| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-26 06:18:05 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the branchpointer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/branchpointer.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 231/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| branchpointer 1.27.0 (landing page) Beth Signal
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: branchpointer |
| Version: 1.27.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:branchpointer.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings branchpointer_1.27.0.tar.gz |
| StartedAt: 2023-05-26 04:27:34 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:35:07 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 452.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: branchpointer.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:branchpointer.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings branchpointer_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/branchpointer.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘branchpointer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘branchpointer’ version ‘1.27.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘branchpointer’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
R 4.1Mb
extdata 1.1Mb
* 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotBranchpointWindow 5.500 0.132 5.656
makeBranchpointWindowForSNP 2.455 0.267 8.110
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘branchpointer.Rnw’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
l.1 \Rdcontents
{\R{} topics documented:}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.1 \Rdcontents{\R
{} topics documented:}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.2 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.3 \HeaderA
{exonsToIntrons}{Convert exon annotation GRanges to intron locat...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.4 \keyword
{internal}{exonsToIntrons}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Description}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Usage undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Arguments undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment ldescription undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{ldescription}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Arguments}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Value undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Value}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Author undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Author}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.34 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.35 \HeaderA
{getBranchpointSequence}{Get branchpoint sequence features Gets...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.36 \keyword
{internal}{getBranchpointSequence}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Description}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Usage undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Arguments undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment ldescription undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.69 ...to use in parallelisation (default = \code
{1})
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{ldescription}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Arguments}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Value undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Value}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Author undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Author}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.83 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.84 \HeaderA
{getCanonical3SS}{Get locations of the first five AG 3' splice ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.85 \keyword
{internal}{getCanonical3SS}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Description}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Usage undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Arguments undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment ldescription undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{ldescription}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Arguments}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Value undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Value}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Author undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Author}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.113 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.114 \HeaderA
{getExonDists}{Get the closest 3' and 5' exons}{getExonDists}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.115 \keyword
{internal}{getExonDists}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Description}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Usage undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Arguments undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment ldescription undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{ldescription}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Arguments}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Value undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Value}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Author undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Author}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! Undefined control sequence.
l.150 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.151 \HeaderA
{getPPT}{Get the best polypyramidine tract}{getPPT}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.152 \keyword
{internal}{getPPT}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Description}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Usage undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Arguments undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment ldescription undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{ldescription}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Arguments}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Value undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Value}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Author undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Author}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! Undefined control sequence.
l.179 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.180 \HeaderA
{getQueryLoc}{Find the closest 3' and 5' exons to a branchpoin...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.181 \keyword
{internal}{getQueryLoc}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Description}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Usage undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Arguments undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment ldescription undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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Type H <return> for immediate help.
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! Undefined control sequence.
l.199 ...ode{queryType}] type of query file (\code
{"SNP"} or \code{"region"})
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.199 ...type of query file (\code{"SNP"} or \code
{"region"})
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{ldescription}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Arguments}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Value undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Value}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Author undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Author}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! Undefined control sequence.
l.217 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.218 \HeaderA
{gtfToExons}{Convert GTF file to exon location file}{gtfToExons}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Description}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Usage undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Arguments undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment ldescription undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{ldescription}.
See the LaTeX manual or LaTeX Companion for explanation.
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! LaTeX Error: \begin{document} ended by \end{Arguments}.
See the LaTeX manual or LaTeX Companion for explanation.
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! LaTeX Error: Environment Value undefined.
See the LaTeX manual or LaTeX Companion for explanation.
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! LaTeX Error: \begin{document} ended by \end{Value}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Author undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: \begin{document} ended by \end{Author}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Examples undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment ExampleCode undefined.
See the LaTeX manual or LaTeX Companion for explanation.
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! LaTeX Error: \begin{document} ended by \end{ExampleCode}.
See the LaTeX manual or LaTeX Companion for explanation.
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! LaTeX Error: \begin{document} ended by \end{Examples}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! Undefined control sequence.
l.251 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.252 \HeaderA
{makeBranchpointWindowForExons}{Make branchpoint window region...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Description}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
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! LaTeX Error: Environment Usage undefined.
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...
! LaTeX Error: \begin{document} ended by \end{Usage}.
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! LaTeX Error: Environment Arguments undefined.
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! LaTeX Error: Environment ldescription undefined.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! Undefined control sequence.
l.269 ... match in the exon annotation file (\code
{"gene\_id"},
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.270 \code
{"transcript\_id"}, or \code{"exon\_id"})
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.270 \code{"transcript\_id"}, or \code
{"exon\_id"})
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: \begin{document} ended by \end{ldescription}.
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! LaTeX Error: Environment Value undefined.
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! LaTeX Error: Environment Examples undefined.
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! LaTeX Error: Environment ExampleCode undefined.
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! Missing $ inserted.
<inserted text>
$
l.291 ...ndowForExons("ENSG00000139618.14", "gene_
id", exons)
! LaTeX Error: \begin{document} ended by \end{ExampleCode}.
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! Missing $ inserted.
<inserted text>
$
l.294 \end{ExampleCode}
! LaTeX Error: \begin{document} ended by \end{Examples}.
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! Undefined control sequence.
l.296 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.297 \HeaderA
{makeBranchpointWindowForSNP}{Makes a branchpointer formatted ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
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! LaTeX Error: \begin{document} ended by \end{Description}.
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! LaTeX Error: Environment Usage undefined.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
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! LaTeX Error: Environment Arguments undefined.
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! LaTeX Error: Environment ldescription undefined.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: \begin{document} ended by \end{ldescription}.
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! Missing $ inserted.
<inserted text>
$
l.339 mart.snp <- biomaRt::useMart("ENSEMBL_
MART_SNP", dataset="hsapiens_snp...
! LaTeX Error: \begin{document} ended by \end{ExampleCode}.
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<inserted text>
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l.341 \end{ExampleCode}
! LaTeX Error: \begin{document} ended by \end{Examples}.
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! Undefined control sequence.
l.343 \inputencoding
{utf8}
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of your error message was never \def'ed. If you have
! Undefined control sequence.
l.344 \HeaderA
{plotBranchpointWindow}{Plots branchpointer predictions}{plotB...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
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! LaTeX Error: \begin{document} ended by \end{Description}.
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! LaTeX Error: Environment Usage undefined.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: \begin{document} ended by \end{Author}.
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! Missing $ inserted.
<inserted text>
$
l.389 querySNPFile <- system.file("extdata","SNP_
example.txt", package = "br...
! LaTeX Error: \begin{document} ended by \end{ExampleCode}.
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! LaTeX Error: \begin{document} ended by \end{Examples}.
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! Undefined control sequence.
l.396 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.397 \HeaderA
{plotStructure}{Plots transcript structures}{plotStructure}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.398 \keyword
{internal}{plotStructure}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
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! LaTeX Error: \begin{document} ended by \end{Description}.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
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! LaTeX Error: Environment Arguments undefined.
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! LaTeX Error: Environment ldescription undefined.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! Undefined control sequence.
l.416 ...cripts}] which transcripts to plot (\code
{"overlapping"} or \code{"...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.416 ...ts to plot (\code{"overlapping"} or \code
{"withExon"})
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.417 \code
{"overlapping"} will plot all transcripts overlapping the exon,
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.418 whereas \code
{"withExon"} will plot all transcripts containing the exon.
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: \begin{document} ended by \end{ldescription}.
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! LaTeX Error: \begin{document} ended by \end{Arguments}.
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! LaTeX Error: \begin{document} ended by \end{Author}.
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! Undefined control sequence.
l.429 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.430 \HeaderA
{predictBranchpoints}{Predict branchpoint probability scores}{...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
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! LaTeX Error: Environment Arguments undefined.
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! LaTeX Error: Environment ldescription undefined.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! Undefined control sequence.
l.462 ...o use in parallelisation (default = \code
{1})
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
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! LaTeX Error: \begin{document} ended by \end{ldescription}.
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! LaTeX Error: Environment Value undefined.
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! LaTeX Error: \begin{document} ended by \end{Value}.
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! LaTeX Error: Environment Author undefined.
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! LaTeX Error: Environment Examples undefined.
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! LaTeX Error: Environment ExampleCode undefined.
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! Missing $ inserted.
<inserted text>
$
l.484 querySNPFile <- system.file("extdata","SNP_
example.txt", package = "br...
! LaTeX Error: \begin{document} ended by \end{ExampleCode}.
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! Missing $ inserted.
<inserted text>
$
l.487 \end{ExampleCode}
! LaTeX Error: \begin{document} ended by \end{Examples}.
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Type H <return> for immediate help.
...
! Undefined control sequence.
l.489 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.490 \HeaderA
{predictionsToSummary}{Convert SNP branchpoint predictions acr...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
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! LaTeX Error: Environment Usage undefined.
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! LaTeX Error: \begin{document} ended by \end{Usage}.
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! LaTeX Error: Environment Arguments undefined.
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! LaTeX Error: Environment ldescription undefined.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! LaTeX Error: Lonely \item--perhaps a missing list environment.
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! Undefined control sequence.
l.513 (default = \code
{0.52})
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Lonely \item--perhaps a missing list environment.
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...
! Undefined control sequence.
l.517 a SNP (default = \code
{0.15})
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: \begin{document} ended by \end{ldescription}.
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! LaTeX Error: \begin{document} ended by \end{Arguments}.
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! LaTeX Error: Environment Value undefined.
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! LaTeX Error: \begin{document} ended by \end{Value}.
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! LaTeX Error: Environment Author undefined.
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! LaTeX Error: \begin{document} ended by \end{Author}.
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! LaTeX Error: Environment Examples undefined.
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! Missing $ inserted.
<inserted text>
$
l.536 querySNPFile <- system.file("extdata","SNP_
example.txt", package = "br...
! Missing $ inserted.
<inserted text>
$
l.539
! LaTeX Error: \begin{document} ended by \end{ExampleCode}.
See the LaTeX manual or LaTeX Companion for explanation.
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! LaTeX Error: \begin{document} ended by \end{Examples}.
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! Undefined control sequence.
l.543 \inputencoding
{utf8}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.544 \HeaderA
{readQueryFile}{Read a query file}{readQueryFile}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Environment Description undefined.
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...
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/branchpointer.Rcheck/00check.log’
for details.
branchpointer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL branchpointer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘branchpointer’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (branchpointer)
branchpointer.Rcheck/branchpointer-Ex.timings
| name | user | system | elapsed | |
| gtfToExons | 1.519 | 0.000 | 1.527 | |
| makeBranchpointWindowForExons | 1.927 | 0.003 | 1.934 | |
| makeBranchpointWindowForSNP | 2.455 | 0.267 | 8.110 | |
| plotBranchpointWindow | 5.500 | 0.132 | 5.656 | |
| predictBranchpoints | 3.608 | 0.048 | 3.662 | |
| predictionsToSummary | 3.521 | 0.243 | 3.770 | |
| readQueryFile | 2.417 | 0.000 | 2.421 | |