ggbio 1.35.2
Michael Lawrence
| Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/ggbio |
| Branch: master |
| Last Commit: 6bc94f4 |
| Last Changed Date: 2020-04-09 16:39:52 -0400 (Thu, 09 Apr 2020) |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped |
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### Running command:
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### chmod a+r ggbio -R && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ggbio
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* checking for file 'ggbio/DESCRIPTION' ... OK
* preparing 'ggbio':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'ggbio.Rnw' using Sweave
--- finished re-building 'ggbio.Rnw'
cp realvignettes/*.Rnw .
C:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/Rscript -e "library(knitr); knit2pdf('ggbio.Rnw')"
processing file: ggbio.Rnw
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$ results: chr "asis"
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Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
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clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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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: ggplot2
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Need specific help about ggbio? try mailing
the maintainer or visit http://tengfei.github.com/ggbio/
Attaching package: 'ggbio'
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geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
xlim
use chr1 automatically
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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Loading required package: IRanges
Attaching package: 'IRanges'
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Loading required package: GenomeInfoDb
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Loading required package: AnnotationDbi
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")'.
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Parsing transcripts...
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Parsing transcripts...
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Loading required package: ensembldb
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Loading required package: Rsamtools
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Parsing transcripts...
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ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
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label: unnamed-chunk-38 (with options)
List of 2
$ fig.width : num 5
$ fig.height: num 4
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
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label: unnamed-chunk-39
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
ERROR: Windows API error 5: Access is denied.
ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
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label: edit-space (with options)
List of 2
$ fig.width : num 5
$ fig.height: num 4
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
ERROR: Windows API error 5: Access is denied.
ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
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label: unnamed-chunk-40 (with options)
List of 2
$ fig.width : num 5
$ fig.height: num 4
ERROR: Windows API error 5: Access is denied.
ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
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List of 1
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label: unnamed-chunk-42
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
Constructing graphics...
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
Constructing graphics...
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
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label: unnamed-chunk-43
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
ERROR: Windows API error 5: Access is denied.
ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
ERROR: Windows API error 5: Access is denied.
ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
ERROR: Windows API error 5: Access is denied.
ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
ERROR: Windows API error 5: Access is denied.
ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
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label: unnamed-chunk-44
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
ERROR: Windows API error 5: Access is denied.
ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
ERROR: Windows API error 5: Access is denied.
ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
ERROR: Line: 111
Sorry, but pdfcrop.exe did not succeed.
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label: session-info
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output file: ggbio.tex
! ERROR: Windows API error 5: Access is denied.
! ERROR: Info: path="cprogramdatamiktex2.9miktexdatale1756f6ade37d5f870f23c05a7f81e257.fndb-5"
! ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
! ERROR: Line: 111
! ERROR: Source: Libraries\MiKTeX\Core\MemoryMappedFile\win\winMemoryMappedFile.cpp
! ERROR: Line: 111
! ERROR: Line: 111
! Sorry, but C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\pdflatex.exe did not succeed.
Error: LaTeX failed to compile ggbio.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See ggbio.log for more info.
In addition: There were 49 warnings (use warnings() to see them)
Execution halted
make: *** [Makefile:15: ggbio.pdf] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted