BioC 3.6: BUILD report for AneuFinder on malbec1

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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data AneuFinder
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* checking for file ‘AneuFinder/DESCRIPTION’ ... OK
* preparing ‘AneuFinder’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: GenomicRanges
Loading required package: stats4
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:stats':

IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame,
cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get,
grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: cowplot
Loading required package: ggplot2

Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

ggsave

Loading required package: AneuFinderData

Please visit https://github.com/ataudt/aneufinder for the latest bugfixes and features.

Aneufinder package:AneuFinder R Documentation

_W_r_a_p_p_e_r _f_u_n_c_t_i_o_n _f_o_r _t_h_e '_A_n_e_u_F_i_n_d_e_r' _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

This function is an easy-to-use wrapper to bin the data, find
copy-number-variations, find sister-chromatid-exchange events,
plot genomewide heatmaps, distributions, profiles and karyograms.

_U_s_a_g_e:

Aneufinder(inputfolder, outputfolder, configfile = NULL, numCPU = 1,
reuse.existing.files = TRUE, binsizes = 1e+06,
variable.width.reference = NULL, reads.per.bin = NULL,
pairedEndReads = FALSE, assembly = NULL, chromosomes = NULL,
remove.duplicate.reads = TRUE, min.mapq = 10, blacklist = NULL,
use.bamsignals = FALSE, reads.store = FALSE, correction.method = NULL,
GC.BSgenome = NULL, method = c("dnacopy", "HMM"), strandseq = FALSE,
eps = 0.1, max.time = 60, max.iter = 5000, num.trials = 15,
states = c("zero-inflation", paste0(0:10, "-somy")),
most.frequent.state = "2-somy", most.frequent.state.strandseq = "1-somy",
resolution = c(3, 6), min.segwidth = 2, bw = 4 * binsizes[1],
pval = 1e-08, cluster.plots = TRUE)

_A_r_g_u_m_e_n_t_s:

inputfolder: Folder with either BAM or BED files.

outputfolder: Folder to output the results. If it does not exist it
will be created.

configfile: A file specifying the parameters of this function (without
'inputfolder', 'outputfolder' and 'configfile'). Having the
parameters in a file can be handy if many samples with the
same parameter settings are to be run. If a 'configfile' is
specified, it will take priority over the command line
parameters.

numCPU: The numbers of CPUs that are used. Should not be more than
available on your machine.

reuse.existing.files: A logical indicating whether or not existing
files in 'outputfolder' should be reused.

binsizes: An integer vector with bin sizes. If more than one value is
given, output files will be produced for each bin size.

variable.width.reference: A BAM file that is used as reference to
produce variable width bins. See 'variableWidthBins' for
details.

reads.per.bin: Approximate number of desired reads per bin. The bin
size will be selected accordingly. Output files are produced
for each value.

pairedEndReads: Set to 'TRUE' if you have paired-end reads in your BAM
files (not implemented for BED files).

assembly: Please see 'fetchExtendedChromInfoFromUCSC' for available
assemblies. Only necessary when importing BED files. BAM
files are handled automatically. Alternatively a data.frame
with columns 'chromosome' and 'length'.

chromosomes: If only a subset of the chromosomes should be imported,
specify them here.

remove.duplicate.reads: A logical indicating whether or not duplicate
reads should be removed.

min.mapq: Minimum mapping quality when importing from BAM files. Set
'min.mapq=NULL' to keep all reads.

blacklist: A 'GRanges' or a bed(.gz) file with blacklisted regions.
Reads falling into those regions will be discarded.

use.bamsignals: If 'TRUE' the 'bamsignals' package will be used for
binning. This gives a tremendous performance increase for the
binning step. 'reads.store' and 'calc.complexity' will be set
to 'FALSE' in this case.

reads.store: Set 'reads.store=TRUE' to store read fragments as RData in
folder 'data' and as BED files in 'BROWSERFILES/data'. This
option will force 'use.bamsignals=FALSE'.

correction.method: Correction methods to be used for the binned read
counts. Currently only ''GC''.

GC.BSgenome: A 'BSgenome' object which contains the DNA sequence that
is used for the GC correction.

method: Any combination of 'c('HMM','dnacopy')'. Option
'method='HMM'' uses a Hidden Markov Model as described in
doi:10.1186/s13059-016-0971-7 to call copy numbers. Option
''dnacopy'' uses the 'DNAcopy' package to call copy numbers
similarly to the method proposed in doi:10.1038/nmeth.3578,
which gives more robust but less sensitive results.

strandseq: A logical indicating whether the data comes from Strand-seq
experiments. If 'TRUE', both strands carry information and
are treated separately.

eps: Convergence threshold for the Baum-Welch algorithm.

max.time: The maximum running time in seconds for the Baum-Welch
algorithm. If this time is reached, the Baum-Welch will
terminate after the current iteration finishes. Set 'max.time
= -1' for no limit.

max.iter: The maximum number of iterations for the Baum-Welch
algorithm. Set 'max.iter = -1' for no limit.

num.trials: The number of trials to find a fit where state
'most.frequent.state' is most frequent. Each time, the HMM is
seeded with different random initial values.

states: A subset or all of
'c("zero-inflation","0-somy","1-somy","2-somy","3-somy","4-somy",...)'.
This vector defines the states that are used in the Hidden
Markov Model. The order of the entries must not be changed.

most.frequent.state: One of the states that were given in 'states'. The
specified state is assumed to be the most frequent one when
running the univariate HMM. This can help the fitting
procedure to converge into the correct fit. Default is
'2-somy'.

most.frequent.state.strandseq: One of the states that were given in
'states'. The specified state is assumed to be the most
frequent one when option 'strandseq=TRUE'. This can help the
fitting procedure to converge into the correct fit. Default
is '1-somy'.

resolution: An integer vector specifying the resolution at bin level at
which to scan for SCE events.

min.segwidth: Segments below this width will be removed before scanning
for SCE events.

bw: Bandwidth for SCE hotspot detection (see 'hotspotter' for
further details).

pval: P-value for SCE hotspot detection (see 'hotspotter' for
further details).

cluster.plots: A logical indicating whether plots should be clustered
by similarity.

_V_a_l_u_e:

'NULL'

_A_u_t_h_o_r(_s):

Aaron Taudt

_E_x_a_m_p_l_e_s:

## Not run:

## The following call produces plots and genome browser files for all BAM files in "my-data-folder"
Aneufinder(inputfolder="my-data-folder", outputfolder="my-output-folder")
## End(Not run)

Reading file hg19_diploid.bam.bed.gz ... 6.5s
Fetching chromosome lengths from UCSC ...Warning in FUN(genome = names(SUPPORTED_UCSC_GENOMES)[idx], circ_seqs = supported_genome$circ_seqs, :
NCBI seqlevel was set to NA for hg19 UCSC seqlevel(s) not in the NCBI assembly:
chrM
Warning in file(file, "rt") :
URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.13_GRCh37/GCF_000001405.13_GRCh37_assembly_report.txt': status was 'Couldn't connect to server'
Quitting from lines 108-130 (AneuFinder.Rnw)
Error: processing vignette 'AneuFinder.Rnw' failed with diagnostics:
cannot open the connection to 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.13_GRCh37/GCF_000001405.13_GRCh37_assembly_report.txt'
Execution halted

BioC 3.6: BUILD report for AneuFinder on malbec1

Summary

Command output