##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SpliceWiz_1.1.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SpliceWiz.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.1.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SpliceWiz’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   9.0Mb
* 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 R 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 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 ... NOTE
Killed
* checking Rd files ... 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 ... NOTE
Killed
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SpliceWiz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ASE-GLM-edgeR
> ### Title: Using Generalised linear models to analyse differential ASEs
> ###   using edgeR
> ### Aliases: ASE-GLM-edgeR fitASE_edgeR fitASE_edgeR_custom testASE_edgeR
> ###   addPSI_edgeR
> 
> ### ** Examples
> 
> # Load the NxtSE object and set up the annotations
> # - see ?makeSE on example code of generating this NxtSE object
> se <- SpliceWiz_example_NxtSE()
> 
> colData(se)$treatment <- rep(c("A", "B"), each = 3)
> colData(se)$replicate <- rep(c("P","Q","R"), 2)
> require("edgeR")
Loading required package: edgeR
Loading required package: limma
> 
> fit <- fitASE_edgeR(
+     se, 
+     strModelFormula = "~0 + replicate + treatment", 
+     strASEFormula = "~0 + replicate + treatment + treatment:ASE"
+ )
Feb 07 16:45:23 Fitting edgeR contrast for included / excluded counts separately
Feb 07 16:45:24 Fitting edgeR contrast for included / excluded counts together
> 
> # Get coefficient terms of Included / Excluded counts isolated model
> colnames(fit$model_IncExc)
[1] "replicateP" "replicateQ" "replicateR" "treatmentB"
> # [1] "replicateP" "replicateQ" "replicateR" "treatmentB"
> 
> # Get coefficient terms of PSI model
> colnames(fit$model_ASE)
[1] "replicateP"             "replicateQ"             "replicateR"            
[4] "treatmentB"             "treatmentA:ASEIncluded" "treatmentB:ASEIncluded"
> # [1] "replicateP" "replicateQ" "replicateR" "treatmentB"            
> # [5] "treatmentA:ASEIncluded" "treatmentB:ASEIncluded"
> 
> # Contrast between treatment "B" against treatment "A"
> res <- testASE_edgeR(se, fit,
+     contrast_IncExc = c(0,0,0,1),
+     contrast_ASE = c(0,0,0,0,-1,1)
+ )
> 
> ### # Add mean PSI values to results:
> res_withPSI <- addPSI_edgeR(res, se, "treatment", c("B", "A"))
> 
> 
> ### Using custom model matrices to model counts
> #   - the equivalent analysis can be performed as follows:
> 
> # Sample annotations for isoform count expressions
> colData <- as.data.frame(colData(se))
> 
> # Sample annotations for isoform count PSI analysis
> colData_ASE <- rbind(colData, colData)
> colData_ASE$ASE <- rep(c("Included", "Excluded"), each = nrow(colData))
> rownames(colData_ASE) <- c(
+     paste0(rownames(colData), ".Included"),
+     paste0(rownames(colData), ".Excluded")
+ )
> 
> model_IncExc <- model.matrix(
+     ~0 + replicate + treatment,
+     data = colData
+ )
> 
> model_ASE <- model.matrix(
+     ~0 + replicate + treatment + treatment:ASE,
+     data = colData_ASE
+ )
> 
> fit <- fitASE_edgeR_custom(se, model_IncExc, model_ASE)
Feb 07 16:45:28 Fitting edgeR contrast for included / excluded counts separately
Feb 07 16:45:28 Fitting edgeR contrast for included / excluded counts together
> 
> res_customModel <- testASE_edgeR(se, fit,
+     contrast_IncExc = c(0,0,0,1),
+     contrast_ASE = c(0,0,0,0,-1,1)
+ )
> 
> # Check this produces identical results:
> identical(res_customModel, res)
[1] TRUE
> 
> ### Time series examples using edgeR and splines 
> # - similar to section 4.8 in the edgeR vignette
> 
> colData(se)$timepoint <- rep(c(1,2,3), each = 2)
> colData(se)$batch <- rep(c("1", "2"), 3)
> 
> # First, we set up a polynomial spline with 2 degrees of freedom:
> Time <- poly(colData(se)$timepoint, df = 2)
> 
> # Next, we define the batch factor:
> Batch <- factor(colData(se)$batch)
> 
> # Finally, we construct the same factors for ASE analysis. Note that
> #   each factor must be repeated twice
> 
> Time_ASE <- rbind(Time, Time)
> Batch_ASE <- c(Batch, Batch)
> ASE <- factor(
+     rep(c("Included", "Excluded"), each = nrow(colData(se)))
+ )
> 
> # Now, we set up the model matrices for isoform and PSI count modelling
> model_IncExc <- model.matrix(~0 + Batch + Time)
> model_ASE <- model.matrix(~0 + Batch_ASE + Time_ASE + Time_ASE:ASE)
> 
> fit <- fitASE_edgeR_custom(se, model_IncExc, model_ASE)
Feb 07 16:45:28 Fitting edgeR contrast for included / excluded counts separately
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ||                           Annotations : transcripts.gtf (GTF)              ||
  ||                                                                            ||
  \\============================================================================//
  
  //=============== Running (07-Feb-2023 16:46:02, pid=4178521) ================\\
  ||                                                                            ||
  || Check the input reads.                                                     ||
  || The input file contains base space reads.                                  ||
  || Initialise the memory objects.                                             ||
  || Estimate the mean read length.                                             ||
  || Create the output BAM file.                                                ||
  || Check the index.                                                           ||
  Unable top open index './reference_index'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. 
  
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SW_Cookbook.Rmd’ using ‘UTF-8’... OK
  ‘SW_QuickStart.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘SW_Cookbook.Rmd’ using rmarkdown
--- finished re-building ‘SW_Cookbook.Rmd’

--- re-building ‘SW_QuickStart.Rmd’ using rmarkdown
Killed
SUMMARY: processing the following file failed:
  ‘SW_QuickStart.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SpliceWiz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘SpliceWiz’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c BAM2blocks.cpp -o BAM2blocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c FastaReader.cpp -o FastaReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c FragmentBlocks.cpp -o FragmentBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c GZTools.cpp -o GZTools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c covTools.cpp -o covTools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c main.cpp -o main.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c swEngine.cpp -o swEngine.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fPIC  -g -O2  -Wall -c synthReadGenerator.cpp -o synthReadGenerator.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o SpliceWiz.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_FragmentsMap.o ReadBlockProcessor_TandemJunctions.o covTools.o main.o swEngine.o synthReadGenerator.o -fopenmp -DSPLICEWIZ -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-SpliceWiz/00new/SpliceWiz/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 (SpliceWiz)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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(SpliceWiz)
Loading required package: NxtIRFdata
SpliceWiz package loaded with 2 threads
Use setSWthreads() to set the number of SpliceWiz threads
> 
> test_check("SpliceWiz")
Loading required package: Rsubread
Feb 07 16:45:53 Converting FASTA to local TwoBitFile...done
Feb 07 16:45:55 Connecting to genome TwoBitFile...done
Feb 07 16:45:55 Making local copy of GTF file...done
Feb 07 16:45:55 Extracting temp genome FASTA from TwoBit file
Feb 07 16:46:02 Generating synthetic reads, saving to /tmp/Rtmpb6n8cv/refWithMapExcl/Mappability/Reads.fa
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Feb 07 16:46:02 Cleaning temp genome / gene annotation files


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.13.2

//================================= setting ==================================\\
||                                                                            ||
|| Function      : Read alignment + Junction detection (RNA-Seq)              ||
|| Input file    : Reads.fa                                                   ||
|| Output file   : AlignedReads.bam (BAM)                                     ||
|| Index name    : reference_index                                            ||
||                                                                            ||
||                    ------------------------------------                    ||
||                                                                            ||
||                               Threads : 1                                  ||
||                          Phred offset : 33                                 ||
||                             Min votes : 1 / 14                             ||
||                        Max mismatches : 3                                  ||
||                      Max indel length : 5                                  ||
||            Report multi-mapping reads : yes                                ||
|| Max alignments per multi-mapping read : 1                                  ||
||                           Annotations : transcripts.gtf (GTF)              ||
||                                                                            ||
\\============================================================================//

//=============== Running (07-Feb-2023 16:46:02, pid=4178521) ================\\
||                                                                            ||
|| Check the input reads.                                                     ||
|| The input file contains base space reads.                                  ||
|| Initialise the memory objects.                                             ||
|| Estimate the mean read length.                                             ||
|| Create the output BAM file.                                                ||
|| Check the index.                                                           ||
Unable top open index './reference_index'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix. 

Killed