##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/nucleR_2.20.0.tar.gz && rm -rf nucleR.buildbin-libdir && mkdir nucleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nucleR.buildbin-libdir nucleR_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL nucleR_2.20.0.zip && rm nucleR_2.20.0.tar.gz nucleR_2.20.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 806k 100 806k 0 0 12.5M 0 --:--:-- --:--:-- --:--:-- 14.0M
install for i386
* installing *source* package 'nucleR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Loading required package: usethis
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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, 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
Welcome at Fri Oct 16 18:34:54 2020
Goodbye at Fri Oct 16 18:35:00 2020
** help
*** installing help indices
converting help for package 'nucleR'
finding HTML links ... done
controlCorrection html
coverage.rpm html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/coverage.rpm.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/coverage.rpm.Rd:35: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/coverage.rpm.Rd:22: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/coverage.rpm.Rd:22: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/coverage.rpm.Rd:51: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
dot-fftRegion html
dot-getThreshold html
dot-loadFiles html
dot-loadPairedBam html
dot-loadSingleBam html
dot-mid html
dot-processStrand html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/dot-processStrand.Rd:16: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
dot-unlist_as_integer html
dot-vectorizedAll html
dot-xlapply html
export.bed html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/export.bed.Rd:51: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/export.bed.Rd:52: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/export.bed.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
export.wig html
filterFFT html
fragmentLenDetect html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/fragmentLenDetect.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
mergeCalls html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/mergeCalls.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/mergeCalls.Rd:31: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
nucleR-package html
nucleosome_htseq html
nucleosome_tiling html
pcKeepCompDetect html
peakDetection html
peakScoring html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/peakScoring.Rd:74: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
plotPeaks html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/plotPeaks.Rd:98: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
processReads html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/processReads.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/processReads.Rd:49: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/processReads.Rd:39: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/processReads.Rd:109: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
processTilingArray html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/processTilingArray.Rd:129: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
readBAM html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/readBAM.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
readBowtie html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpKgUjFl/R.INSTALL23d837252346/nucleR/man/readBowtie.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
syntheticNucMap html
** building package indices
Loading required package: usethis
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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, 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
Welcome at Fri Oct 16 18:35:07 2020
Goodbye at Fri Oct 16 18:35:07 2020
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading required package: usethis
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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, 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
Welcome at Fri Oct 16 18:35:12 2020
Goodbye at Fri Oct 16 18:35:18 2020
** testing if installed package can be loaded from final location
Loading required package: usethis
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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, 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
Welcome at Fri Oct 16 18:35:22 2020
Goodbye at Fri Oct 16 18:35:28 2020
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'nucleR' ...
** testing if installed package can be loaded
Loading required package: usethis
Loading required package: BiocGenerics
Loading required package: utils
Loading required package: graphics
Loading required package: stats
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, 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
Welcome at Fri Oct 16 18:35:34 2020
Goodbye at Fri Oct 16 18:35:41 2020
* MD5 sums
packaged installation of 'nucleR' as nucleR_2.20.0.zip
* DONE (nucleR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'nucleR' successfully unpacked and MD5 sums checked
