CRAN Package Check Results for Package rtfbs

Last updated on 2019-12-07 07:56:29 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.9 63.91 41.40 105.31 ERROR
r-devel-linux-x86_64-debian-gcc 0.3.9 48.44 37.26 85.70 WARN
r-devel-linux-x86_64-fedora-clang 0.3.9 137.91 NOTE
r-devel-linux-x86_64-fedora-gcc 0.3.9 144.28 WARN
r-devel-windows-ix86+x86_64 0.3.9 143.00 164.00 307.00 OK
r-devel-windows-ix86+x86_64-gcc8 0.3.9 156.00 172.00 328.00 WARN
r-patched-linux-x86_64 0.3.9 52.13 45.10 97.23 WARN
r-patched-solaris-x86 0.3.9 200.30 OK
r-release-linux-x86_64 0.3.9 53.77 45.39 99.16 WARN
r-release-windows-ix86+x86_64 0.3.9 206.00 142.00 348.00 OK
r-release-osx-x86_64 0.3.9 OK
r-oldrel-windows-ix86+x86_64 0.3.9 159.00 158.00 317.00 OK
r-oldrel-osx-x86_64 0.3.9 OK

Check Details

Version: 0.3.9
Check: examples
Result: ERROR
    Running examples in 'rtfbs-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: build.mm
    > ### Title: Build Markov Model to represent sequences in an MS object
    > ### Aliases: build.mm
    >
    > ### ** Examples
    >
    > require("rtfbs")
    > exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
    > seqFile <- "input.fas"
    > unzip(exampleArchive, seqFile)
    > # Read in FASTA file "input.fas" from the examples into an
    > # MS (multiple sequences) object
    > ms <- read.ms(seqFile)
    > # Build a 3rd order Markov Model to represent the sequences
    > # in the MS object "ms". The Model will be a list of
    > # matrices corrisponding in size to the order of the
    > # Markov Model
    > mm <- build.mm(ms, 3);
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    rtfbs
     --- call from context ---
    label.matrix(mat[[entry]], columnsOnly)
     --- call from argument ---
    if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
    } else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
    }
     --- R stacktrace ---
    where 1: label.matrix(mat[[entry]], columnsOnly)
    where 2: label.matrix(x)
    where 3: build.mm(ms, 3)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (mat, columnsOnly = FALSE)
    {
     check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     }
     else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     mat
    }
    <bytecode: 0x39db9e0>
    <environment: namespace:rtfbs>
     --- function search by body ---
    Function label.matrix in namespace rtfbs has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(mat) == "list") { : the condition has length > 1
    Calls: build.mm -> label.matrix -> label.matrix
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.9
Check: tests
Result: ERROR
     Running 'build_mm.R' [1s/1s]
     Running 'calc_fdr.R' [1s/1s]
     Running 'gcContent_ms.R' [0s/0s]
     Running 'groupByGC_ms.R' [1s/1s]
     Running 'makeFdrPlot.R' [1s/1s]
     Running 'output_sites.R' [1s/2s]
     Running 'read_ms.R' [0s/1s]
     Running 'read_pwm.R' [1s/2s]
     Running 'score_ms.R' [1s/2s]
     Running 'simulate_ms.R' [1s/2s]
    Running the tests in 'tests/build_mm.R' failed.
    Complete output:
     > require("rtfbs")
     Loading required package: rtfbs
     > exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
     > seqFile <- "input.fas"
     > unzip(exampleArchive, seqFile)
     > # Read in FASTA file "input.fas" from the examples into an
     > # MS (multiple sequences) object
     > ms <- read.ms(seqFile)
     > # Build a 3rd order Markov Model to represent the sequences
     > # in the MS object "ms". The Model will be a list of
     > # matrices corrisponding in size to the order of the
     > # Markov Model
     > mm <- build.mm(ms, 3);
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     rtfbs
     --- call from context ---
     label.matrix(mat[[entry]], columnsOnly)
     --- call from argument ---
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     } else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     --- R stacktrace ---
     where 1: label.matrix(mat[[entry]], columnsOnly)
     where 2: label.matrix(x)
     where 3: build.mm(ms, 3)
    
     --- value of length: 2 type: logical ---
     [1] FALSE FALSE
     --- function from context ---
     function (mat, columnsOnly = FALSE)
     {
     check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     }
     else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     mat
     }
     <bytecode: 0x4e4d9a8>
     <environment: namespace:rtfbs>
     --- function search by body ---
     Function label.matrix in namespace rtfbs has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(mat) == "list") { : the condition has length > 1
     Calls: build.mm -> label.matrix -> label.matrix
     Execution halted
    Running the tests in 'tests/calc_fdr.R' failed.
    Complete output:
     > require("rtfbs")
     Loading required package: rtfbs
     > exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
     > seqFile <- "input.fas"
     > unzip(exampleArchive, seqFile)
     > # Read in FASTA file "input.fas" from the examples into an
     > # MS (multiple sequences) object
     > ms <- read.ms(seqFile);
     > pwmFile <- "pwm.meme"
     > unzip(exampleArchive, pwmFile)
     > # Read in Position Weight Matrix (PWM) from MEME file from
     > # the examples into a Matrix object
     > pwm <- read.pwm(pwmFile)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     rtfbs
     --- call from context ---
     label.matrix(x, columnsOnly = TRUE)
     --- call from argument ---
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     } else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     --- R stacktrace ---
     where 1: label.matrix(x, columnsOnly = TRUE)
     where 2: read.pwm(pwmFile)
    
     --- value of length: 2 type: logical ---
     [1] FALSE FALSE
     --- function from context ---
     function (mat, columnsOnly = FALSE)
     {
     check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     }
     else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     mat
     }
     <bytecode: 0x38c77c8>
     <environment: namespace:rtfbs>
     --- function search by body ---
     Function label.matrix in namespace rtfbs has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(mat) == "list") { : the condition has length > 1
     Calls: read.pwm -> label.matrix
     Execution halted
    Running the tests in 'tests/makeFdrPlot.R' failed.
    Complete output:
     > require("rtfbs")
     Loading required package: rtfbs
     > exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
     > seqFile <- "input.fas"
     > unzip(exampleArchive, seqFile)
     > # Read in FASTA file "input.fas" from the examples into an
     > # MS (multiple sequences) object
     > ms <- read.ms(seqFile);
     > pwmFile <- "pwm.meme"
     > unzip(exampleArchive, pwmFile)
     > # Read in Position Weight Matrix (PWM) from MEME file from
     > # the examples into a Matrix object
     > pwm <- read.pwm(pwmFile)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     rtfbs
     --- call from context ---
     label.matrix(x, columnsOnly = TRUE)
     --- call from argument ---
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     } else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     --- R stacktrace ---
     where 1: label.matrix(x, columnsOnly = TRUE)
     where 2: read.pwm(pwmFile)
    
     --- value of length: 2 type: logical ---
     [1] FALSE FALSE
     --- function from context ---
     function (mat, columnsOnly = FALSE)
     {
     check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     }
     else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     mat
     }
     <bytecode: 0x2fec7c8>
     <environment: namespace:rtfbs>
     --- function search by body ---
     Function label.matrix in namespace rtfbs has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(mat) == "list") { : the condition has length > 1
     Calls: read.pwm -> label.matrix
     Execution halted
    Running the tests in 'tests/output_sites.R' failed.
    Complete output:
     > require("rtfbs")
     Loading required package: rtfbs
     > exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
     > seqFile <- "input.fas"
     > unzip(exampleArchive, seqFile)
     > # Read in FASTA file "input.fas" from the examples into an
     > # MS (multiple sequences) object
     > ms <- read.ms(seqFile);
     > pwmFile <- "pwm.meme"
     > unzip(exampleArchive, pwmFile)
     > # Read in Position Weight Matrix (PWM) from MEME file from
     > # the examples into a Matrix object
     > pwm <- read.pwm(pwmFile)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     rtfbs
     --- call from context ---
     label.matrix(x, columnsOnly = TRUE)
     --- call from argument ---
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     } else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     --- R stacktrace ---
     where 1: label.matrix(x, columnsOnly = TRUE)
     where 2: read.pwm(pwmFile)
    
     --- value of length: 2 type: logical ---
     [1] FALSE FALSE
     --- function from context ---
     function (mat, columnsOnly = FALSE)
     {
     check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     }
     else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     mat
     }
     <bytecode: 0x30667c8>
     <environment: namespace:rtfbs>
     --- function search by body ---
     Function label.matrix in namespace rtfbs has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(mat) == "list") { : the condition has length > 1
     Calls: read.pwm -> label.matrix
     Execution halted
    Running the tests in 'tests/read_pwm.R' failed.
    Complete output:
     > require("rtfbs")
     Loading required package: rtfbs
     > exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
     > pwmFile <- "pwm.meme"
     > unzip(exampleArchive, pwmFile)
     > # Read in Position Weight Matrix (PWM) from MEME file from
     > # the examples into a Matrix object
     > pwm <- read.pwm(pwmFile)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     rtfbs
     --- call from context ---
     label.matrix(x, columnsOnly = TRUE)
     --- call from argument ---
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     } else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     --- R stacktrace ---
     where 1: label.matrix(x, columnsOnly = TRUE)
     where 2: read.pwm(pwmFile)
    
     --- value of length: 2 type: logical ---
     [1] FALSE FALSE
     --- function from context ---
     function (mat, columnsOnly = FALSE)
     {
     check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     }
     else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     mat
     }
     <bytecode: 0x3de3d90>
     <environment: namespace:rtfbs>
     --- function search by body ---
     Function label.matrix in namespace rtfbs has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(mat) == "list") { : the condition has length > 1
     Calls: read.pwm -> label.matrix
     Execution halted
    Running the tests in 'tests/score_ms.R' failed.
    Complete output:
     > require("rtfbs")
     Loading required package: rtfbs
     > exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
     > seqFile <- "input.fas"
     > unzip(exampleArchive, seqFile)
     > # Read in FASTA file "input.fas" from the examples into an
     > # MS (multiple sequences) object
     > ms <- read.ms(seqFile);
     > pwmFile <- "pwm.meme"
     > unzip(exampleArchive, pwmFile)
     > # Read in Position Weight Matrix (PWM) from MEME file from
     > # the examples into a Matrix object
     > pwm <- read.pwm(pwmFile)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     rtfbs
     --- call from context ---
     label.matrix(x, columnsOnly = TRUE)
     --- call from argument ---
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     } else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     --- R stacktrace ---
     where 1: label.matrix(x, columnsOnly = TRUE)
     where 2: read.pwm(pwmFile)
    
     --- value of length: 2 type: logical ---
     [1] FALSE FALSE
     --- function from context ---
     function (mat, columnsOnly = FALSE)
     {
     check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     }
     else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     mat
     }
     <bytecode: 0x36287c8>
     <environment: namespace:rtfbs>
     --- function search by body ---
     Function label.matrix in namespace rtfbs has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(mat) == "list") { : the condition has length > 1
     Calls: read.pwm -> label.matrix
     Execution halted
    Running the tests in 'tests/simulate_ms.R' failed.
    Complete output:
     > require("rtfbs")
     Loading required package: rtfbs
     > exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
     > seqFile <- "input.fas"
     > unzip(exampleArchive, seqFile)
     > # Read in FASTA file "input.fas" from the examples into an
     > # MS (multiple sequences) object
     > ms <- read.ms(seqFile);
     > # Build a 3rd order Markov Model to represent the sequences
     > # in the MS object "ms". The Model will be a list of
     > # matrices corrisponding in size to the order of the
     > # Markov Model
     > mm <- build.mm(ms, 3);
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     rtfbs
     --- call from context ---
     label.matrix(mat[[entry]], columnsOnly)
     --- call from argument ---
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     } else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     --- R stacktrace ---
     where 1: label.matrix(mat[[entry]], columnsOnly)
     where 2: label.matrix(x)
     where 3: build.mm(ms, 3)
    
     --- value of length: 2 type: logical ---
     [1] FALSE FALSE
     --- function from context ---
     function (mat, columnsOnly = FALSE)
     {
     check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     }
     else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     mat
     }
     <bytecode: 0x37ed9a8>
     <environment: namespace:rtfbs>
     --- function search by body ---
     Function label.matrix in namespace rtfbs has this body.
     ----------- END OF FAILURE REPORT --------------
     Error in if (class(mat) == "list") { : the condition has length > 1
     Calls: build.mm -> label.matrix -> label.matrix
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.9
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'vignette.Rnw' using Sweave
    Loading required package: rtfbs
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    rtfbs
     --- call from context ---
    label.matrix(x, columnsOnly = TRUE)
     --- call from argument ---
    if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
    } else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
    }
     --- R stacktrace ---
    where 1: label.matrix(x, columnsOnly = TRUE)
    where 2: read.pwm("pwm.meme")
    where 3: eval(expr, .GlobalEnv)
    where 4: eval(expr, .GlobalEnv)
    where 5: withVisible(eval(expr, .GlobalEnv))
    where 6: doTryCatch(return(expr), name, parentenv, handler)
    where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 8: tryCatchList(expr, classes, parentenv, handlers)
    where 9: tryCatch(expr, error = function(e) {
     call <- conditionCall(e)
     if (!is.null(call)) {
     if (identical(call[[1L]], quote(doTryCatch)))
     call <- sys.call(-4L)
     dcall <- deparse(call)[1L]
     prefix <- paste("Error in", dcall, ": ")
     LONG <- 75L
     sm <- strsplit(conditionMessage(e), "\n")[[1L]]
     w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
     if (is.na(w))
     w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
     type = "b")
     if (w > LONG)
     prefix <- paste0(prefix, "\n ")
     }
     else prefix <- "Error : "
     msg <- paste0(prefix, conditionMessage(e), "\n")
     .Internal(seterrmessage(msg[1L]))
     if (!silent && isTRUE(getOption("show.error.messages"))) {
     cat(msg, file = outFile)
     .Internal(printDeferredWarnings())
     }
     invisible(structure(msg, class = "try-error", condition = e))
    })
    where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
    where 11: evalFunc(ce, options)
    where 12: tryCatchList(expr, classes, parentenv, handlers)
    where 13: tryCatch(evalFunc(ce, options), finally = {
     cat("\n")
     sink()
    })
    where 14: driver$runcode(drobj, chunk, chunkopts)
    where 15: utils::Sweave(...)
    where 16: engine$weave(file, quiet = quiet, encoding = enc)
    where 17: doTryCatch(return(expr), name, parentenv, handler)
    where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 19: tryCatchList(expr, classes, parentenv, handlers)
    where 20: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 21: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rtfbs.Rcheck/vign_test/rtfbs",
     ser_elibs = "/tmp/Rtmp233pOV/file33cfd960d51.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (mat, columnsOnly = FALSE)
    {
     check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
     if (class(mat) == "list") {
     for (entry in 1:length(mat)) {
     mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
     }
     }
     else if (class(mat) == "matrix") {
     name <- list()
     bases <- list("A", "C", "G", "T")
     if (columnsOnly == FALSE) {
     if (nrow(mat) == 1) {
     name = c("*")
     }
     else {
     for (row in 0:(nrow(mat))) {
     name[row] <- ""
     for (s in 1:log(nrow(mat), 4)) {
     base <- (ceiling(row/(4^(s - 1)))%%4)
     if (base == 0)
     base <- 4
     name[row] <- paste(bases[base], name[row],
     sep = "")
     }
     }
     }
     rownames(mat) <- name
     }
     colnames(mat) <- bases
     }
     mat
    }
    <bytecode: 0x34f70a0>
    <environment: namespace:rtfbs>
     --- function search by body ---
    Function label.matrix in namespace rtfbs has this body.
     ----------- END OF FAILURE REPORT --------------
    
    Error: processing vignette 'vignette.Rnw' failed with diagnostics:
     chunk 1 (label = rarAnalysis1)
    Error in if (class(mat) == "list") { : the condition has length > 1
    
    --- failed re-building 'vignette.Rnw'
    
    SUMMARY: processing the following file failed:
     'vignette.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.9
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'input.fas'
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.9
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
     bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
     bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
     /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.3.9
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     ‘input.fas’ ‘pwm.meme’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.3.9
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
     bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
     bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
     /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.3.9
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
     bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
     bgc_hmm.c:241:31: warning: ', ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
     rph_tfbs.c:371:11: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
     rph_tfbs.c:351:11: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
     rph_tfbs.c:819:5: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
Flavor: r-devel-windows-ix86+x86_64-gcc8

Version: 0.3.9
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
     rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
     rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
     rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64