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CHECK report for exomePeak on merida2

This page was generated on 2019-04-09 13:28:46 -0400 (Tue, 09 Apr 2019).

Package 518/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
exomePeak 2.17.0
Lin Zhang , Lian Liu , Jia Meng
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/exomePeak
Branch: master
Last Commit: 979b0d0
Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: exomePeak
Version: 2.17.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:exomePeak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings exomePeak_2.17.0.tar.gz
StartedAt: 2019-04-09 00:48:51 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:52:09 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 198.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: exomePeak.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:exomePeak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings exomePeak_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exomePeak/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomePeak’ version ‘2.17.0’
* 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 ‘exomePeak’ 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 ... NOTE
Packages in Depends field not imported from:
  ‘GenomicAlignments’ ‘GenomicFeatures’ ‘Rsamtools’ ‘rtracklayer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.bed2grangeslist: no visible global function definition for ‘head’
.bed2grangeslist: no visible global function definition for ‘makeTxDb’
.bed2grangeslist: no visible global function definition for ‘exonsBy’
.exomepeak_notification: no visible global function definition for
  ‘mcols<-’
.get.bam.chrs: no visible global function definition for ‘indexBam’
.get.bam.chrs: no visible global function definition for ‘ScanBamParam’
.get.bam.chrs: no visible global function definition for ‘scanBam’
.get.bam.read.length: no visible global function definition for
  ‘indexBam’
.get.bam.read.length: no visible global function definition for
  ‘ScanBamParam’
.get.bam.read.length: no visible global function definition for
  ‘scanBam’
.get.bam.read.length: no visible global function definition for
  ‘median’
.get.check.points.reads.count: no visible global function definition
  for ‘IRangesList’
.get.check.points.reads.count: no visible global function definition
  for ‘IRanges’
.get.check.points.reads.count: no visible global function definition
  for ‘ScanBamParam’
.get.check.points.reads.count: no visible global function definition
  for ‘scanBam’
.read.gtf: no visible global function definition for ‘makeTxDbFromUCSC’
.read.gtf: no visible global function definition for ‘makeTxDbFromGFF’
.read.gtf: no visible global function definition for ‘columns’
.read.gtf: no visible global function definition for ‘keys’
.read.gtf: no visible global function definition for ‘select’
.readTxDb2: no visible global function definition for
  ‘makeTxDbFromUCSC’
.readTxDb2: no visible global function definition for ‘makeTxDbFromGFF’
.report.diff.peak.based.on.result: no visible global function
  definition for ‘write.table’
.report.peak.based.on.result: no visible global function definition for
  ‘write.table’
.xls2Grangeslist: no visible global function definition for
  ‘read.table’
.xls2Grangeslist: no visible global function definition for ‘head’
.xls2Grangeslist: no visible global function definition for ‘makeTxDb’
.xls2Grangeslist: no visible global function definition for ‘exonsBy’
.xls2Grangeslist: no visible global function definition for ‘mcols<-’
RMT: no visible global function definition for ‘read.table’
RMT: no visible global function definition for ‘write.table’
RMT: no visible global function definition for ‘findOverlaps’
RMT: no visible global function definition for ‘queryHits’
RMT: no visible global function definition for ‘subjectHits’
RMT: no visible global function definition for ‘ranges’
RMT: no visible global function definition for ‘exonsBy’
RMT: no visible global function definition for ‘readGAlignments’
RMT: no visible global function definition for ‘ScanBamParam’
RMT: no visible global function definition for ‘scanBam’
RMT: no visible global function definition for ‘countOverlaps’
RMT: no visible global function definition for ‘width’
RMT: no visible global function definition for ‘var’
bltest: no visible global function definition for ‘pchisq’
bltest: no visible global function definition for ‘p.adjust’
ctest: no visible global function definition for ‘pbinom’
ctest: no visible global function definition for ‘p.adjust’
exomepeak: no visible global function definition for ‘indexBam’
rhtest: no visible global function definition for ‘phyper’
rhtest: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  IRanges IRangesList ScanBamParam columns countOverlaps exonsBy
  findOverlaps head indexBam keys makeTxDb makeTxDbFromGFF
  makeTxDbFromUCSC mcols<- median p.adjust pbinom pchisq phyper
  queryHits ranges read.table readGAlignments scanBam select
  subjectHits var width write.table
Consider adding
  importFrom("stats", "median", "p.adjust", "pbinom", "pchisq", "phyper",
             "var")
  importFrom("utils", "head", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: RMT.Rd:60-62: Dropping empty section \details
prepare_Rd: RMT.Rd:74-76: Dropping empty section \note
prepare_Rd: RMT.Rd:80-82: Dropping empty section \seealso
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘exomePeak-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RMT
> ### Title: Extract a combinatorial RNA methylome from multiple biological
> ###   conditions or replicates.
> ### Aliases: RMT
> ### Keywords: MeRIP-Seq
> 
> ### ** Examples
> 
> # the RESPECT R-package has two main functions:
> # 1. exome-based peak
> # 2. compute reads counts, rpkm and fold change
> # please feel free to contact liulian19860905@163.com for any questions
> 
> # load library and specify the parameters
> gene_anno_gtf <- system.file("extdata", "example.gtf", package="exomePeak")
> f1 <- system.file("extdata", "IP1.bam", package="exomePeak")
> f2 <- system.file("extdata", "IP2.bam", package="exomePeak")
> f3 <- system.file("extdata", "IP3.bam", package="exomePeak")
> f4 <- system.file("extdata", "IP4.bam", package="exomePeak")
> ip_bam <- c(f1,f2,f3,f4)
> f1 <- system.file("extdata", "Input1.bam", package="exomePeak")
> f2 <- system.file("extdata", "Input2.bam", package="exomePeak")
> f3 <- system.file("extdata", "Input3.bam", package="exomePeak")
> input_bam <- c(f1,f2,f3)
> input2bam <- list(4)
> input2bam[[1]] <- c(1,2) # the 1st ip sample uses the 1st & 2nd input samples as control
> input2bam[[2]] <- c(1,2) # the 2nd ip sample uses the 1st & 2nd input samples as control
> input2bam[[3]] <- c(1,2) # the 3rd ip sample uses the 1st & 2nd input samples as control
> input2bam[[4]] <- c(3)   # the 4th ip sample uses the 3rd input sample as control
> 
> # Extract the combinatorial RNA methylome
> # unfortunately, this function has not been optimized for parallel processing.
> # This part will take a really long time on real data
> RMT(INPUT_BAM=input_bam, IP_BAM=ip_bam, INPUT2IP=input2bam, GENE_ANNO_GTF=gene_anno_gtf)
[1] "Processing IP sample 1"
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:many mapping between keys and columns
[1] "Divide transcriptome into chr-gene-batch sections ..."
[1] "Get Reads Count ..."
[1] "This step may take a few hours ..."
[1] "100 %"
[1] "Get all the peaks ..."
[1] "Get the consistent peaks ..."
[1] "---------------------------------"
[1] "The bam files used:"
[1] "1 IP replicate(s)"
[1] "2 Input replicate(s)"
[1] "---------------------------------"
[1] "Peak calling result: "
[1] "15 peaks detected on merged data."
[1] "Please check 'peak.bed/xls' under /Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck/RMT_Result/temp/IP_rep_1"
[1] "15 consistent peaks detected on every replicates. (Recommended list)"
[1] "Please check 'con_peak.bed/xls' under /Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck/RMT_Result/temp/IP_rep_1"
[1] "Processing IP sample 2"
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:many mapping between keys and columns
[1] "Divide transcriptome into chr-gene-batch sections ..."
[1] "Get Reads Count ..."
[1] "This step may take a few hours ..."
[1] "100 %"
[1] "Get all the peaks ..."
[1] "Get the consistent peaks ..."
[1] "---------------------------------"
[1] "The bam files used:"
[1] "1 IP replicate(s)"
[1] "2 Input replicate(s)"
[1] "---------------------------------"
[1] "Peak calling result: "
[1] "19 peaks detected on merged data."
[1] "Please check 'peak.bed/xls' under /Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck/RMT_Result/temp/IP_rep_2"
[1] "19 consistent peaks detected on every replicates. (Recommended list)"
[1] "Please check 'con_peak.bed/xls' under /Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck/RMT_Result/temp/IP_rep_2"
[1] "Processing IP sample 3"
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:many mapping between keys and columns
[1] "Divide transcriptome into chr-gene-batch sections ..."
[1] "Get Reads Count ..."
[1] "This step may take a few hours ..."
[1] "100 %"
[1] "Get all the peaks ..."
[1] "Get the consistent peaks ..."
[1] "---------------------------------"
[1] "The bam files used:"
[1] "1 IP replicate(s)"
[1] "2 Input replicate(s)"
[1] "---------------------------------"
[1] "Peak calling result: "
[1] "14 peaks detected on merged data."
[1] "Please check 'peak.bed/xls' under /Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck/RMT_Result/temp/IP_rep_3"
[1] "14 consistent peaks detected on every replicates. (Recommended list)"
[1] "Please check 'con_peak.bed/xls' under /Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck/RMT_Result/temp/IP_rep_3"
[1] "Processing IP sample 4"
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:many mapping between keys and columns
[1] "Divide transcriptome into chr-gene-batch sections ..."
[1] "Get Reads Count ..."
[1] "This step may take a few hours ..."
[1] "100 %"
[1] "Get all the peaks ..."
[1] "Get the consistent peaks ..."
[1] "---------------------------------"
[1] "The bam files used:"
[1] "1 IP replicate(s)"
[1] "1 Input replicate(s)"
[1] "---------------------------------"
[1] "Peak calling result: "
[1] "5 peaks detected on merged data."
[1] "Please check 'peak.bed/xls' under /Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck/RMT_Result/temp/IP_rep_4"
[1] "5 consistent peaks detected on every replicates. (Recommended list)"
[1] "Please check 'con_peak.bed/xls' under /Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck/RMT_Result/temp/IP_rep_4"
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
exomePeak
 --- call from context --- 
RMT(INPUT_BAM = input_bam, IP_BAM = ip_bam, INPUT2IP = input2bam, 
    GENE_ANNO_GTF = gene_anno_gtf)
 --- call from argument --- 
if (x < y) {
    num[matrix_overlap[i, 1][1][[1]]] <- matrix_overlap[i, 1][1][[1]]
} else if (x > y) {
    num[matrix_overlap[i, 2][1][[1]]] <- matrix_overlap[i, 2][1][[1]]
} else {
    num[matrix_overlap[i, 1][1][[1]]] <- matrix_overlap[i, 1][1][[1]]
    num[matrix_overlap[i, 2][1][[1]]] <- matrix_overlap[i, 2][1][[1]]
}
 --- R stacktrace ---
where 1: RMT(INPUT_BAM = input_bam, IP_BAM = ip_bam, INPUT2IP = input2bam, 
    GENE_ANNO_GTF = gene_anno_gtf)

 --- value of length: 4 type: logical ---
[1] FALSE  TRUE FALSE  TRUE
 --- function from context --- 
function (INPUT_BAM, IP_BAM, INPUT2IP = NA, GENE_ANNO_GTF = NA, 
    GENOME = NA, UCSC_TABLE_NAME = "knownGene", TXDB = NA, EXOME_OUTPUT_DIR = NA, 
    RMT_OUTPUT_DIR = NA, RMT_EXPERIMENT_NAME = "RMT_Result") 
{
    PARAMETERS = list()
    PARAMETERS$INPUT_BAM = INPUT_BAM
    PARAMETERS$IP_BAM = IP_BAM
    PARAMETERS$INPUT2IP = INPUT2IP
    PARAMETERS$EXOME_OUTPUT_DIR = EXOME_OUTPUT_DIR
    PARAMETERS$GO_OUTPUT_DIR = RMT_OUTPUT_DIR
    PARAMETERS$GO_EXPERIMENT_NAME = RMT_EXPERIMENT_NAME
    PARAMETERS$GENE_ANNO_GTF = GENE_ANNO_GTF
    PARAMETERS$GENOME = GENOME
    PARAMETERS$UCSC_TABLE_NAME = UCSC_TABLE_NAME
    PARAMETERS$TXDB = TXDB
    if (is.na(PARAMETERS$EXOME_OUTPUT_DIR)) {
        PARAMETERS$EXOME_OUTPUT_DIR <- getwd()
    }
    if (is.na(PARAMETERS$GO_OUTPUT_DIR)) {
        PARAMETERS$GO_OUTPUT_DIR <- getwd()
    }
    input_length <- length(PARAMETERS$INPUT_BAM)
    ip_length <- length(PARAMETERS$IP_BAM)
    all_filepath <- vector()
    temp1 <- is.na(PARAMETERS$INPUT2IP)
    flag <- temp1[1]
    if (flag) {
        for (i in 1:ip_length) {
            experiment_name = paste(PARAMETERS$GO_EXPERIMENT_NAME, 
                "/temp/IP_rep_", i, sep = "")
            all_filepath[i] = PARAMETERS$IP_BAM[i]
            print(paste("Processing IP sample", i))
            temp <- exomepeak(GENE_ANNO_GTF = GENE_ANNO_GTF, 
                GENOME = GENOME, UCSC_TABLE_NAME = UCSC_TABLE_NAME, 
                TXDB = TXDB, IP_BAM = c(PARAMETERS$IP_BAM[i]), 
                INPUT_BAM = c(PARAMETERS$INPUT_BAM[i]), OUTPUT_DIR = PARAMETERS$EXOME_OUTPUT_DIR, 
                POISSON_MEAN_RATIO = 1, EXPERIMENT_NAME = experiment_name)
        }
    }
    else {
        for (i in 1:ip_length) {
            experiment_name = paste(PARAMETERS$GO_EXPERIMENT_NAME, 
                "/temp/IP_rep_", i, sep = "")
            input_bam = PARAMETERS$INPUT_BAM[PARAMETERS$INPUT2IP[[i]][1]]
            if (length(PARAMETERS$INPUT2IP[[i]]) > 1) {
                for (j in 2:length(PARAMETERS$INPUT2IP[[i]])) {
                  input_bam = c(input_bam, c(PARAMETERS$INPUT_BAM[PARAMETERS$INPUT2IP[[i]][j]]))
                }
            }
            all_filepath[i] <- paste(PARAMETERS$EXOME_OUTPUT_DIR, 
                experiment_name, sep = "/")
            print(paste("Processing IP sample", i))
            temp <- exomepeak(GENE_ANNO_GTF = GENE_ANNO_GTF, 
                GENOME = GENOME, UCSC_TABLE_NAME = UCSC_TABLE_NAME, 
                TXDB = TXDB, IP_BAM = c(PARAMETERS$IP_BAM[i]), 
                INPUT_BAM = input_bam, OUTPUT_DIR = PARAMETERS$EXOME_OUTPUT_DIR, 
                POISSON_MEAN_RATIO = 1, EXPERIMENT_NAME = experiment_name)
        }
    }
    for (i in 1:length(all_filepath)) {
        path <- paste(all_filepath[i], "peak.xls", sep = "/")
        bam_file <- read.table(path, sep = "\t", header = FALSE)
        if (i == 1) {
            all_peak <- bam_file
        }
        else {
            all_peak = rbind(all_peak, bam_file[2:nrow(bam_file), 
                ])
        }
    }
    dir.create(paste(PARAMETERS$GO_OUTPUT_DIR, PARAMETERS$GO_EXPERIMENT_NAME, 
        sep = "/"), recursive = TRUE, showWarnings = FALSE)
    dir = paste(PARAMETERS$GO_OUTPUT_DIR, PARAMETERS$GO_EXPERIMENT_NAME, 
        sep = "/")
    write.table(all_peak, paste(dir, "all_peak.xls", sep = "/"), 
        sep = "\t", quote = FALSE, col.names = FALSE, row.names = FALSE)
    filepath = paste(dir, "all_peak.xls", sep = "/")
    matrix_peak_read = read.table(filepath, header = TRUE, stringsAsFactors = FALSE)
    ori_peak <- .xls2Grangeslist(filepath)
    overlaps <- findOverlaps(ori_peak, ori_peak)
    matrix_overlap <- matrix(0, length(overlaps), 2)
    matrix_overlap[, 1] <- queryHits(overlaps)
    matrix_overlap[, 2] <- subjectHits(overlaps)
    num <- c(rep(0, length(ori_peak)))
    for (i in 1:nrow(matrix_overlap)) {
        if (matrix_overlap[i, 1][1][[1]] != matrix_overlap[i, 
            2][1][[1]]) {
            x <- ranges(ori_peak[matrix_overlap[i, 1]])[[1]]@width
            y <- ranges(ori_peak[matrix_overlap[i, 2]])[[1]]@width
            if (x < y) {
                num[matrix_overlap[i, 1][1][[1]]] <- matrix_overlap[i, 
                  1][1][[1]]
            }
            else if (x > y) {
                num[matrix_overlap[i, 2][1][[1]]] <- matrix_overlap[i, 
                  2][1][[1]]
            }
            else {
                num[matrix_overlap[i, 1][1][[1]]] <- matrix_overlap[i, 
                  1][1][[1]]
                num[matrix_overlap[i, 2][1][[1]]] <- matrix_overlap[i, 
                  2][1][[1]]
            }
        }
    }
    peak <- ori_peak[num == 0]
    tab <- which(num == 0)
    write.table(matrix_peak_read[tab, ], paste(dir, "merged_peak.xls", 
        sep = "/"), sep = "\t", quote = FALSE, col.names = TRUE, 
        row.names = FALSE)
    write.table(matrix_peak_read[tab, 1:12], paste(dir, "merged_peak.bed", 
        sep = "/"), sep = "\t", quote = FALSE, col.names = FALSE, 
        row.names = FALSE)
    txdb <- .readTxDb2(PARAMETERS)
    exonRanges <- exonsBy(txdb, "gene")
    rpkm_input <- matrix(0, length(peak), length(PARAMETERS$INPUT_BAM))
    rpkm_ip <- matrix(0, length(peak), length(PARAMETERS$IP_BAM))
    count_input <- matrix(0, length(peak), length(PARAMETERS$INPUT_BAM))
    count_ip <- matrix(0, length(peak), length(PARAMETERS$IP_BAM))
    for (i in 1:length(PARAMETERS$INPUT_BAM)) {
        filepath <- PARAMETERS$INPUT_BAM[i]
        aligns <- readGAlignments(filepath)
        para <- ScanBamParam(what = "mapq")
        mapq <- scanBam(filepath, param = para)[[1]][[1]]
        mapq[is.na(mapq)] <- 255
        ID_keep <- (mapq > 30)
        filtered <- aligns[ID_keep]
        id <- countOverlaps(filtered, exonRanges)
        transcriptome_filtered_aligns <- filtered[id > 0]
        counts <- countOverlaps(peak, transcriptome_filtered_aligns)
        count_input[, i] <- counts
        numBases <- sum(width(peak))
        geneLengthsInKB <- numBases/1000
        millionsMapped <- length(transcriptome_filtered_aligns)/1e+06
        rpm <- counts/millionsMapped
        rpkm_input[, i] <- rpm/geneLengthsInKB
    }
    write.table(count_input, paste(dir, "count_input.xls", sep = "/"), 
        sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
    write.table(rpkm_input, paste(dir, "rpkm_input.xls", sep = "/"), 
        sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
    for (i in 1:length(PARAMETERS$IP_BAM)) {
        filepath <- PARAMETERS$IP_BAM[i]
        aligns <- readGAlignments(filepath)
        para <- ScanBamParam(what = "mapq")
        mapq <- scanBam(filepath, param = para)[[1]][[1]]
        mapq[is.na(mapq)] <- 255
        ID_keep <- (mapq > 30)
        filtered <- aligns[ID_keep]
        id <- countOverlaps(filtered, exonRanges)
        transcriptome_filtered_aligns <- filtered[id > 0]
        counts <- countOverlaps(peak, transcriptome_filtered_aligns)
        count_ip[, i] <- counts
        numBases <- sum(width(peak))
        geneLengthsInKB <- numBases/1000
        millionsMapped <- length(transcriptome_filtered_aligns)/1e+06
        rpm <- counts/millionsMapped
        rpkm_ip[, i] <- rpm/geneLengthsInKB
    }
    write.table(count_ip, paste(dir, "count_ip.xls", sep = "/"), 
        sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
    write.table(rpkm_ip, paste(dir, "rpkm_ip.xls", sep = "/"), 
        sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
    matrix_log2_fc = matrix(0, length(peak), ip_length)
    if (is.na(PARAMETERS$INPUT2IP)) {
        for (i in 1:ip_length) {
            matrix_log2_fc[, i] <- log2(rpkm_ip[, i] + 0.01) - 
                log2(rpkm_input[, i] + 0.01)
        }
    }
    else {
        for (i in 1:ip_length) {
            if (length(PARAMETERS$INPUT2IP[[i]]) == 1) {
                matrix_log2_fc[, i] <- log2(rpkm_ip[, i] + 0.01) - 
                  log2(rpkm_input[, PARAMETERS$INPUT2IP[[i]]] + 
                    0.01)
            }
            else {
                sum = matrix(0, length(peak), 1)
                for (j in 1:length(PARAMETERS$INPUT2IP[i])) {
                  sum = sum + rpkm_input[, PARAMETERS$INPUT2IP[[i]][j]]
                }
                matrix_log2_fc[, i] <- log2(rpkm_ip[, i] + 0.01) - 
                  log2(sum + 0.01)
            }
        }
    }
    v <- matrix_log2_fc[, 1]
    for (i in 1:nrow(matrix_log2_fc)) {
        v[i] <- var(matrix_log2_fc[i, ])
    }
    matrix_log2_fc <- cbind(tab, matrix_log2_fc[1:nrow(matrix_log2_fc), 
        ], matrix_peak_read[tab, ])
    write.table(matrix_log2_fc, paste(dir, "all_information.xls", 
        sep = "/"), sep = "\t", quote = FALSE, col.names = TRUE, 
        row.names = FALSE)
    file.remove(paste(dir, "all_peak.xls", sep = "/"))
    file.remove(paste(dir, "all_information.xls", sep = "/"))
    print("***************************")
    print("***************************")
    print(paste("The combinatorial RNA methylome is generated under:", 
        dir))
    print("Including:")
    print("1. Merged Peaks")
    print("2. Merged Peaks in BED format")
    print("3. Reads count for every peak in every bam file")
    print("4. RPKM for every peak in every bam file")
}
<bytecode: 0x7fb77a1985f8>
<environment: namespace:exomePeak>
 --- function search by body ---
Function RMT in namespace exomePeak has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
* 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 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/exomePeak.Rcheck/00check.log’
for details.


Installation output

exomePeak.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL exomePeak
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘exomePeak’ ...
** 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 (exomePeak)

Tests output


Example timings

exomePeak.Rcheck/exomePeak-Ex.timings

nameusersystemelapsed