Last updated on 2020-10-25 05:47:37 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.99 | 15.71 | 182.67 | 198.38 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 0.99 | 13.36 | 133.29 | 146.65 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 0.99 | 245.21 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 0.99 | 230.18 | WARN | |||
| r-devel-windows-ix86+x86_64 | 0.99 | 38.00 | 203.00 | 241.00 | WARN | |
| r-patched-linux-x86_64 | 0.99 | 15.71 | 167.54 | 183.25 | WARN | |
| r-patched-solaris-x86 | 0.99 | 316.80 | WARN | |||
| r-release-linux-x86_64 | 0.99 | 15.64 | 164.90 | 180.54 | WARN | |
| r-release-macos-x86_64 | 0.99 | OK | ||||
| r-release-windows-ix86+x86_64 | 0.99 | 29.00 | 144.00 | 173.00 | WARN | |
| r-oldrel-macos-x86_64 | 0.99 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 0.99 | 33.00 | 195.00 | 228.00 | WARN |
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'my-vignette.Rmd' using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
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, 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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
% 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 9339 100 9339 0 0 28300 0 --:--:-- --:--:-- --:--:-- 28300
% 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 9339 100 9339 0 0 79144 0 --:--:-- --:--:-- --:--:-- 79144
% 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 9339 100 9339 0 0 75314 0 --:--:-- --:--:-- --:--:-- 75314
% 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 9339 100 9339 0 0 81921 0 --:--:-- --:--:-- --:--:-- 81921
% 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 9339 100 9339 0 0 75926 0 --:--:-- --:--:-- --:--:-- 75926
% 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 9339 100 9339 0 0 82646 0 --:--:-- --:--:-- --:--:-- 82646
% 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 9339 100 9339 0 0 74119 0 --:--:-- --:--:-- --:--:-- 74119
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in file(file, "rt") :
'raw = FALSE' but '/tmp/Rtmp3Jm7mE/VSE_samples/' is not a regular file
Warning in file(file, "rt") :
cannot open file '/tmp/Rtmp3Jm7mE/VSE_samples/': it is a directory
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'my-vignette.Rmd'
SUMMARY: processing the following file failed:
'my-vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
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, 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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
% 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 9339 100 9339 0 0 24837 0 --:--:-- --:--:-- --:--:-- 24837
% 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 9339 100 9339 0 0 63530 0 --:--:-- --:--:-- --:--:-- 63530
% 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 9339 100 9339 0 0 69694 0 --:--:-- --:--:-- --:--:-- 69694
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
70 9339 70 6593 0 0 51507 0 --:--:-- --:--:-- --:--:-- 51108
100 9339 100 9339 0 0 72960 0 --:--:-- --:--:-- --:--:-- 72395
% 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 9339 100 9339 0 0 72960 0 --:--:-- --:--:-- --:--:-- 72960
% 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 9339 100 9339 0 0 72395 0 --:--:-- --:--:-- --:--:-- 72395
% 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 9339 100 9339 0 0 77181 0 --:--:-- --:--:-- --:--:-- 77181
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in file(file, "rt") :
'raw = FALSE' but '/home/hornik/tmp/scratch/Rtmp8t4aZ0/VSE_samples/' is not a regular file
Warning in file(file, "rt") :
cannot open file '/home/hornik/tmp/scratch/Rtmp8t4aZ0/VSE_samples/': it is a directory
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
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, 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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 9339 100 9339 0 0 25172 0 --:--:-- --:--:-- --:--:-- 25104
% 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 9339 100 9339 0 0 77825 0 --:--:-- --:--:-- --:--:-- 78478
% 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 9339 100 9339 0 0 76549 0 --:--:-- --:--:-- --:--:-- 76549
% 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 9339 100 9339 0 0 78478 0 --:--:-- --:--:-- --:--:-- 78478
% 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 9339 100 9339 0 0 75314 0 --:--:-- --:--:-- --:--:-- 75314
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
67 9339 67 6276 0 0 51442 0 --:--:-- --:--:-- --:--:-- 51024
100 9339 100 9339 0 0 76549 0 --:--:-- --:--:-- --:--:-- 75926
% 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 9339 100 9339 0 0 54296 0 --:--:-- --:--:-- --:--:-- 54296
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in file(file, "rt") :
'raw = FALSE' but '/tmp/RtmpFZ2E7K/working_dir/Rtmps2vLFx/VSE_samples/' is not a regular file
Warning in file(file, "rt") :
cannot open file '/tmp/RtmpFZ2E7K/working_dir/Rtmps2vLFx/VSE_samples/': it is a directory
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown
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, 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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
% 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 9339 100 9339 0 0 37207 0 --:--:-- --:--:-- --:--:-- 37207
% 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 9339 100 9339 0 0 77181 0 --:--:-- --:--:-- --:--:-- 77181
% 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 9339 100 9339 0 0 75926 0 --:--:-- --:--:-- --:--:-- 75926
% 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 9339 100 9339 0 0 75926 0 --:--:-- --:--:-- --:--:-- 75926
% 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 9339 100 9339 0 0 78478 0 --:--:-- --:--:-- --:--:-- 78478
% 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 9339 100 9339 0 0 79144 0 --:--:-- --:--:-- --:--:-- 79144
% 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 9339 100 9339 0 0 74119 0 --:--:-- --:--:-- --:--:-- 75926
Warning in file(file, "rt") :
'raw = FALSE' but '/tmp/RtmpgUjTZN/working_dir/RtmpfYsx3k/VSE_samples/' is not a regular file
Warning in file(file, "rt") :
cannot open file '/tmp/RtmpgUjTZN/working_dir/RtmpfYsx3k/VSE_samples/': it is a directory
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 9339 100 9339 0 0 18753 0 --:--:-- --:--:-- --:--:-- 18753
% 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 9339 100 9339 0 0 37207 0 --:--:-- --:--:-- --:--:-- 37356
% 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 9339 100 9339 0 0 60642 0 --:--:-- --:--:-- --:--:-- 60642
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 9339 100 9339 0 0 24007 0 --:--:-- --:--:-- --:--:-- 24007
% 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 9339 100 9339 0 0 66234 0 --:--:-- --:--:-- --:--:-- 66707
% 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 9339 100 9339 0 0 61440 0 --:--:-- --:--:-- --:--:-- 61440
% 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 9339 100 9339 0 0 64854 0 --:--:-- --:--:-- --:--:-- 64854
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in file(file, "rt") :
cannot open file 'D:\temp\RtmpCSEFf0/VSE_samples/': Permission denied
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'my-vignette.Rmd'
SUMMARY: processing the following file failed:
'my-vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
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, 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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 9339 100 9339 0 0 29932 0 --:--:-- --:--:-- --:--:-- 29837
% 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 9339 100 9339 0 0 77181 0 --:--:-- --:--:-- --:--:-- 77181
% 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 9339 100 9339 0 0 75314 0 --:--:-- --:--:-- --:--:-- 75314
% 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 9339 100 9339 0 0 78478 0 --:--:-- --:--:-- --:--:-- 78478
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
24 9339 24 2249 0 0 5512 0 0:00:01 --:--:-- 0:00:01 5498
100 9339 100 9339 0 0 22889 0 --:--:-- --:--:-- --:--:-- 22833
% 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 9339 100 9339 0 0 75314 0 --:--:-- --:--:-- --:--:-- 75314
% 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 9339 100 9339 0 0 79820 0 --:--:-- --:--:-- --:--:-- 79820
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in file(file, "rt") :
'raw = FALSE' but '/tmp/RtmpfgIVxw/VSE_samples/' is not a regular file
Warning in file(file, "rt") :
cannot open file '/tmp/RtmpfgIVxw/VSE_samples/': it is a directory
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
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, 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 object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
100 9339 100 9339 0 0 1867 0 0:00:05 0:00:05 --:--:-- 2232
100 9339 100 9339 0 0 1867 0 0:00:05 0:00:05 --:--:-- 2934
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
100 9339 100 9339 0 0 2334 0 0:00:04 0:00:04 --:--:-- 1941
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
100 9339 100 9339 0 0 2334 0 0:00:04 0:00:04 --:--:-- 2456
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
100 9339 100 9339 0 0 2334 0 0:00:04 0:00:04 --:--:-- 2458
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
100 9339 100 9339 0 0 2334 0 0:00:04 0:00:04 --:--:-- 2462
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
100 9339 100 9339 0 0 2334 0 0:00:04 0:00:04 --:--:-- 2458
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:04 --:--:-- 0
100 9339 100 9339 0 0 2334 0 0:00:04 0:00:04 --:--:-- 2459
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in file(file, "rt") :
'raw = FALSE' but '/tmp/RtmpOFaO6I/working_dir/RtmpHmaGiE/VSE_samples/' is not a regular file
Warning in file(file, "rt") :
cannot open file '/tmp/RtmpOFaO6I/working_dir/RtmpHmaGiE/VSE_samples/': it is a directory
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
% 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 9339 100 9339 0 0 24383 0 --:--:-- --:--:-- --:--:-- 24383
% 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 9339 100 9339 0 0 71838 0 --:--:-- --:--:-- --:--:-- 71838
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
24 9339 24 2249 0 0 17708 0 --:--:-- --:--:-- --:--:-- 17570
100 9339 100 9339 0 0 73535 0 --:--:-- --:--:-- --:--:-- 72960
% 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 9339 100 9339 0 0 74119 0 --:--:-- --:--:-- --:--:-- 74119
% 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 9339 100 9339 0 0 79144 0 --:--:-- --:--:-- --:--:-- 79144
% 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 9339 100 9339 0 0 85678 0 --:--:-- --:--:-- --:--:-- 85678
% 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 9339 100 9339 0 0 82646 0 --:--:-- --:--:-- --:--:-- 82646
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in file(file, "rt") :
'raw = FALSE' but '/tmp/RtmpydLQTC/VSE_samples/' is not a regular file
Warning in file(file, "rt") :
cannot open file '/tmp/RtmpydLQTC/VSE_samples/': it is a directory
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘my-vignette.Rmd’
SUMMARY: processing the following file failed:
‘my-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
% 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 9339 100 9339 0 0 26759 0 --:--:-- --:--:-- --:--:-- 26759
% 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 9339 100 9339 0 0 68167 0 --:--:-- --:--:-- --:--:-- 68167
% 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 9339 100 9339 0 0 65767 0 --:--:-- --:--:-- --:--:-- 65767
% 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 9339 100 9339 0 0 69177 0 --:--:-- --:--:-- --:--:-- 69177
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
71 9339 71 6655 0 0 48576 0 --:--:-- --:--:-- --:--:-- 48576
100 9339 100 9339 0 0 68167 0 --:--:-- --:--:-- --:--:-- 68167
% 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 9339 100 9339 0 0 71838 0 --:--:-- --:--:-- --:--:-- 71838
% 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 9339 100 9339 0 0 68167 0 --:--:-- --:--:-- --:--:-- 68167
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in file(file, "rt") :
cannot open file 'D:\temp\RtmpS0gOG5/VSE_samples/': Permission denied
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'my-vignette.Rmd'
SUMMARY: processing the following file failed:
'my-vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-ix86+x86_64
Version: 0.99
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-macos-x86_64
Version: 0.99
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'my-vignette.Rmd' using rmarkdown
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
% 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 9339 100 9339 0 0 20615 0 --:--:-- --:--:-- --:--:-- 37356
% 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 9339 100 9339 0 0 28472 0 --:--:-- --:--:-- --:--:-- 29932
% 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 9339 100 9339 0 0 37356 0 --:--:-- --:--:-- --:--:-- 37356
% 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 9339 100 9339 0 0 28472 0 --:--:-- --:--:-- --:--:-- 29932
% 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 9339 100 9339 0 0 37506 0 --:--:-- --:--:-- --:--:-- 37506
% 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 9339 100 9339 0 0 35241 0 --:--:-- --:--:-- --:--:-- 37506
% 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 9339 100 9339 0 0 66234 0 --:--:-- --:--:-- --:--:-- 74712
Warning in block_exec(params) :
Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
Warning in file(file, "rt") :
cannot open file 'D:\temp\RtmpELvzPA/VSE_samples/': Permission denied
Quitting from lines 136-146 (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'my-vignette.Rmd'
SUMMARY: processing the following file failed:
'my-vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64