Multiple platform build/check report for BioC 3.8 - CHECK report for bcSeq on merida1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bcSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bcSeq_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/bcSeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bcSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bcSeq’ version ‘1.4.1’
* 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 ‘bcSeq’ can be installed ... OK
* 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 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 ... OK
* 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 ... 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 compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_bcSeq.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/bcSeq.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bcSeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘bcSeq’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Matrix/include" -I/usr/local/include  -pthread -fPIC  -Wall -g -O2 -c CRISPR_matching.cpp -o CRISPR_matching.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Matrix/include" -I/usr/local/include  -pthread -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Matrix/include" -I/usr/local/include  -pthread -fPIC  -Wall -g -O2 -c Trie_edit.cpp -o Trie_edit.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Matrix/include" -I/usr/local/include  -pthread -fPIC  -Wall -g -O2 -c Trie_hamming.cpp -o Trie_hamming.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Matrix/include" -I/usr/local/include  -pthread -fPIC  -Wall -g -O2 -c Trie_util.cpp -o Trie_util.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Matrix/include" -I/usr/local/include  -pthread -fPIC  -Wall -g -O2 -c alignment.cpp -o alignment.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Matrix/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Matrix/include" -I/usr/local/include  -pthread -fPIC  -Wall -g -O2 -c trimRead.cpp -o trimRead.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Matrix/include" -I/usr/local/include  -pthread -fPIC  -Wall -g -O2 -c uniqueBar.cpp -o uniqueBar.o
uniqueBar.cpp:21:9: warning: unused variable 'length' [-Wunused-variable]
    int length = 0;
        ^
1 warning generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o bcSeq.so CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/bcSeq/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
* DONE (bcSeq)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(bcSeq)
> #devtools::load_all("../")
> #### Set the seed
> set.seed(4523)
> 
> #### Generate barcode
> lFName    <- "./libFile.fasta"
> bases     <- c(rep('A', 4), rep('C',4), rep('G',4), rep('T',4))
> numOfBars <- 7
> Barcodes  <- rep(NA, numOfBars*2)
> for (i in 1:numOfBars){
+     Barcodes[2*i-1] <- paste0(">barcode_ID: ", i)
+     Barcodes[2*i]   <- paste(sample(bases, length(bases)), collapse = '')
+ }
> write(Barcodes, lFName)
> 
> #### Generate reads and phred score
> rFName     <- "./readFile.fastq"
> numOfReads <- 8
> Reads      <- rep(NA, numOfReads*4)
> for (i in 1:numOfReads){
+     Reads[4*i-3] <- paste0("@read_ID_",i)
+     Reads[4*i-2] <- Barcodes[2*sample(1:numOfBars,1,
+                   replace=TRUE, prob=seq(1:numOfBars))]
+     Reads[4*i-1] <- "+"
+     Reads[4*i]   <- paste(rawToChar(as.raw(
+                   33+sample(20:30, length(bases),replace=TRUE))),
+                   collapse='')
+ }
> write(Reads, rFName)
> 
> #### perform alignment 
> ReadFile <- "./readFile.fastq"
> BarFile  <- "./libFile.fasta"
> outFile  <- "./countH.csv"
> 
> #### with default output for bcSeq_hamming
> res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
+     tMat = NULL, numThread = 2, count_only = TRUE )
Running hamming search with 4 sequences per thread in 2 threads
Compiling results
> res <- read.csv(outFile, header=FALSE)
> res
                V1 V2
1 TCCGACGCAAGTGATT  0
2 TATCGCTGAATGAGCC  0
3 AATCGGTGGCACATCT  2
4 GAGTCTCTGGATACAC  1
5 CGACAGTAATCGCTTG  2
6 ACCAGTAGTCAGGTTC  1
7 TAAGCAGGCGTCTTAC  2
> 
> #### with return of alignment probability matrix to R
> #outFile  <- "./countH2.csv"
> #res <- bcSeq_hamming(ReadFile, BarFile, outFile, misMatch = 2,
> #    tMat = NULL, numThread = 2, count_only = FALSE )
> #res 
> 
> #### with default output for bcSeq_edit
> outFile  <- "./countE.csv"
> res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
+     tMat = NULL, numThread = 2, count_only = TRUE,
+     gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
+     pen_max = 7)
Running levenshtein search with 4 sequences per thread in 2 threads
Compiling results
> res <- read.csv(outFile, header=FALSE)
> res
                V1 V2
1 TCCGACGCAAGTGATT  0
2 TATCGCTGAATGAGCC  0
3 AATCGGTGGCACATCT  2
4 GAGTCTCTGGATACAC  1
5 CGACAGTAATCGCTTG  2
6 ACCAGTAGTCAGGTTC  1
7 TAAGCAGGCGTCTTAC  2
> 
> #### with return of alignment probability matrix to R
> #outFile  <- "./countE2.csv"
> #res <- bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
> #    tMat = NULL, numThread = 2, count_only = FALSE,
> #    gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
> #    pen_max = 7)
> #res
> 
> #### user-defined probability model
> comstomizeP <- function(m, x, y)
+ {
+     x * (1 - log(2) + log(1 + m / (m + y) ) )
+ }
> outFile = "comstomizeP.csv"
> bcSeq_edit(ReadFile, BarFile, outFile, misMatch = 2,
+     tMat = NULL, numThread = 2, count_only = TRUE,
+     gap_left = 2, ext_left = 1, gap_right = 2, ext_right = 1,
+     pen_max = 7, userProb = comstomizeP)
Running levenshtein search with 4 sequences per thread in 2 threads
Compiling results
> 
> proc.time()
   user  system elapsed 
  4.650   0.294   4.945

name	user	system	elapsed
bcSeq-package	0.201	0.012	0.098
bcSeq_edit	3.657	0.034	1.078
bcSeq_hamming	0.141	0.028	0.170
trimRead	0.098	0.037	0.136
uniqueBar	0.009	0.001	0.010

CHECK report for bcSeq on merida1

Summary

Command output

Installation output

Tests output

Example timings