##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:cobindR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings cobindR_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/cobindR.Rcheck’
* using R Under development (unstable) (2020-01-28 r77731)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cobindR/DESCRIPTION’ ... OK
* this is package ‘cobindR’ version ‘1.25.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘genoPlotR’
* 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 ‘cobindR’ can be installed ... WARNING
Found the following significant warnings:
Warning: multiple methods tables found for ‘path’
Warning: multiple methods tables found for ‘path<-’
See ‘/home/biocbuild/bbs-3.11-bioc/meat/cobindR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Warning: multiple methods tables found for ‘path’
Warning: multiple methods tables found for ‘path<-’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘MotifDb’ ‘parallel’ ‘snowfall’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
plot.detrending plot.gc plot.pairdistance plot.positionprofile
plot.positions plot.positions.simple plot.tfbs.heatmap
plot.tfbs.venndiagram plot.tfbslogo
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compare.samples: no visible global function definition for
‘wilcox.test’
input.pfm.similarity: no visible global function definition for ‘combn’
parallelize: no visible global function definition for
‘installed.packages’
parallelize: no visible global function definition for ‘mclapply’
parallelize: no visible global function definition for ‘sfCpus’
parallelize: no visible global function definition for ‘sfInit’
parallelize: no visible global function definition for ‘sfLapply’
parallelize: no visible global function definition for ‘sfStop’
query.motifDb: no visible binding for global variable ‘MotifDb’
find.pairs,cobindr: no visible global function definition for ‘combn’
plot.detrending,cobindr: no visible global function definition for
‘par’
plot.detrending,cobindr: no visible global function definition for
‘plot’
plot.detrending,cobindr: no visible global function definition for
‘lines’
plot.detrending,cobindr: no visible global function definition for
‘title’
plot.gc,cobindr: no visible global function definition for
‘txtProgressBar’
plot.gc,cobindr: no visible global function definition for
‘setTxtProgressBar’
plot.gc,cobindr: no visible global function definition for ‘rainbow’
plot.gc,cobindr: no visible global function definition for ‘par’
plot.gc,cobindr: no visible global function definition for ‘matplot’
plot.gc,cobindr: no visible global function definition for ‘points’
plot.gc,cobindr: no visible global function definition for ‘legend’
plot.pairdistance,cobindr: no visible global function definition for
‘hist’
plot.pairdistribution,cobindr: no visible global function definition
for ‘plot’
plot.positionprofile,cobindr: no visible global function definition for
‘rainbow’
plot.positionprofile,cobindr: no visible global function definition for
‘matplot’
plot.positionprofile,cobindr: no visible global function definition for
‘legend’
plot.positions.simple,cobindr: no visible global function definition
for ‘rainbow’
plot.positions.simple,cobindr: no visible global function definition
for ‘par’
plot.positions.simple,cobindr: no visible global function definition
for ‘plot’
plot.positions.simple,cobindr: no visible global function definition
for ‘points’
plot.positions.simple,cobindr: no visible global function definition
for ‘legend’
plot.positions,cobindr: no visible global function definition for
‘rainbow’
plot.positions,cobindr: no visible binding for global variable ‘n.cpu’
plot.positions,cobindr: no visible global function definition for
‘hclust’
plot.positions,cobindr: no visible global function definition for
‘dist’
plot.positions,cobindr: no visible global function definition for
‘order.dendrogram’
plot.positions,cobindr: no visible global function definition for
‘as.dendrogram’
plot.positions,cobindr: no visible global function definition for
‘grid.newpage’
plot.positions,cobindr: no visible global function definition for
‘pushViewport’
plot.positions,cobindr: no visible global function definition for
‘viewport’
plot.positions,cobindr: no visible global function definition for
‘plot_gene_map’
plot.positions,cobindr: no visible global function definition for
‘popViewport’
plot.positions,cobindr: no visible global function definition for
‘gpar’
plot.positions,cobindr: no visible global function definition for
‘grid_legend’
plot.tfbs.heatmap,cobindr: no visible global function definition for
‘phyper’
plot.tfbs.heatmap,cobindr: no visible global function definition for
‘heat.colors’
plot.tfbs.venndiagram,cobindr: no visible global function definition
for ‘venn.diagram’
plot.tfbs.venndiagram,cobindr: no visible global function definition
for ‘grid.draw’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
definition for ‘makePWM’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
definition for ‘seqLogo’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
definition for ‘grid.text’
plot.tfbslogo,cobindr : <anonymous>: no visible global function
definition for ‘gpar’
read.pfm,configuration: no visible global function definition for
‘read.table’
read.sequences,configuration: no visible global function definition for
‘txtProgressBar’
read.sequences,configuration: no visible global function definition for
‘setTxtProgressBar’
read.sequences,configuration: no visible global function definition for
‘read.table’
search.gadem,cobindr : <anonymous>: no visible global function
definition for ‘GADEM’
search.gadem,cobindr: no visible global function definition for ‘GADEM’
search.gadem,cobindr: no visible global function definition for
‘nMotifs’
search.pwm,cobindr: no visible global function definition for ‘error’
testCpG,cobindr: no visible global function definition for ‘hist’
testCpG,cobindr: no visible global function definition for ‘layout’
testCpG,cobindr: no visible global function definition for ‘par’
testCpG,cobindr: no visible global function definition for ‘barplot’
write.bindingsites.table,cobindr: no visible global function definition
for ‘mcols’
write.bindingsites.table,cobindr: no visible global function definition
for ‘write.table’
write.bindingsites,cobindr: no visible global function definition for
‘write.table’
write,cobindr-character: no visible global function definition for
‘write.table’
Undefined global functions or variables:
GADEM MotifDb as.dendrogram barplot combn dist error gpar grid.draw
grid.newpage grid.text grid_legend hclust heat.colors hist
installed.packages layout legend lines makePWM matplot mclapply mcols
n.cpu nMotifs order.dendrogram par phyper plot plot_gene_map points
popViewport pushViewport rainbow read.table seqLogo setTxtProgressBar
sfCpus sfInit sfLapply sfStop title txtProgressBar venn.diagram
viewport wilcox.test write.table
Consider adding
importFrom("grDevices", "heat.colors", "rainbow")
importFrom("graphics", "barplot", "hist", "layout", "legend", "lines",
"matplot", "par", "plot", "points", "title")
importFrom("stats", "as.dendrogram", "dist", "hclust",
"order.dendrogram", "phyper", "wilcox.test")
importFrom("utils", "combn", "installed.packages", "read.table",
"setTxtProgressBar", "txtProgressBar", "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘cobindR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: search.pwm
> ### Title: function to predict transcription factor binding sites using the
> ### method matchPWM from package Biostrings
> ### Aliases: search.pwm search.pwm-method search.pwm,cobindr-method
> ### Keywords: manip iteration methods
>
> ### ** Examples
>
> ############################################################
> # use simulated sequences
> library(Biostrings)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:cobindR’:
path, path<-
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
>
> n <- 400 # number of input sequences
> l <- 500 # length of sequences
> n.hits <- 250 # number of 'true' binding sites
> bases <- c("A","C","G","T") # alphabet
> # generate random input sequences with two groups with differing GC content
> seqs <- sapply(1:(3*n/4), function(x) paste(sample(bases, l, replace=TRUE,
+ prob=c(.3,.22,.2,.28)), collapse=""))
> seqs <- append(seqs, sapply(1:(n/4), function(x) paste(sample(bases, l, replace=TRUE,
+ prob=c(.25,.25,.25,.25)), collapse="")))
> path <- system.file('extdata/pfms/myod.tfpfm',package='cobindR')
> motif <- read.transfac.pfm(path)[[1]] # get PFM of binding site
[1] "ES_Sox2_1_c1058"
[1] "ES_Klf4_3_c1373"
> # add binding sites with distance specificity
> for(position in c(110, 150)) {
+ hits <- apply(apply(motif, 2, function(x) sample(x=bases, size=n.hits, prob=x,
+ replace=TRUE)), 1, paste, collapse='')
+ pos.hits <- round(rnorm(n.hits, mean=position, sd=8))
+ names(pos.hits) <- sample(1:n, n.hits)
+ for(i in 1:n.hits) substr(seqs[as.integer(names(pos.hits)[i])], start=pos.hits[i],
+ stop=pos.hits[i]+ncol(motif)) <- hits[i]
+ }
> #save sample sequences in fasta file
> tmp.file <- tempfile(pattern = "cobindr_sample_seq", tmpdir = tempdir(), fileext = ".fasta")
> writeXStringSet(DNAStringSet(seqs), tmp.file)
> #run cobindr
> cfg <- cobindRConfiguration()
Warning in .local(.Object, ...) :
no config-file defined, generating configuration-object with default values
> sequence_type(cfg) <- 'fasta'
> sequence_source(cfg) <- tmp.file
> sequence_origin(cfg) <- 'artificial sequences'
> pfm_path(cfg) <- system.file('extdata/pfms',package='cobindR')
> pairs(cfg) <- 'V$MYOD_01 V$MYOD_01'
> runObj <- cobindr(cfg, name='cobindr test using sampled sequences')
[1] "Creating a new experiment!"
reading file /tmp/Rtmp8Cpw2r/cobindr_sample_seq1d2c68a56f7b.fasta ...
|
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implicit list embedding of S4 objects is deprecated
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|=================== | 27%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=================== | 28%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|==================== | 28%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|==================== | 29%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|===================== | 30%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|====================== | 31%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|====================== | 32%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================= | 32%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================= | 33%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================= | 34%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================== | 34%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================== | 35%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|========================= | 35%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|========================= | 36%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|========================== | 36%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|========================== | 37%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|========================== | 38%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=========================== | 38%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=========================== | 39%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================ | 40%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================= | 41%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================= | 42%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================== | 42%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================== | 43%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================== | 44%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=============================== | 44%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=============================== | 45%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================ | 45%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================ | 46%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================= | 46%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================= | 47%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================= | 48%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================== | 48%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================== | 49%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=================================== | 50%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|==================================== | 51%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|==================================== | 52%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|===================================== | 52%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|===================================== | 53%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|===================================== | 54%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|====================================== | 54%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|====================================== | 55%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|======================================= | 55%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|======================================= | 56%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|======================================== | 56%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================================== | 57%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================================== | 58%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|========================================= | 58%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|========================================= | 59%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|========================================== | 60%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=========================================== | 61%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=========================================== | 62%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================================ | 62%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================================ | 63%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================================ | 64%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================================= | 64%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================================= | 65%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================================== | 65%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|============================================== | 66%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=============================================== | 66%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=============================================== | 67%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=============================================== | 68%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================================ | 68%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================================ | 69%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================================= | 70%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================================== | 71%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|================================================== | 72%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=================================================== | 72%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=================================================== | 73%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|=================================================== | 74%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|==================================================== | 74%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|==================================================== | 75%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|===================================================== | 75%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|===================================================== | 76%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|====================================================== | 76%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|====================================================== | 77%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|====================================================== | 78%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================================================= | 78%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================================================= | 79%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|======================================================== | 80%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
|
|========================================================= | 81%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|========================================================= | 82%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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|========================================================== | 82%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|========================================================== | 83%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|========================================================== | 84%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|=========================================================== | 84%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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|============================================================ | 85%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|============================================================ | 86%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|============================================================= | 86%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|============================================================= | 87%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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|============================================================= | 88%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|============================================================== | 88%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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implicit list embedding of S4 objects is deprecated
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|============================================================== | 89%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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|=============================================================== | 90%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|================================================================ | 91%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|================================================================ | 92%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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|================================================================= | 92%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|================================================================= | 93%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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|================================================================= | 94%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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implicit list embedding of S4 objects is deprecated
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|================================================================== | 95%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|=================================================================== | 95%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|=================================================================== | 96%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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|==================================================================== | 96%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|==================================================================== | 97%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|==================================================================== | 98%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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|===================================================================== | 98%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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implicit list embedding of S4 objects is deprecated
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|===================================================================== | 99%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
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|======================================================================| 100%Warning in `[<-`(`*tmp*`, id, value = new.seq) :
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Warning in `[<-`(`*tmp*`, id, value = new.seq) :
implicit list embedding of S4 objects is deprecated
ready retrieving sequences!
reading pfm files: /home/biocbuild/bbs-3.11-bioc/R/library/cobindR/extdata/pfms ...
[1] "ES_Sox2_1_c1058"
[1] "ES_Klf4_3_c1373"
[1] "ES_Oct4_1_c570"
[1] "ES_Sox2_1_c1058"
ignored files:
Using the parallel (multicore) version of cobindR - function cpg.gc.content with 20 cores
> # perform tfbs prediction using matchPWM
> runObj.bs <- search.pwm(runObj, min.score = '90')
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
cobindR
--- call from context ---
FUN(X[[i]], ...)
--- call from argument ---
if (class(res) == "try-error") warning("PFM-PWM conversion failed for matrix ",
names(x@pfm)[x], "!")
--- R stacktrace ---
where 1: FUN(X[[i]], ...)
where 2: lapply(1:length(x@pfm), function(y) {
pwm = x@pfm[[y]]
is.float = any(pwm != apply(pwm, c(1, 2), as.integer))
if (is.float) {
return(pwm)
}
else {
res = try(pfm2pwm(pwm))
if (class(res) == "try-error")
warning("PFM-PWM conversion failed for matrix ",
names(x@pfm)[x], "!")
return(res)
}
})
where 3: lapply(1:length(x@pfm), function(y) {
pwm = x@pfm[[y]]
is.float = any(pwm != apply(pwm, c(1, 2), as.integer))
if (is.float) {
return(pwm)
}
else {
res = try(pfm2pwm(pwm))
if (class(res) == "try-error")
warning("PFM-PWM conversion failed for matrix ",
names(x@pfm)[x], "!")
return(res)
}
})
where 4: .local(x, ...)
where 5: search.pwm(runObj, min.score = "90")
where 6: search.pwm(runObj, min.score = "90")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (y)
{
pwm = x@pfm[[y]]
is.float = any(pwm != apply(pwm, c(1, 2), as.integer))
if (is.float) {
return(pwm)
}
else {
res = try(pfm2pwm(pwm))
if (class(res) == "try-error")
warning("PFM-PWM conversion failed for matrix ",
names(x@pfm)[x], "!")
return(res)
}
}
<environment: 0x55cc008eb328>
--- function search by body ---
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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 ERROR, 1 WARNING, 6 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc/meat/cobindR.Rcheck/00check.log’
for details.