* using log directory ‘/srv/hornik/tmp/CRAN_pretest/OlinkAnalyze.Rcheck’ * using R Under development (unstable) (2025-01-26 r87642) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.6 (1+b1) Debian flang-new version 19.1.6 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘OlinkAnalyze/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OlinkAnalyze’ version ‘4.1.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/8s] OK * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OlinkAnalyze’ can be installed ... [7s/7s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [14s/14s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [6s/6s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [86s/86s] ERROR Running ‘testthat.R’ [85s/85s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(OlinkAnalyze) > > test_check("OlinkAnalyze") Variables and covariates converted from character to factors: Site ANOVA model fit to each assay: NPX~Site Variables and covariates converted from character to factors: Time ANOVA model fit to each assay: NPX~Time Variables and covariates converted from character to factors: Site, Time ANOVA model fit to each assay: NPX~Site*Time Variables and covariates converted from character to factors: Site Means estimated for each assay from ANOVA model: NPX~Site Variables and covariates converted from character to factors: Time Means estimated for each assay from ANOVA model: NPX~Time 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment2 ANOVA model fit to each assay: NPX~treatment2 Duplicate SampleID(s) detected: sample1_1 sample2_1 sample4_1 MM55111 XY32341 MN86751 YY35111 UY45551 cs2_1 S81771 SA0F71 S52F71 S8FCB1 S7EF01 S897C1 S65FC1 NEG-SOAP-11 SFCC51 S4DFE1 S0C651 S15B31 SD4171 NEG-SOAP-12 S17811 S0D6D1 S16F21 S53B71 S161F1 S6D2C1 SA17C1 SD4DD1 SACD01 SAC111 PC-SOAP-11 SF14F1 S353F1 S14C51 SE8771 PC-SOAP-12 SCF7B1 S84D41 SA1DC1 S45E31 S1DB31 S38321 sample5_2 sample6_2 sample7_2 KJ23652 OO34092 VX55552 cs1_2 ZK43212 SD50562 MN86752 XW43972 YY35112 LH84092 SD8172 SA0F72 S52F72 SA33F2 S7EF02 S939C2 S65FC2 NEG-SOAP-21 SFCC52 S4DFE2 S275F2 S857F2 S87C02 S10642 S0C652 NEG-SOAP-22 SC17B2 S0D6D2 S16F22 SCF472 S53B72 NEG-SOAP-23 S161F2 S6D2C2 S35EB2 S445F2 SD13C2 SAC412 SAC112 PC-SOAP-21 SBE1D2 S353F2 S14C52 S10262 SE8772 SCF7B2 SA1DC2 S7BD12 S4E5F2 S45BF2 SD7702 S38322 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment1 ANOVA model fit to each assay: NPX~treatment1 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment2 Means estimated for each assay from ANOVA model: NPX~treatment2 Duplicate SampleID(s) detected: sample1_1 sample2_1 sample4_1 MM55111 XY32341 MN86751 YY35111 UY45551 cs2_1 S81771 SA0F71 S52F71 S8FCB1 S7EF01 S897C1 S65FC1 NEG-SOAP-11 SFCC51 S4DFE1 S0C651 S15B31 SD4171 NEG-SOAP-12 S17811 S0D6D1 S16F21 S53B71 S161F1 S6D2C1 SA17C1 SD4DD1 SACD01 SAC111 PC-SOAP-11 SF14F1 S353F1 S14C51 SE8771 PC-SOAP-12 SCF7B1 S84D41 SA1DC1 S45E31 S1DB31 S38321 sample5_2 sample6_2 sample7_2 KJ23652 OO34092 VX55552 cs1_2 ZK43212 SD50562 MN86752 XW43972 YY35112 LH84092 SD8172 SA0F72 S52F72 SA33F2 S7EF02 S939C2 S65FC2 NEG-SOAP-21 SFCC52 S4DFE2 S275F2 S857F2 S87C02 S10642 S0C652 NEG-SOAP-22 SC17B2 S0D6D2 S16F22 SCF472 S53B72 NEG-SOAP-23 S161F2 S6D2C2 S35EB2 S445F2 SD13C2 SAC412 SAC112 PC-SOAP-21 SBE1D2 S353F2 S14C52 S10262 SE8772 SCF7B2 SA1DC2 S7BD12 S4E5F2 S45BF2 SD7702 S38322 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment2 Means estimated for each assay from ANOVA model: NPX~treatment2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Using max LOD as filter criteria... Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Using plate LOD as filter criteria... Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Using plate LOD as filter criteria... Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 0 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Samples removed due to missing variable CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables converted from character to factors: Site Kruskal model fit to each assay: NPX~Site Samples removed due to missing variable CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables converted from character to factors: Time Friedman model fit to each assay: NPX~Time Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Samples removed due to missing variable: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables converted from character to factors: Site Pairwise comparisons for Kruskal-Wallis test using Dunn test were performed Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Samples removed due to missing variable: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables converted from character to factors: Time Pairwise comparisons for Friedman test using paired Wilcoxon signed-rank test were performed 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables converted from character to factors: treatment2 Kruskal model fit to each assay: NPX~treatment2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables converted from character to factors: treatment2 Pairwise comparisons for Kruskal-Wallis test using Dunn test were performed Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables and covariates converted from character to factors: Treatment, Time ANOVA model fit to each assay: NPX~Treatment*Time Duplicate SampleID(s) detected: CONTROL_SAMPLE_AS 1 CONTROL_SAMPLE_AS 2 Samples removed due to missing variable or covariate levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variables and covariates converted from character to factors: Treatment, Time Means estimated for each assay from ANOVA model: NPX~Treatment*Time NOTE: Results may be misleading due to involvement in interactions 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment2 ANOVA model fit to each assay: NPX~treatment2 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Variables and covariates converted from character to factors: treatment2 Means estimated for each assay from ANOVA model: NPX~treatment2 Random assignment of SAMPLES to plates Assigning subjects to plates . Random assignment of SUBJECTS to plates `study` column detected in manifest. Optional study argument is set to "study". Assigning subjects to plates. Keeping studies together during randomization. Testing with 0 empty well(s) in the plate. . study1 successful! Testing with 0 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 1 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 2 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 3 empty well(s) in the plate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Testing with 4 empty well(s) in the plate. . study2 successful! Random assignment of SUBJECTS to plates Totally included 4 empty well(s) in first and/or intermediate plate(s) to accomplish the randomization. Please try another seed or increase the number of iterations if there are indications that another randomization might leave fewer empty wells. `study` column detected in manifest. Optional study argument is set to "study". Assigning subjects to plates. Multi-study project detected. Studies will be kept together during randomization. Random assignment of SAMPLES to plates by study Assigning subjects to plates . Random assignment of SUBJECTS to plates Random assignment of SAMPLES to plates Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variable converted from character to factor: Treatment T-test is performed on Treated - Untreated. Variable converted from character to factor: Time Paired t-test is performed on Baseline - Week.6. Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variable converted from character to factor: Time Variable converted from character to factor: treatment1 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. T-test is performed on control - treated. Target 96 data in wide form detected. QUANT data detected. Some downstream functions may not be supported. 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 326 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variable converted from character to factor: Treatment Mann-Whitney U Test is performed on Treated - Untreated. Variable converted from character to factor: Time Paired Mann-Whitney U Test is performed on Baseline - Week.6. Samples removed due to missing variable levels: CONTROL_SAMPLE_AS 1, CONTROL_SAMPLE_AS 2 Variable converted from character to factor: Time Variable converted from character to factor: treatment1 8 assay(s) exhibited assay QC warning. For more information see the Assay_Warning column. Mann-Whitney U Test is performed on control - treated. [ FAIL 1 | WARN 0 | SKIP 30 | PASS 461 ] ══ Skipped tests (30) ══════════════════════════════════════════════════════════ • On CRAN (12): 'test-Olink_boxplot.R:1:1', 'test-Olink_plate_randomizer.R:60:3', 'test-Read_NPX_data.R:52:5', 'test-Volcano_plot.R:17:3', 'test-dist_plot.R:18:5', 'test-linear_mixed_model.R:1:1', 'test-npxProcessing.R:121:3', 'test-olink_Pathway_Enrichment.R:1:1', 'test-olink_Pathway_Heatmap.R:1:1', 'test-olink_Pathway_Visualization.R:1:1', 'test-olink_qc_plot.R:16:5', 'test-pca_plot.R:2:1' • file.exists(test_path("data", "example_3k_data.rds")) is not TRUE (14): 'test-olink_normalization.R:474:5', 'test-olink_normalization.R:739:5', 'test-olink_normalization_product.R:7:5', 'test-olink_normalization_product.R:122:5', 'test-olink_normalization_product.R:218:5', 'test-olink_normalization_product.R:342:5', 'test-olink_normalization_product.R:469:5', 'test-olink_normalization_utils.R:146:5', 'test-olink_normalization_utils.R:2429:5', 'test-olink_normalization_utils.R:2523:5', 'test-olink_normalization_utils.R:2598:5', 'test-olink_normalization_utils.R:2645:5', 'test-olink_normalization_utils.R:2764:5', 'test-olink_normalization_utils.R:3810:5' • file.exists(test_path("data", "ref_results_norm.rds")) is not TRUE (4): 'test-olink_normalization.R:17:5', 'test-olink_normalization.R:131:5', 'test-olink_normalization.R:249:5', 'test-olink_normalization.R:367:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Read_NPX_data.R:220:9'): read_npx_parquet - RUO file ─────────── Error: NotImplemented: Support for codec 'gzip' not built Backtrace: ▆ 1. └─withr::with_tempfile(...) at test-Read_NPX_data.R:192:5 2. └─base::eval(substitute(code), envir = env) 3. └─base::eval(substitute(code), envir = env) 4. └─arrow::write_parquet(x = df, sink = pfile_ruo, compression = "gzip") at test-Read_NPX_data.R:220:9 5. └─writer$WriteTable(x, chunk_size = chunk_size) 6. └─arrow:::parquet___arrow___FileWriter__WriteTable(...) [ FAIL 1 | WARN 0 | SKIP 30 | PASS 461 ] Deleting unused snapshots: • Olink_boxplot/boxplot-site-10prots.svg • Olink_boxplot/boxplot-site-2prots.svg • Olink_boxplot/boxplot-time-and-site.svg • Olink_boxplot/boxplot-time-with-coloroption.svg • Olink_boxplot/boxplot-time.svg • Volcano_plot/volcano-plot-with-coloroption.svg • dist_plot/distribution-plot-col-by-treatment.svg • linear_mixed_model/lmer-plot-more-prots-than-space.svg • linear_mixed_model/lmer-plot.svg • olink_Pathway_Heatmap/gsea-heatmap.svg • olink_Pathway_Heatmap/ora-heatmap-with-keyword.svg • olink_Pathway_Visualization/gsea-vis-with-keyword.svg • olink_Pathway_Visualization/gsea-visualization.svg • olink_Pathway_Visualization/ora-vis-with-keyword.svg • olink_Pathway_Visualization/ora-vis-with-terms.svg • olink_qc_plot/qc-plot-with-coloroption.svg Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [51s/50s] OK * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR