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### Running command:
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### chmod a+r profileplyr -R && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data profileplyr
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* checking for file 'profileplyr/DESCRIPTION' ... OK
* preparing 'profileplyr':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'profileplyr.Rmd' using rmarkdown
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, 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: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
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
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'profileplyr'
The following object is masked from 'package:S4Vectors':
params
Read 1 item
Matrix contained 'NA' values, these will be replaced with zeros
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Making ChIPprofile object from signal files.
Reading Bam header information.....Done
Filtering regions which extend outside of genome boundaries.....Done
Filtered 0 of 3 regions
Splitting regions by Watson and Crick strand....Done
..Done
Found 3 Watson strand regions
Found 0 Crick strand regions
Extending regions.....done
Reading tags from F:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpoLE0gp/Rinst1a31c208c1883/profileplyr/extdata/Sorted_Hindbrain_day_12_1_filtered.bam..Done.
Read in 7763 reads
Extending reads to fragmentlength of 150..done
Calculating coverage....done
Making windows.
Windowing positive 5' flanking
Windowing positive regions
Windowing positive 3' flank
..done
Calculating bin scores for regions.
Processing per contig
contig: 1
Processing inner region windows in chr4
..done
Processing flanking windows in chr4
contig: 2
Processing inner region windows in chr13
..done
Processing flanking windows in chr13
contig: 3
Processing inner region windows in chr15
..done
Processing flanking windows in chr15
Reading Bam header information.....Done
Filtering regions which extend outside of genome boundaries.....Done
Filtered 0 of 3 regions
Splitting regions by Watson and Crick strand....Done
..Done
Found 3 Watson strand regions
Found 0 Crick strand regions
Extending regions.....done
Reading tags from F:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpoLE0gp/Rinst1a31c208c1883/profileplyr/extdata/Sorted_Liver_day_12_1_filtered.bam..Done.
Read in 0 reads
Extending reads to fragmentlength of 150..done
Calculating coverage....done
Making windows.
Windowing positive 5' flanking
Windowing positive regions
Windowing positive 3' flank
..done
Calculating bin scores for regions.
Processing per contig
contig: 1
Processing inner region windows in chr4
..done
Processing flanking windows in chr4
contig: 2
Processing inner region windows in chr13
..done
Processing flanking windows in chr13
contig: 3
Processing inner region windows in chr15
..done
Processing flanking windows in chr15
Read 1 item
Matrix contained 'NA' values, these will be replaced with zeros
Read 1 item
Matrix contained 'NA' values, these will be replaced with zeros
No 'kmeans_k' or 'cutree_rows' arguments specified. profileplyr object will be returned new column with hierarchical order from hclust
K means clustering used.
A column has been added to the range metadata with the column name 'cluster', and the 'rowGroupsInUse' has been set to this column.
K means clustering used.
A column has been added to the range metadata with the column name 'cluster', and the 'rowGroupsInUse' has been set to this column.
Hierarchical clustering used. It is advised to avoid this option with large matrices as the clustering can take a long time. Kmeans is more suitable for large matrices.
A column has been added to the range metadata with the column name 'cluster', and the 'rowGroupsInUse' has been set to this column.
Attaching package: 'magrittr'
The following object is masked from 'package:GenomicRanges':
subtract
Read 1 item
Matrix contained 'NA' values, these will be replaced with zeros
K means clustering used.
A column has been added to the range metadata with the column name 'cluster', and the 'rowGroupsInUse' has been set to this column.
Loading required package: org.Mm.eg.db
Loading required package: AnnotationDbi
'select()' returned 1:1 mapping between keys and columns
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21047 ms: Timed out
failed with the request, try after 0 min (1st try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21179 ms: Timed out
failed with the request, try after 0 min (2nd try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21019 ms: Timed out
failed with the request, try after 0 min (3th try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21020 ms: Timed out
failed with the request, try after 0 min (4th try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21102 ms: Timed out
failed with the request, try after 0 min (5th try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21051 ms: Timed out
failed with the request, try after 0 min (6th try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21116 ms: Timed out
failed with the request, try after 0 min (7th try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21023 ms: Timed out
failed with the request, try after 0 min (8th try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21238 ms: Timed out
failed with the request, try after 0 min (9th try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21004 ms: Timed out
failed with the request, try after 0 min (10th try)
Error in function (type, msg, asError = TRUE) :
Failed to connect to great.stanford.edu port 80 after 21023 ms: Timed out
Quitting from lines 446-450 (profileplyr.Rmd)
Error: processing vignette 'profileplyr.Rmd' failed with diagnostics:
max try: 10 reached. Stop with error.
--- failed re-building 'profileplyr.Rmd'
SUMMARY: processing the following file failed:
'profileplyr.Rmd'
Error: Vignette re-building failed.
Execution halted