Number of nodes: 600   Number of edges: 16701      Running Louvain algorithm...   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|      Modularity: 0.7658   Number of communities: 10   Elapsed time: 0 seconds   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 37129   **|   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 37129   **|   Dataset 1:    NPM1, SAT1, VIM, FTH1, BTG1, ISG15, GBP1, RSAD2, HSP90AB1   Shared:    NMB, ANXA1, GPR183, NDUFC2, GAPDH, VIM, EIF1, SRGN, JUNB, S100A10, TMSB4X, PABPC1, H3F3B, SAT1, HIST1H2AC, RGCC, ANXA2, RPLP1, LYZ, RPL18, HLA-A, RPS15A, TMEM66, RSAD2, UBC, HSPA8, MALAT1, RPLP0, RPS6, RPS12   Dataset 2    RSAD2, VIM, ISG15, GBP1, HSP90AB1, SAT1, NPM1, FTH1, BTG1   Dataset 1:    CD83, VIM, CXCR4, MARCKSL1, GAPDH, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, SOD2, SAT1, IFI27, CCL2, CCL8, CCL3, CCL4, APOBEC3A, TYMP   Shared:    RPL23A, RPS2, CD79A, RPL18A, RPL12, RPL13A, RPL3, RPL27A, RPS23, RPL15, RPLP0, RPL10, RPL19, RPS8, RPS4X, RPS5, RPL10A, RPL11, RPS19, RPL18, RPS3A, RPL34, RPS18, PTMA, RPL7, RPS6, RPS27, RPLP1, RPL32, RPL14   Dataset 2    PLAC8, GBP1, IFI27, TYMP, ISG15, SELL, RSAD2, CXCL10, SOD2, SAT1, CCL2, CCL8, CCL3, CCL4, APOBEC3A, MARCKSL1, CXCR4, CD83, VIM, GAPDH, FTL   Dataset 1:    FCGR3A, LGALS1, RPLP0, RPL18, RPS12, RPS3A, RPL23A, S100A4, ACTB, RPL7, ISG15, GBP1, RSAD2, SAT1, CCNH   Shared:    CST7, CHRNB1, NKG7, APOBEC3G, CLIC3, CXCR4, GNLY, HLA-A, CD7, HLA-C, GZMB, SRGN, BAK1, TMSB4X, NDUFC2, HLA-B, B2M, BTG1, JTB, CCNH, FOXN3, H2AFZ, UBC, CREM, MALAT1, PTMA, ANXA1, H3F3B, VIM, RABL5   Dataset 2    CCNH, ISG15, RSAD2, SAT1, GBP1, S100A4, FCGR3A, RPS3A, RPS12, ACTB, RPL7, RPLP0, RPL23A, RPL18, LGALS1   Dataset 1:    CXCL10, GBP1, PTMA, S100A10, CD14, LGALS1, TIMP1, FAM26F, RPS3A, RPL10A, RPL3, S100A6, H2AFZ, CCL3, S100A8, GPX1, IL8, HLA-DQA1, LGALS3, ISG15, RSAD2, CD83, HSPA1A, GIMAP7, IDO1, TXN, MS4A7, IFI27, CCL2, CCL8   Shared:    FCGR3A, MS4A7, VMO1, FAM26F, GBP1, CXCL10, TYROBP, PLAC8, FCER1G, TIMP1, S100A11, FTH1, SAT1, SOD2, JUNB, TMSB4X, TYMP, HLA-C, SRGN, HLA-B, B2M, ACTB, HLA-DPA1, CST3, RPS19, APOBEC3A, MALAT1, TMEM66, S100A4, H3F3B   Dataset 2    ISG15, IFI27, MS4A7, APOBEC3A, HSPA1A, GIMAP7, CD83, RSAD2, GBP1, CXCL10, FAM26F, IDO1, TXN, CCL2, CCL8, CCL3, S100A10, S100A8, S100A6, PTMA, GPX1, IL8, H2AFZ, RPS3A, CD14, HLA-DQA1, RPL10A, TIMP1, LGALS3, LGALS1   Dataset 1:    RPL10A, H2AFZ, GAPDH, PABPC1, ISG15, GBP1, CXCL10, CD83, SAT1, EIF1, HERC6   Shared:    MIR155HG, MYC, ID3, CD83, NPM1, HLA-DQA1, HSP90AB1, CCR7, CCL3, HLA-DRB1, HSPA8, EIF1, HLA-DRA, RPLP0, RPS5, CCL4, JTB, RPL14, RPS23, RPL19, RPL10A, RPL7, RPS12, RPL18A, RPS2, PTMA, CD74, RPL23A, RPS8, RPLP1   Dataset 2    GBP1, EIF1, CD83, CXCL10, HERC6, ISG15, SAT1, H2AFZ, RPL10A, PABPC1, GAPDH   Dataset 1:    RPS8, RPS23, RPL15, RPL21, RPL7, RPL13A, MARCKSL1, RPS3A, TIMP1, RPS6, RPS3, ISG15, GBP1, RSAD2, CXCL10, HSPA1A, FAM26F, HSPB1, IDO1, CREM, CCL8, APOBEC3A, APOBEC3G, TYMP, THRAP3   Shared:    CXCL3, SERPINB2, IL8, CCL7, CCL2, CTSL, CTSB, RABL5, ANXA5, CD63, SOD2, FCER1G, FTL, CSTB, CD14, ANXA2, CCL3, FTH1, VIM, NFKBIA, LGALS1, GAPDH, ANXA1, SRGN, LGALS3, S100A6, S100A9, H3F3B, TYMP, TIMP1   Dataset 2    CCL8, THRAP3, HSPA1A, TYMP, HSPB1, CREM, APOBEC3G, ISG15, GBP1, RSAD2, CXCL10, FAM26F, IDO1, APOBEC3A, MARCKSL1, RPS8, RPL15, RPS3A, RPS23, TIMP1, RPL7, RPS6, RPS3, RPL21, RPL13A   Dataset 1:    RSAD2, ISG15, APOBEC3A, CD14, GPX1, GAPDH, MARCKSL1, RPL10, JTB, RPS3A, RPL21, RPS5, SAT1, RPS27A, RPL3, RPS8, RPL32, RPL7, RPS12, RPL15, PABPC1, RPL11, RPLP0, RPL10A, IL8, RPL19, S100A8, S100A6, DUSP2, CXCR4   Shared:    RSAD2, ISG15, APOBEC3A, CCL8, CXCL10, CCL2, CTSB, IDO1, SOD2, ANXA5, TYMP, FTL, CD63, HSPA1A, GBP1, CSTB, CTSL, IFI27, C15orf48, FAM26F, CCL7, FCER1G, LGALS3, LGALS1, FTH1, S100A11, TYROBP, ANXA2, HSPB1, TIMP1   Dataset 2    IDO1, HSPA1A, CCL4, CCL7, NFKBIA, CCL3, CXCL10, FAM26F, IFI27, RPS19, HERC6, ISG15, RSAD2, HSPB1, SAT1, CCL2, CCL8, APOBEC3A, RPL11, MARCKSL1, RPS8, S100A8, S100A6, RPS27A, DUSP2, CXCR4, PTMA, RPL32, RPL15, RPL14   Dataset 1:    BIRC3, S100A6, FTH1, CCL8, ID3, HLA-DPB1, GAPDH, CD79A, FTL, ISG15, GBP1, SELL, RSAD2, CXCL10, PLAC8, HSP90AB1, GIMAP7, SAT1, CREM, HSPA8, IFI27, CCL2, CCR7, H3F3B, APOBEC3A, TYMP, HERC6   Shared:    TMEM66, RPL13, RPL31, LTB, RPS18, RPL34, RPL32, RPS14, SELL, RPL21, RPS6, RPS15A, RPS27A, RPS12, RPL7, RPL3, RPS4X, RPS3, RPS3A, RPL9, RPL10, RPL11, RPL13A, RPS19, RPL10A, PABPC1, RPS23, RPS8, RPL27A, RPS2   Dataset 2    GIMAP7, PLAC8, CCR7, IFI27, H3F3B, SELL, GBP1, ISG15, RSAD2, CXCL10, HSP90AB1, SAT1, CREM, HSPA8, CCL2, CCL8, APOBEC3A, TYMP, HERC6, ID3, S100A6, HLA-DPB1, FTH1, BIRC3, GAPDH, CD79A, FTL   Dataset 1:    TEX264, FTH1, VIM, CCNH, UBC, RGCC, ISG15, GBP1, RSAD2, CXCL10, PLAC8, CD74, SAT1, CD79A   Shared:    GIMAP7, RGCC, ACAT2, BTG1, THRAP3, RELB, LTB, H2AFZ, EIF2AK1, CXCR4, HERC6, BIRC3, SELL, HSPA8, GPR183, CCR7, BAK1, HIST1H2AC, CHCHD10, EIF1, HSPB1, RPS27, JTB, MALAT1, H3F3B, PTMA, TMEM66, HSP90AB1, ANXA1, HLA-B   Dataset 2    GBP1, RSAD2, RGCC, UBC, ISG15, CXCL10, PLAC8, CD74, SAT1, CD79A, TEX264, VIM, FTH1, CCNH   Dataset 1:    CD14, S100A8, IFI27, RPL31, RPL27A, RPL21, RPL7, GBP1, MARCKSL1, RPS8, S100A6, S100A4, RPS27A, IL1B, PTMA, RPL15, RPL14, GPX1, IL8, CXCL3, H2AFZ, RPL34, RPS3A, RPS23, RPL10A, RPS4X, RPS6, RPS3, GAPDH, RGCC   Shared:    MARCKSL1, TIMP1, C15orf48, SOD2, FTH1, CD63, ANXA5, CSTB, SRGN, GAPDH, FTL, TYROBP, FCER1G, S100A11, EIF1, IL8, LGALS1, TYMP, B2M, LGALS3, ANXA2, CTSB, VIM, TXN, S100A10, ACTB, CCL2, NFKBIA, LYZ, HLA-B   Dataset 2    TXN, CST3, IDO1, APOBEC3A, MARCKSL1, PLAC8, S100A6, S100A4, HERC6, RPL19, RPS3, ISG15, GBP1, SELL, RSAD2, CXCL10, HIST1H2AC, HLA-C, HSPA1A, FAM26F, HSPB1, SAT1, CTSL, BIRC3, IFI27, CCL2, CCL7, CCL8, CCR7, APOBEC3B   Dataset 1:    IDO1, CST7, VMO1, IL8, SAT1, RPS5, TYMP, LAGE3, CXCR4, TIMP1, RGCC, RPL3, ISG15, GBP1, S100A4, SELL, RSAD2, CXCL10, HSPA1A, HSP90AB1, FAM26F, HSPB1, CTSB, ANXA1, HSPA8, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B   Shared:    HLA-DPA1, HLA-DPB1, HLA-DRA, CD74, HLA-DRB1, TXN, HLA-DQA1, IDO1, CST3, CCR7, CD83, ANXA2, GPR183, MARCKSL1, ACTB, BIRC3, LYZ, CST7, TMSB4X, C15orf48, S100A10, LGALS1, B2M, GPX1, CD79A, NFKBIA, H2AFZ, RELB, ISG15, HSPA1A   Dataset 2    CXCL10, HSPA1A, ISG15, FAM26F, HSPB1, HERC6, GBP1, S100A4, APOBEC3G, RSAD2, HSP90AB1, HSPA8, SELL, SAT1, CTSB, IDO1, ANXA1, IFI27, CCL2, H3F3B, APOBEC3A, APOBEC3B, TYMP, CXCR4, IL8, TIMP1, RGCC, VMO1, CST7, RPS5   Dataset 1:    H3F3B, BIRC3, ISG15, HLA-C   Shared:    DUSP2, JUNB, GADD45B, HIST1H2AC, MYC, NFKBIA, BIRC3, BTG1, GZMK, CD83, PABPC1, APOBEC3G, TMEM66, H3F3B, EIF1, PTMA, UBC, HLA-C, NDUFC2, RPS19, GPR183, MALAT1, RPS5, RPL18, HLA-A, RPL19, RPS27, SRGN, RPL3, RPL27A   Dataset 2    HLA-C, ISG15, BIRC3, H3F3B   Dataset 1:    GAPDH, RPL12, FTL, ISG15, FCER1G, RSAD2, TYMP   Shared:    GZMH, FGFBP2, CCL5, CLIC3, NKG7, GZMB, CST7, GZMK, HLA-B, APOBEC3G, B2M, HLA-C, PTMA, TMSB4X, NDUFC2, RGCC, ANXA1, HLA-A, GAPDH, ACTN1, PLAC8, RPS19, MALAT1, RPL15, JTB, KLRD1, RPS3, TMEM66, RPS15A, RPL3   Dataset 2    TYMP, FCER1G, ISG15, RSAD2, RPL12, GAPDH, FTL   Dataset 1:    CCL2, H2AFZ, CD14, CTSL, RPL10A, RPS8, RPS6, TIMP1, S100A8, RPS27, RPLP0, RPL21, RPL14, RPL34, RPL7, RPL18A, ID3, RPL11, MARCKSL1, RPL31, IL1B, RPL15, RPL9, IL8, RPS3A, RPS14, NPM1, RPS4X, RPL10, PABPC1   Shared:    S100A4, LGALS3, CTSL, S100A6, GPX1, S100A11, FTL, S100A10, LGALS1, CTSB, CST3, FCER1G, ACTB, VIM, ANXA2, CD63, TYMP, TYROBP, CSTB, HLA-DRB1, CCL2, FCGR3A, ANXA1, ANXA5, SAT1, ACTN1, JTB, HLA-DRA, HLA-DPB1, H3F3B   Dataset 2    HSPB1, FAM26F, LYZ, HSPA1A, RPS14, RPL9, HIST1H2AC, HLA-A, APOBEC3A, ISG15, GBP1, RSAD2, CXCL10, HLA-C, HSP90AB1, SAT1, IDO1, CTSL, TXN, CREM, CCL2, CCL7, CCL8, APOBEC3B, APOBEC3G, TYMP, HERC6, ID3, RPL11, MARCKSL1   Dataset 1:    HSPA1A, H3F3B, CXCR4, FTL, ISG15, GBP1, RSAD2, RPL34, HLA-A, HLA-C, HLA-B, RPLP1, RPS2   Shared:    UBC, HSPA1A, GADD45G, GADD45B, HSP90AB1, HSPA8, HSPB1, H3F3B, PPBP, CREM, SAT1, BIRC3, CCNH, EIF1, NFKBIA, H2AFZ, JUNB, ID3, TMEM66, BTG1, MALAT1, RPS27, HIST1H2AC, NPM1, GBP1, CXCR4, RPS12, RPL14, RELB, CXCL10   Dataset 2    GBP1, RPLP1, HLA-C, RSAD2, HLA-B, ISG15, RPL34, HLA-A, RPS2, CXCR4, HSPA1A, H3F3B, FTL   Dataset 1:    CXCL3, IL8, FTH1, RPL9, GBP1, MARCKSL1, IL1B, H2AFZ, CD14, ISG15, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, IDO1, CCL8, CST3, APOBEC3A, APOBEC3G   Shared:    IL1B, LYZ, IL8, CST3, NFKBIA, CCL3, S100A10, APOBEC3B, GPX1, ACTB, C15orf48, ANXA2, S100A6, S100A4, HLA-DPB1, CCL4, CXCL3, HLA-DRA, HLA-DRB1, S100A11, TYROBP, IFI27, JTB, HLA-DPA1, VIM, FCER1G, CD74, SRGN, ANXA1, HBA1   Dataset 2    FAM26F, CXCL10, CST3, HSPA1A, IL1B, SAT1, IDO1, ISG15, GBP1, RSAD2, HIST1H2AC, HSPB1, CCL8, APOBEC3A, APOBEC3G, MARCKSL1, RPL9, IL8, CXCL3, H2AFZ, CD14, FTH1   Dataset 1:    APOBEC3B, IL8, S100A4, MARCKSL1, RPS27A, RPL15, RPL7, RPL12, S100A9, PABPC1, S100A8, IL1B, TIMP1, RPS6, BTG1, RPLP0, RGCC, RPL13A, RPL3, ISG15, GBP1, RSAD2, CXCL10, HIST1H2AC, HSPA1A, FAM26F, HSPB1, SAT1, CTSB, IDO1   Shared:    S100A8, S100A9, CD14, GPX1, APOBEC3B, S100A6, TYROBP, LGALS1, S100A4, TYMP, S100A10, IL8, MS4A7, S100A11, FTL, NFKBIA, FTH1, MARCKSL1, APOBEC3A, FCER1G, LYZ, SRGN, SAT1, GAPDH, C15orf48, ANXA5, ACTB, CTSB, ISG15, CD63   Dataset 2    CCL2, HIST1H2AC, S100A8, IDO1, CCL8, CCL7, FAM26F, CTSB, CST3, HSPA1A, APOBEC3G, HSPB1, ISG15, GBP1, RSAD2, CXCL10, SAT1, CTSL, TXN, LGALS3, APOBEC3A, APOBEC3B, MARCKSL1, S100A9, S100A4, RPS27A, IL1B, RPL15, IL8, TIMP1   Dataset 1:    GAPDH, VIM, ACTB, S100A6, TIMP1, RGCC, ISG15, CXCL10, HLA-DPA1, CREM, CD79A   Shared:    RBM10, GZMK, LAGE3, ACAT2, NDUFC2, RPL14, CHCHD10, HSP90AB1, RPLP0, APOBEC3A, RPL12, RSAD2, RPL18A, GAPDH, CSTB, RPS3, RPS6, NPM1, RPL18, RPS15A, RPS19, TMSB4X, RPS12, HLA-A, TYMP, RPS3A, CCL5, RPL15, CD14, LGALS3   Dataset 2    CREM, HLA-DPA1, ISG15, CXCL10, CD79A, S100A6, ACTB, TIMP1, VIM, GAPDH, RGCC   Dataset 1:    TMEM66, BTG1, ISG15, RSAD2, SAT1, ANXA1, HERC6   Shared:    KLRC1, KLRD1, GNLY, APOBEC3G, NKG7, CD7, GZMB, HLA-A, PLAC8, PPBP, LAGE3, CCL5, GPR183, SRGN, HLA-B, TEX264, THRAP3, EIF2AK1, B2M, TMSB4X, CD63, HLA-C, RPL9, XCL2, RPS27A, CXCR4, RPS3, RPLP1, H3F3B, ACTB   Dataset 2    ANXA1, HERC6, ISG15, RSAD2, SAT1, TMEM66, BTG1   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 37129   **|   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   Total iterations: 42   Total time: 0 sec   Objective error: 59878.9   INMF started, niter=2   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   Total time: 0 sec   Objective error: 49910.7   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 45414.7   **|   INMF started, niter=2   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   Total time: 0 sec   Objective error: 41528.3   INMF started, niter=2   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   Total time: 0 sec   Objective error: 47418.4   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 37129   **|   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 37129   **|   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 37129   **|   INMF started, niter=30   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   Total time: 0 sec   Objective error: 35967.3   INMF started, niter=30   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   Total time: 0 sec   Objective error: 35967.3   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 45479.1   **|   INMF started, niter=2   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   Total time: 0 sec   Objective error: 49910.7   completed constructor::A::173x300   time taken:22.3533   completed constructor::A::173x300   time taken:19.4844   completed constructor::A::173x300   time taken:23.7611   completed constructor::A::173x300   time taken:22.0577   completed constructor::A::173x300   time taken:20.7871   completed constructor::A::173x300   time taken:20.932   Working ctrl H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\ctrltest_1e02c3026764d.h5   Working stim H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\stimtest_1e02c497e42ad.h5               Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 45414.7   **|   A liger command record, performed at 03-30-2025 02:16:27 EDT   Call: normalize.liger(object)   Parameters:       useDatasets : "ctrl", "stim"       verbose : TRUE   Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 45414.7   **|   Working ctrl H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\ctrltest_1e02c4f0c1359.h5   Working stim H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\stimtest_1e02c48e075b4.h5                           Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 45414.7   **|   An object of class ligerDataset with 300 cells   Performing log-normalization   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|   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%   [----|----|----|----|----|----|----|----|----|----|   **************************************************|        |     | | 0%     |     |======================================================================| 100%   Working ctrl H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\ctrltest_1e02c18657671.h5   Working stim H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\stimtest_1e02c3db82a55.h5         Working ctrl H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\ctrltest_1e02c1bfb5e92.h5   Working stim H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\stimtest_1e02c8662dcc.h5               Working ctrl H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\ctrltest_1e02c1f5b4c07.h5   Working stim H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\stimtest_1e02c680a6a9b.h5                     Working ctrl H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\ctrltest_1e02c305d1b7c.h5   Working stim H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\stimtest_1e02c4578752c.h5                              Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 37129   **|   Working ctrl H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\ctrltest_1e02c50c83baf.h5   Working stim H5 file path: D:\temp\2025_03_30_01_50_00_20407\RtmpgPqbAv\stimtest_1e02c25e94098.h5                           Starting online iNMF scenario 1, factorize all datasets   0% 10 20 30 40 50 60 70 80 90 100%   [----|----|----|----|----|----|----|----|----|----|   ************************************************Total iterations: 30   Total time: 0 sec   Objective error: 37129   **|                                       [ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]      ══ Skipped tests (1) ═══════════════════════════════════════════════════════════   • {DoubletFinder} is not installed (1): 'test_preprocessing.R:112:5'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_factorization.R:111:5'): UINMF ─────────────────────────────────   <Rcpp::exception/C++Error/error/condition>   Error: k must be <= m   Backtrace:       ▆    1. ├─rliger::runUINMF(pbmc, k = 30, nIteration = 2, nRandomStarts = 2) at test_factorization.R:111:5    2. └─rliger:::runUINMF.liger(pbmc, k = 30, nIteration = 2, nRandomStarts = 2)    3. └─rliger:::.runUINMF.list(...)    4. └─RcppPlanc::uinmf(...)    5. └─RcppPlanc:::.uinmf_rcpp(...)   ── Error ('test_factorization.R:130:5'): Optimize new parameters ───────────────   <Rcpp::exception/C++Error/error/condition>   Error: Must provide 2 V matrices   Backtrace:       ▆    1. └─rliger::optimizeNewLambda(pbmc, lambdaNew = 5.5, nIteration = 2) at test_factorization.R:130:5    2. ├─rliger::runINMF(...)    3. └─rliger:::runINMF.liger(...)    4. └─rliger:::.runINMF.list(...)    5. └─RcppPlanc::inmf(...)    6. └─RcppPlanc:::.bppinmf(...)   ── Error ('test_factorization.R:180:5'): Online iNMF - in-memory ───────────────   <std::invalid_argument/C++Error/error/condition>   Error: Must provide 2 H matrices   Backtrace:       ▆    1. ├─rliger::runOnlineINMF(...) at test_factorization.R:180:5    2. └─rliger:::runOnlineINMF.liger(...)    3. └─rliger:::.runOnlineINMF.list(...)    4. └─RcppPlanc::onlineINMF(...)    5. └─RcppPlanc:::.onlineINMF_withInitial(...)      [ FAIL 3 | WARN 0 | SKIP 1 | PASS 1329 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [5s] OK
• checking PDF version of manual ... [28s] OK
• checking HTML version of manual ... [26s] OK
• DONE

Status: 2 ERRORs