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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:FRASER.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings FRASER_2.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/FRASER.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-05 03:39:51 UTC
* checking for file ‘FRASER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FRASER’ version ‘2.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘FRASER’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.6Mb
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::selectSome' 'ggbio:::.buildFacetsFromArgs'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateRangesWithTxDb: no visible binding for global variable
  ‘include’
calculatePadjValuesOnSubset : <anonymous>: no visible binding for
  global variable ‘gene_rowIdx’
estimateBestQ: no visible binding for global variable ‘oht’
hyperParams: no visible binding for global variable ‘oht’
loadFraserDataSet: no visible global function definition for
  ‘slotNames’
plotEncDimSearch.FRASER: no visible binding for global variable ‘oht’
plotEncDimSearch.FRASER: no visible binding for global variable
  ‘singular_values’
plotVolcano.FRASER: no visible binding for global variable
  ‘aberrantLabel’
updateSeqlevelsStyle: no visible binding for global variable
  ‘NCBI_Genome_Name’
updateSeqlevelsStyle: no visible global function definition for
  ‘setNames’
updateSeqlevelsStyle: no visible global function definition for
  ‘seqnames<-’
updateSeqlevelsStyle: no visible binding for global variable
  ‘UCSC_Genome_Name’
plotEncDimSearch,FraserDataSet: no visible binding for global variable
  ‘oht’
plotEncDimSearch,FraserDataSet: no visible binding for global variable
  ‘singular_values’
plotVolcano,FraserDataSet: no visible binding for global variable
  ‘aberrantLabel’
results,FraserDataSet: no visible binding for global variable ‘padjust’
results,FraserDataSet: no visible binding for global variable
  ‘pValueGene’
results,FraserDataSet: no visible binding for global variable
  ‘padjustGene’
Undefined global functions or variables:
  NCBI_Genome_Name UCSC_Genome_Name aberrantLabel gene_rowIdx include
  oht pValueGene padjust padjustGene seqnames<- setNames
  singular_values slotNames
Consider adding
  importFrom("methods", "slotNames")
  importFrom("stats", "setNames")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotFunctions.Rd: aberrant
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 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 compiled code ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘FRASER-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotManhattan
> ### Title: Visualization functions for FRASER
> ### Aliases: plotManhattan plotFunctions plotAberrantPerSample plotVolcano
> ###   plotQQ plotExpression plotCountCorHeatmap plotFilterExpression
> ###   plotExpectedVsObservedPsi plotEncDimSearch plotBamCoverage
> ###   plotBamCoverageFromResultTable plotVolcano,FraserDataSet-method
> ###   plotAberrantPerSample,FraserDataSet-method plotSpliceMetricRank
> ###   plotQQ,FraserDataSet-method plotEncDimSearch,FraserDataSet-method
> ###   plotFilterVariability plotCountCorHeatmap,FraserDataSet-method
> ###   plotManhattan,FraserDataSet-method
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(42)
> ## End(Don't show)
> # create full FRASER object 
> fds <- makeSimulatedFraserDataSet(m=40, j=200)
> fds <- calculatePSIValues(fds)
Mon May  4 23:50:14 2026: Calculate the PSI 5 and 3 values ...
Mon May  4 23:50:17 2026: Calculate the theta values ...
Mon May  4 23:50:18 2026: Calculate the total nonsplit counts for each intron ...
Mon May  4 23:50:19 2026: Calculate the Jaccard Intron values ...
Mon May  4 23:50:19 2026: Calculate the delta for jaccard values ...
Mon May  4 23:50:20 2026: Calculate the delta for psi5 values ...
Mon May  4 23:50:20 2026: Calculate the delta for psi3 values ...
Mon May  4 23:50:20 2026: Calculate the delta for theta values ...
> fds <- filterExpressionAndVariability(fds, filter=FALSE)
Mon May  4 23:50:20 2026: Filtering out introns with low read support ...
Mon May  4 23:50:21 2026: Filtering out non-variable introns ...
Mon May  4 23:50:21 2026: Filtering done!
> # this step should be done for more dimensions in practice
> fds <- estimateBestQ(fds, type="jaccard", useOHT=FALSE, q_param=c(2,5,10,25))
dPsi filter:FALSE: 10	TRUE: 190
Exclusion matrix: TRUE: 200
Mon May  4 23:50:23 2026: Injecting 102 outliers ...
Mon May  4 23:50:28 2026: Run hyper optimization with 4 options.
1 ;	 2 ;	 0
Mon May  4 23:50:28 2026 ; q: 2 ; noise:  0
Mon May  4 23:50:28 2026: Running fit with correction method: PCA
Mon May  4 23:50:29 2026: Computing PCA ...
Mon May  4 23:50:29 2026: Fitting rho ...
Mon May  4 23:50:29 2026: rho fit:
	   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
	0.01267 0.14117 0.22709 0.22407 0.29927 0.47212 
Mon May  4 23:50:31 2026:  adjusting junction-level pvalues ...
Mon May  4 23:50:32 2026:  genome-wide FDR for junction-level pvalues ...
Mon May  4 23:50:32 2026: Calculating AUC-PR ...
2 ;	 5 ;	 0
Mon May  4 23:50:32 2026 ; q: 5 ; noise:  0
Mon May  4 23:50:33 2026: Running fit with correction method: PCA
Mon May  4 23:50:33 2026: Computing PCA ...
Mon May  4 23:50:33 2026: Fitting rho ...
Mon May  4 23:50:34 2026: rho fit:
	   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
	0.01227 0.10201 0.16777 0.16629 0.21851 0.42562 
Mon May  4 23:50:36 2026:  adjusting junction-level pvalues ...
Mon May  4 23:50:36 2026:  genome-wide FDR for junction-level pvalues ...
Mon May  4 23:50:37 2026: Calculating AUC-PR ...
3 ;	 10 ;	 0
Mon May  4 23:50:37 2026 ; q: 10 ; noise:  0
Mon May  4 23:50:37 2026: Running fit with correction method: PCA
Mon May  4 23:50:37 2026: Computing PCA ...
Mon May  4 23:50:37 2026: Fitting rho ...
Mon May  4 23:50:38 2026: rho fit:
	    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
	0.009201 0.065373 0.104685 0.108464 0.140767 0.470132 
Mon May  4 23:50:40 2026:  adjusting junction-level pvalues ...
Mon May  4 23:50:41 2026:  genome-wide FDR for junction-level pvalues ...
Mon May  4 23:50:41 2026: Calculating AUC-PR ...
4 ;	 25 ;	 0
Mon May  4 23:50:41 2026 ; q: 25 ; noise:  0
Mon May  4 23:50:42 2026: Running fit with correction method: PCA
Mon May  4 23:50:42 2026: Computing PCA ...
Mon May  4 23:50:42 2026: Fitting rho ...
Mon May  4 23:50:43 2026: rho fit:
	    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
	0.001306 0.016561 0.025216 0.031793 0.036894 0.393650 
Mon May  4 23:50:44 2026:  adjusting junction-level pvalues ...
Mon May  4 23:50:45 2026:  genome-wide FDR for junction-level pvalues ...
Mon May  4 23:50:45 2026: Calculating AUC-PR ...
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  span too small.   fewer data values than degrees of freedom.
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  pseudoinverse used at 1.885
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  neighborhood radius 8.115
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  reciprocal condition number  0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
  There are other near singularities as well. 404.61
Warning in sqrt(sum.squares/one.delta) : NaNs produced
Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
  span too small.   fewer data values than degrees of freedom.
Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
  pseudoinverse used at 1.885
Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
  neighborhood radius 8.115
Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
  reciprocal condition number  0
Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
  There are other near singularities as well. 404.61
Warning in stats::qt(level/2 + 0.5, pred$df) : NaNs produced
Warning in max(ids, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
> 
> # assign gene names to show functionality on test dataset
> # use fds <- annotateRanges(fds) on real data
> mcols(fds, type="j")$hgnc_symbol <- 
+     paste0("gene", sample(1:25, nrow(fds), replace=TRUE))
> 
> # fit and calculate pvalues
> genesOfInterest <- rep(list(paste0("gene", sample(1:25, 10))), 4)
> names(genesOfInterest) <- c("sample1", "sample6", "sample15", "sample23")
> fds <- FRASER(fds, subsets=list("testSet"=genesOfInterest))
Mon May  4 23:50:46 2026: Calculate the PSI 5 and 3 values ...
Mon May  4 23:50:49 2026: Calculate the theta values ...
Mon May  4 23:50:51 2026: Calculate the total nonsplit counts for each intron ...
Mon May  4 23:50:51 2026: Calculate the Jaccard Intron values ...
Mon May  4 23:50:51 2026: Calculate the delta for jaccard values ...
Mon May  4 23:50:51 2026: Calculate the delta for psi5 values ...
Mon May  4 23:50:52 2026: Calculate the delta for psi3 values ...
Mon May  4 23:50:52 2026: Calculate the delta for theta values ...

Mon May  4 23:50:52 2026: Fit step for: 'jaccard'.
Mon May  4 23:50:52 2026: Running fit with correction method: PCA
Mon May  4 23:50:53 2026: Computing PCA ...
Mon May  4 23:50:53 2026: Fitting rho ...
Mon May  4 23:50:53 2026: rho fit:
	   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
	0.01025 0.05837 0.09145 0.09641 0.13341 0.27426 
Mon May  4 23:50:54 2026: Compute p values for: 'jaccard'.
Mon May  4 23:50:55 2026: Adjust p values for: 'jaccard'.
Mon May  4 23:50:55 2026:  adjusting junction-level pvalues ...
Mon May  4 23:50:56 2026:  genome-wide FDR for junction-level pvalues ...
Mon May  4 23:50:56 2026:  calculating gene-level pvalues ...
Mon May  4 23:50:56 2026:   starting gene-level pval computation for type jaccard
Mon May  4 23:50:56 2026:   gene-level pval computation per gene (n=25)
Mon May  4 23:50:56 2026:   genome-wide FDR for gene-level pvals for type jaccard
Mon May  4 23:50:56 2026:   finished gene-level pval computation for type jaccard
Mon May  4 23:50:56 2026: starting FDR calculation on subset of genes...
Mon May  4 23:50:57 2026: finished FDR calculation on subset of genes.
> 
> # QC plotting
> plotFilterExpression(fds)
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
> plotFilterVariability(fds)
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
> plotCountCorHeatmap(fds, "jaccard")
> plotCountCorHeatmap(fds, "jaccard", normalized=TRUE)
> plotEncDimSearch(fds, type="jaccard")
Warning in .local(object, ...) :
  Please use `estimateBestQ` to compute the singular values using OHT before visualizing them.
NULL
> 
> # extract results 
> plotAberrantPerSample(fds, aggregate=FALSE)
Warning in scale_y_log10(limits = c(1, max(unlist(outliers)))) :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10(limits = c(1, max(unlist(outliers)))) :
  log-10 transformation introduced infinite values.
Warning: `label` cannot be a <ggplot2::element_blank> object.
> plotAberrantPerSample(fds, aggregate=TRUE, subsetName="testSet")
Warning in scale_y_log10(limits = c(1, max(unlist(outliers)))) :
  log-10 transformation introduced infinite values.
Warning: Removed 4 rows containing missing values or values outside the scale range
(`geom_hline()`).
Warning: `label` cannot be a <ggplot2::element_blank> object.
> plotVolcano(fds, "sample2", "jaccard", label="aberrant")
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
> plotVolcano(fds, "sample1", "jaccard", aggregate=TRUE, subsetName="testSet")
> 
> # dive into gene/sample level results
> res <- data.table::as.data.table(results(fds))
Mon May  4 23:51:01 2026: Collecting results for: jaccard (transcriptome-wide)
Mon May  4 23:51:01 2026: Process chunk: 1 for: jaccard
Mon May  4 23:51:03 2026: Collecting results for: jaccard (testSet)
Mon May  4 23:51:03 2026: Process chunk: 1 for: jaccard
> res
    seqnames start   end width strand sampleID hgncSymbol    type     pValue
      <fctr> <int> <int> <int> <fctr>   <char>     <char>  <char>      <num>
 1:     chr1   134   134     1      * sample20     gene10 jaccard 1.9225e-09
 2:     chr1   133   133     1      * sample36     gene13 jaccard 3.0340e-06
 3:     chr1   140   140     1      * sample12     gene16 jaccard 1.8227e-05
 4:     chr1   157   157     1      * sample14      gene6 jaccard 2.7918e-05
 5:     chr1   146   146     1      * sample21      gene6 jaccard 3.2925e-05
 6:     chr1    55    55     1      *  sample2     gene22 jaccard 3.8333e-05
 7:     chr1   131   131     1      * sample20      gene6 jaccard 4.7675e-05
 8:     chr1    53    53     1      * sample15      gene5 jaccard 8.0140e-05
 9:     chr1   165   165     1      * sample26     gene22 jaccard 8.1956e-05
10:     chr1    33    33     1      * sample15     gene19 jaccard 1.1989e-04
11:     chr1   169   169     1      *  sample2      gene5 jaccard 1.2681e-04
12:     chr1   106   106     1      * sample20     gene19 jaccard 1.7649e-04
13:     chr1   118   118     1      * sample20     gene16 jaccard 1.9974e-04
14:     chr1     8     8     1      *  sample1     gene16 jaccard 2.1493e-04
15:     chr1    35    35     1      * sample20      gene3 jaccard 3.7079e-04
       padjust psiValue deltaPsi counts totalCounts meanCounts meanTotalCounts
         <num>    <num>    <num>  <int>       <num>      <num>           <num>
 1: 2.2601e-06     0.90     0.86    184         204     101.35         9892.35
 2: 3.5668e-03     0.94     0.53     29          31     143.43         4046.48
 3: 2.1427e-02     0.57     0.41    330         580      70.67         4989.88
 4: 3.2821e-02     0.35     0.29    712        2018      65.38         5758.12
 5: 3.8707e-02     0.37    -0.49   3717       10155    4982.95         6180.00
 6: 4.5065e-02     0.07    -0.84     38         514    3037.38         4392.32
 7: 2.8023e-02     0.65     0.51   2128        3250     437.22         6008.88
 8: 7.0472e-02     0.30    -0.49   2997       10145    3562.72         5864.88
 9: 9.6348e-02     0.20    -0.39     46         234     168.75         6614.35
10: 7.0472e-02     0.28     0.26   1645        5975     367.80         7470.15
11: 7.4538e-02     0.40     0.27  16576       41090     611.95         4973.10
12: 5.8704e-02     0.08    -0.56    734        9286    3124.25         4404.05
13: 5.8704e-02     0.06    -0.50     11         171   12187.92        20062.32
14:         NA     0.13    -0.65    331        2615    1344.75         4665.45
15: 8.7181e-02     0.04    -0.57    205        5097    3762.35         5683.75
    nonsplitCounts nonsplitProportion nonsplitProportion_99quantile
             <num>              <num>                         <num>
 1:              8               0.04                          0.82
 2:              2               0.06                          1.00
 3:            182               0.31                          1.00
 4:           1280               0.63                          1.00
 5:           5924               0.58                          0.72
 6:              2               0.00                            NA
 7:           1116               0.34                            NA
 8:              0               0.00                          0.59
 9:              6               0.03                          0.73
10:            458               0.08                          0.99
11:          24514               0.60                          1.00
12:            636               0.07                          0.71
13:             46               0.27                          0.68
14:              0               0.00                          1.00
15:             84               0.02                          0.86
    padjust_testSet
              <num>
 1:              NA
 2:              NA
 3:              NA
 4:              NA
 5:              NA
 6:              NA
 7:              NA
 8:        0.025247
 9:              NA
10:        0.025247
11:              NA
12:              NA
13:              NA
14:        0.090522
15:              NA
> plotExpression(fds, result=res[1])
> plotQQ(fds, result=res[1])
> plotExpectedVsObservedPsi(fds, res=res[1])
> plotSpliceMetricRank(fds, res=res[1])
> 
> # other ways to call these plotting functions
> plotExpression(fds, idx=10, sampleID="sample1", type="jaccard")
> plotExpression(fds, result=res[1], subsetName="testSet")
> plotQQ(fds, idx=10, sampleID="sample1", type="jaccard")
> plotQQ(fds, result=res[1], subsetName="testSet")
> plotExpectedVsObservedPsi(fds, idx=10, sampleID="sample1", type="jaccard")
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
> plotExpectedVsObservedPsi(fds, result=res[1], subsetName="testSet")
> plotSpliceMetricRank(fds, idx=10, sampleID="sample1", type="jaccard")
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
> plotSpliceMetricRank(fds, result=res[1], subsetName="testSet")
> 
> # create manhattan plot of pvalues by genomic position
> if(require(ggbio)){
+     plotManhattan(fds, type="jaccard", sampleID="sample10")
+ }
Loading required package: ggbio
Loading required package: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit https://lawremi.github.io/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

highlighting 0 outliers ...
using coord:genome to parse x scale
> 
> # plot splice graph and coverage from bam files in a given region
> if(require(SGSeq)){
+     fds <- createTestFraserSettings()
+     gr <- GRanges(seqnames="chr19", 
+         IRanges(start=7587496, end=7598895), 
+         strand="+")
+     plotBamCoverage(fds, gr=gr, sampleID="sample3", 
+         control_samples="sample2", min_junction_count=5,
+         curvature_splicegraph=1, curvature_coverage=1, 
+         mar=c(1, 7, 0.1, 3))
+ 
+     # plot coverage from bam file for a row in the result table
+     fds <- createTestFraserDataSet()
+     require(TxDb.Hsapiens.UCSC.hg19.knownGene)
+     txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
+     require(org.Hs.eg.db)
+     orgDb <- org.Hs.eg.db
+  
+     res <- results(fds, padjCutoff=NA, deltaPsiCutoff=NA)
+     res_dt <- data.table::as.data.table(res)
+     res_dt <- res_dt[sampleID == "sample2",]
+     
+     # plot full range of gene containing outlier junction
+     plotBamCoverageFromResultTable(fds, result=res_dt[1,], show_full_gene=TRUE,
+         txdb=txdb, orgDb=orgDb, control_samples="sample3")
+     
+     # plot only certain range around outlier junction
+     plotBamCoverageFromResultTable(fds, result=res_dt[1,], show_full_gene=FALSE, 
+         control_samples="sample3", curvature_splicegraph=0.5, txdb=txdb,
+         curvature_coverage=0.5, right_extension=5000, left_extension=5000,
+         splicegraph_labels="id")
+ }
Loading required package: SGSeq

Attaching package: 'SGSeq'

The following object is masked from 'package:ggplot2':

    annotate

Extracting SGSeq sample info from BAM files for samples sample3, sample2 ...
sample2 complete.
sample3 complete.
Warning: Custom tag 'XS' not found in BAM file:
   ''

Spliced alignments must include a custom tag 'XS'.
Compatible BAM files can be obtained with an alignment
program for RNA-seq data (e.g. GSNAP, HISAT, STAR, TopHat).
Predict features...
sample2 complete.
sample3 complete.
Process features...
Obtain counts...
sample2 complete.
sample3 complete.
Mon May  4 23:51:24 2026: Folder with the merged split read counts exists already and will be used. If you want to count the split reads again, use the option recount=TRUE or remove this folder: 
FRASER_output/savedObjects/Data_Analysis/splitCounts
Mon May  4 23:51:24 2026: Folder with the merged non-split read counts exists already and will be used. If you want to count the non-split reads again, use the option recount=TRUE or remove this folder: 
FRASER_output/savedObjects/Data_Analysis/nonSplitCounts
Mon May  4 23:51:24 2026: Writing final FRASER object ('FRASER_output/savedObjects/Data_Analysis/fds-object.RDS').
Mon May  4 23:51:24 2026: Calculate the PSI 5 and 3 values ...
Mon May  4 23:51:25 2026: Calculate the theta values ...
Mon May  4 23:51:26 2026: Calculate the total nonsplit counts for each intron ...
Mon May  4 23:51:26 2026: Calculate the Jaccard Intron values ...
Mon May  4 23:51:27 2026: Calculate the delta for jaccard values ...
Mon May  4 23:51:27 2026: Calculate the delta for psi5 values ...
Mon May  4 23:51:27 2026: Calculate the delta for psi3 values ...
Mon May  4 23:51:28 2026: Calculate the delta for theta values ...
Mon May  4 23:51:28 2026: Filtering out introns with low read support ...
Keeping 24 junctions out of 48. This is 50% of the junctions
Mon May  4 23:51:28 2026: Filtering out non-variable introns ...
Keeping 24 junctions out of 24. This is 100% of the junctions
Mon May  4 23:51:28 2026: Filtering done!

Mon May  4 23:51:31 2026: Fit step for: 'jaccard'.
Mon May  4 23:51:31 2026: Running fit with correction method: PCA
Mon May  4 23:51:31 2026: Computing PCA ...
Mon May  4 23:51:32 2026: Fitting rho ...
Mon May  4 23:51:32 2026: rho fit:
	     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
	3.069e-05 5.961e-03 3.601e-02 1.770e-01 1.795e-01 9.978e-01 
Mon May  4 23:51:32 2026: Compute p values for: 'jaccard'.
Mon May  4 23:51:33 2026: Adjust p values for: 'jaccard'.
Mon May  4 23:51:33 2026:  adjusting junction-level pvalues ...
Mon May  4 23:51:33 2026:  genome-wide FDR for junction-level pvalues ...
Mon May  4 23:51:33 2026:  calculating gene-level pvalues ...
Mon May  4 23:51:33 2026:   starting gene-level pval computation for type jaccard
Mon May  4 23:51:33 2026:   gene-level pval computation per gene (n=3)
Mon May  4 23:51:34 2026:   genome-wide FDR for gene-level pvals for type jaccard
Mon May  4 23:51:34 2026:   finished gene-level pval computation for type jaccard
Mon May  4 23:51:39 2026: Writing final FRASER object ('FRASER_output/savedObjects/Data_Analysis/fds-object.RDS').
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: org.Hs.eg.db
Mon May  4 23:51:40 2026: Collecting results for: jaccard (transcriptome-wide)
Mon May  4 23:51:40 2026: Process chunk: 1 for: jaccard
Error: unable to open database file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
FRASER                  40.467  0.556  41.049
injectOutliers          27.044  0.084  25.801
annotateRanges          21.486  0.674  41.268
estimateBestQ           20.860  0.456  21.317
fds-methods             18.684  0.223  20.039
mergeExternalData       18.584  0.136  18.700
calculatePSIValues      17.375  0.977  18.332
filtering               17.647  0.287  17.914
counts                  16.098  0.436  16.503
createTestFraserDataSet 16.040  0.316  16.320
getter_setter_functions 15.899  0.172  16.037
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘FRASER.Rnw’ using knitr

Quitting from FRASER.Rnw:797-831 [bamCoverage_plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     x
  1. \-FRASER::plotBamCoverageFromResultTable(...)
  2.   +-data.table::as.data.table(...)
  3.   +-AnnotationDbi::select(...)
  4.   \-AnnotationDbi::select(...)
  5.     \-AnnotationDbi:::.select(...)
  6.       \-AnnotationDbi::testSelectArgs(...)
  7.         \-AnnotationDbi:::.testForValidKeys(x, keys, keytype, fks)
  8.           +-AnnotationDbi::keys(x, keytype)
  9.           \-AnnotationDbi::keys(x, keytype)
 10.             \-AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
 11.               \-AnnotationDbi:::.keys(x, keytype)
 12.                 \-AnnotationDbi:::.legacyKeys(x, keytype)
 13.                   \-AnnotationDbi:::.queryForKeys(x, keytype)
 14.                     \-AnnotationDbi:::dbQuery(dbconn(x), sql)
 15.                       +-DBI::dbGetQuery(conn, SQL)
 16.                       \-DBI::dbGetQuery(conn, SQL)
 17.                         \-DBI (local) .local(conn, statement, ...)
 18.                           +-DBI::dbFetch(rs, n = n, ...)
 19.                           \-RSQLite::dbFetch(rs, n = n, ...)
 20.                             \-RSQLite (local) .local(res, n, ...)
 21.                               \-RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'FRASER.Rnw' failed with diagnostics:
unable to open database file
--- failed re-building ‘FRASER.Rnw’

SUMMARY: processing the following file failed:
  ‘FRASER.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/FRASER.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL FRASER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘FRASER’ ...
** this is package ‘FRASER’ version ‘2.9.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -DARMA_DONT_USE_OPENMP -fpic  -g -O2  -Wall -Werror=format-security  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.24-bioc/R/lib -L/usr/local/lib -o FRASER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.24-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-FRASER/00new/FRASER/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FRASER)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(FRASER)
Loading required package: BiocParallel
Loading required package: Rsamtools
Loading required package: Seqinfo
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'FRASER'

The following object is masked from 'package:Biobase':

    samples

> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
> library(org.Hs.eg.db)

> 
> # to speed up the testing on windows do it in serial mode
> if(.Platform$OS.type != "unix") {
+     register(SerialParam())
+ }
> 
> set.seed(42)
> test_check("FRASER")
Optimal encoding dimension: 2 
Optimal encoding dimension: 2 
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 109 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 109 ]
> 
> proc.time()
   user  system elapsed 
194.861  57.182 188.755