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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TAPseq.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings TAPseq_1.11.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TAPseq.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TAPseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TAPseq' version '1.11.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'TAPseq' can be installed ... WARNING
Found the following significant warnings:
Warning: Following software required by TAPseq is not installed or not in PATH:
See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TAPseq.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: Following software required by TAPseq is not installed or not in PATH:
primer3_core
makeblastdb
blastn
Please install these tools before trying to use this package!
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'TAPseq-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: inferPolyASites
> ### Title: Infer polyA sites from droplet sequencing data
> ### Aliases: inferPolyASites
>
> ### ** Examples
>
> library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, 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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
>
> # protein-coding exons of genes within chr11 region
> data("chr11_genes")
> target_genes <- split(chr11_genes, f = chr11_genes$gene_name)
>
> # subset of target genes for quick example
> target_genes <- target_genes[18:27]
>
> # bam file containing aligned Drop-seq reads
> dropseq_bam <- system.file("extdata", "chr11_k562_dropseq.bam", package = "TAPseq")
>
> # infer polyA sites for all target genes with adjusted parameters. parameter values depend on the
> # input data and at this stage it's best to try different settings and check the results
> polyA_sites <- inferPolyASites(target_genes, bam = dropseq_bam, polyA_downstream = 50,
+ wdsize = 100, min_cvrg = 1, parallel = TRUE)
Warning in socketConnection(port = port, server = TRUE, blocking = TRUE, :
port 11884 cannot be opened
Error in socketConnection(port = port, server = TRUE, blocking = TRUE, :
cannot open the connection
Calls: inferPolyASites ... <Anonymous> -> <Anonymous> -> newSOCKnode -> socketConnection
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.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, 1 NOTE
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/TAPseq.Rcheck/00check.log'
for details.