| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:06 -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 | ||||
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To the developers/maintainers of the consensusSeekeR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/consensusSeekeR.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 413/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| consensusSeekeR 1.29.0 (landing page) Astrid Deschenes
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: consensusSeekeR |
| Version: 1.29.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings consensusSeekeR_1.29.0.tar.gz |
| StartedAt: 2023-05-26 04:37:08 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:37:30 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 22.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: consensusSeekeR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:consensusSeekeR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings consensusSeekeR_1.29.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/consensusSeekeR.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 ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.29.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
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 ‘consensusSeekeR’ can be installed ... OK
* checking installed package size ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘consensusSeekeR.Rmd’ using ‘UTF-8’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘consensusSeekeR.Rmd’
...
> proc.time()
user system elapsed
0.179 0.023 0.196
... incomplete output. Crash?
* 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
{consensusSeekeR-package}{consensusSeekeR: Detection of consensu...
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 \aliasA
{consensusSeekeR}{consensusSeekeR-package}{consensusSeekeR}
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.5 \keyword
{package}{consensusSeekeR-package}
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 Author undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Author}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment SeeAlso undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.27 \item{} \code
{\LinkA{readNarrowPeakFile}{readNarrowPeakFile}} for extra...
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.27 \item{} \code{\LinkA
{readNarrowPeakFile}{readNarrowPeakFile}} for extra...
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.29 \item{} \code
{\LinkA{findConsensusPeakRegions}{findConsensusPeakRegions...
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.29 \item{} \code{\LinkA
{findConsensusPeakRegions}{findConsensusPeakRegions...
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{SeeAlso}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.35 \inputencoding
{utf8}
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.36 \HeaderA
{A549\_NR3C1\_CFQ\_NarrowPeaks\_partial}{}{A549.Rul.NR3C1.Rul.C...
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.37 \keyword
{datasets}{A549\_NR3C1\_CFQ\_NarrowPeaks\_partial}
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.
...
! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Format undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.54 A \code
{GRanges} containing one entry per site. The ranges are
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.56 \code
{A549\_NR3C1\_CFQ\_Peaks\_partial}.
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{Format}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Details undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Details}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Source undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Source}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment References undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{References}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment SeeAlso undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.82 \item{} \code
{\LinkA{A549\_NR3C1\_CFQ\_Peaks\_partial}{A549.Rul.NR3C1.R...
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.82 \item{} \code{\LinkA
{A549\_NR3C1\_CFQ\_Peaks\_partial}{A549.Rul.NR3C1.R...
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 \item{} \code
{\LinkA{findConsensusPeakRegions}{findConsensusPeakRegions...
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 \item{} \code{\LinkA
{findConsensusPeakRegions}{findConsensusPeakRegions...
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{SeeAlso}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Examples undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment ExampleCode undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! You can't use `macro parameter character #' in vertical mode.
l.94 #
# Loading datasets
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.94 ##
Loading datasets
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! Missing $ inserted.
<inserted text>
$
l.95 data(A549_
NR3C1_CFQ_NarrowPeaks_partial)
! Missing $ inserted.
<inserted text>
$
l.99
! You can't use `macro parameter character #' in vertical mode.
l.100 #
# Assigning experiment name to each row of the dataset.
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.100 ##
Assigning experiment name to each row of the dataset.
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.101 #
# NarrowPeak and Peak datasets from the same experiment must
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.101 ##
NarrowPeak and Peak datasets from the same experiment must
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.102 #
# have identical names.
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.102 ##
have identical names.
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! Missing $ inserted.
<inserted text>
$
l.103 names(A549_
NR3C1_CFQ_NarrowPeaks_partial) <- rep("NR3C1_CFQ",
! Missing $ inserted.
<inserted text>
$
l.111
! You can't use `macro parameter character #' in vertical mode.
l.112 #
# Calculating consensus regions for chromosome 3
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.112 ##
Calculating consensus regions for chromosome 3
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.113 #
# with a default region size of 300 bp (2 * extendingSize)
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.113 ##
with a default region size of 300 bp (2 * extendingSize)
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.114 #
# which is extended to include all genomic regions for the closest
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.114 ##
which is extended to include all genomic regions for the closest
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.115 #
# peak to the median position of all peaks included in the region (for
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.115 ##
peak to the median position of all peaks included in the region (for
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.116 #
# each experiment).
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.116 ##
each experiment).
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.117 #
# Peaks from both experiments must be present in a region to
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.117 ##
Peaks from both experiments must be present in a region to
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.118 #
# be retained as a consensus region.
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in horizontal mode.
l.118 ##
be retained as a consensus region.
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! Missing $ inserted.
<inserted text>
$
l.121 narrowPeaks = c(A549_
NR3C1_CFQ_NarrowPeaks_partial,
! Missing $ inserted.
<inserted text>
$
l.131
! LaTeX Error: \begin{document} ended by \end{ExampleCode}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Examples}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.134 \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.135 \HeaderA
{findConsensusPeakRegions}{Extract regions sharing features in...
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.
...
! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Arguments undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment ldescription undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! 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.172 \item[\code{narrowPeaks}] a \code
{GRanges} containing
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.174 for all analyzed experiments. All \code
{GRanges} entries must
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.176 the called peak. All \code
{GRanges} entries must also
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.178 \code
{peaks} entry must have an associated \code{narrowPeaks} entry.
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.178 ...eaks} entry must have an associated \code
{narrowPeaks} entry.
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.179 A \code
{GRanges} entry is associated to a \code{narrowPeaks} entry by
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.179 ...e{GRanges} entry is associated to a \code
{narrowPeaks} entry by
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.
...
! Undefined control sequence.
l.182 \item[\code{peaks}] a \code
{GRanges} containing called peaks of signal
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.184 for all analyzed experiments. All \code
{GRanges} entries must
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.186 peak. All \code
{GRanges} entries must
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.188 \code
{peaks} entry must have an associated \code{narrowPeaks} entry. A
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.188 ...eaks} entry must have an associated \code
{narrowPeaks} entry. A
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.189 \code
{GRanges} entry is associated to a \code{narrowPeaks} entry by ha...
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.189 ...e{GRanges} entry is associated to a \code
{narrowPeaks} entry by having
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.
...
! Undefined control sequence.
l.192 \item[\code{chrInfo}] a \code
{Seqinfo} containing the name and the len...
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.194 \code
{Seqinfo} will be analyzed.
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.
...
! Undefined control sequence.
l.196 \item[\code{extendingSize}] a \code
{numeric} value indicating the size...
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 equal to twice the value of the \code
{extendingSize} parameter.
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.200 The size of the \code
{extendingSize} must be a positive integer.
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.
...
! Undefined control sequence.
l.203 \item[\code{expandToFitPeakRegion}] a \code
{logical} indicating if the...
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.204 which is set by the \code
{extendingSize} parameter is extended to include
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.207 ...sidered for the extension. Default: \code
{FALSE}.
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.
...
! Undefined control sequence.
l.209 \item[\code{shrinkToFitPeakRegion}] a \code
{logical} indicating if the...
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.210 which is set by the \code
{extendingSize} parameter is shrinked to
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.212 ...than the consensus region. Default: \code
{FALSE}.
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.
...
! Undefined control sequence.
l.214 \item[\code{minNbrExp}] a positive \code
{numeric} or a positive \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.214 ...sitive \code{numeric} or a positive \code
{integer}
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 in the \code
{narrowPeaks} and \code{peaks} parameters. Default = 1.
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 in the \code{narrowPeaks} and \code
{peaks} parameters. Default = 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.
...
! Undefined control sequence.
l.220 \item[\code{nbrThreads}] a \code
{numeric} or a \code{integer} indicati...
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.220 ...{nbrThreads}] a \code{numeric} or a \code
{integer} indicating the
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.221 ... of threads to use in parallel. The \code
{nbrThreads} must be a
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}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Arguments}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Value undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.227 an \code
{list} of \code{class} "consensusRanges" containing :
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.227 an \code{list} of \code
{class} "consensusRanges" containing :
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.230 \item{} \code
{call} the matched call.
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.231 \item{} \code
{consensusRanges} a \code{GRanges} containing the
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.231 \item{} \code{consensusRanges} a \code
{GRanges} containing the
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{Value}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Author undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Author}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Examples undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment ExampleCode undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! You can't use `macro parameter character #' in vertical mode.
l.245 #
# Loading datasets
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.245 ##
Loading datasets
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! Missing $ inserted.
<inserted text>
$
l.246 data(A549_
CTCF_MYN_NarrowPeaks_partial)
! Missing $ inserted.
<inserted text>
$
l.250
! You can't use `macro parameter character #' in vertical mode.
l.251 #
# Assigning experiment name "CTCF_MYJ" to first experiment
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.251 ##
Assigning experiment name "CTCF_MYJ" to first experiment
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! Missing $ inserted.
<inserted text>
$
l.251 ## Assigning experiment name "CTCF_
MYJ" to first experiment
! Missing $ inserted.
<inserted text>
$
l.256
! You can't use `macro parameter character #' in vertical mode.
l.257 #
# Assigning experiment name "CTCF_MYN" to second experiment
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.257 ##
Assigning experiment name "CTCF_MYN" to second experiment
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! Missing $ inserted.
<inserted text>
$
l.257 ## Assigning experiment name "CTCF_
MYN" to second experiment
! Missing $ inserted.
<inserted text>
$
l.262
! You can't use `macro parameter character #' in vertical mode.
l.263 #
# Only choromsome 1 is going to be analysed
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.263 ##
Only choromsome 1 is going to be analysed
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.266 #
# Find consensus regions with both experiments
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.266 ##
Find consensus regions with both experiments
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! Missing $ inserted.
<inserted text>
$
l.268 narrowPeaks = c(A549_
CTCF_MYJ_NarrowPeaks_partial,
! Missing $ inserted.
<inserted text>
$
l.278
! You can't use `macro parameter character #' in vertical mode.
l.279 #
# Print 2 first consensus regions
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! You can't use `macro parameter character #' in vertical mode.
l.279 ##
Print 2 first consensus regions
Sorry, but I'm not programmed to handle this case;
I'll just pretend that you didn't ask for it.
! Missing $ inserted.
<inserted text>
$
l.281
! LaTeX Error: \begin{document} ended by \end{ExampleCode}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: \begin{document} ended by \end{Examples}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Undefined control sequence.
l.284 \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.285 \HeaderA
{findConsensusPeakRegionsForOneChrom}{Extract regions sharing ...
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.286 \keyword
{internal}{findConsensusPeakRegionsForOneChrom}
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.
...
! LaTeX Error: \begin{document} ended by \end{Usage}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment Arguments undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Environment ldescription undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! 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.310 \item[\code{chrName}] a \code
{character}, the name of the chromosome t...
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.
...
! Undefined control sequence.
l.312 \item[\code{allPeaks}] a \code
{GRanges} containing all peaks from all ...
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.
...
! Undefined control sequence.
l.315 \item[\code{allNarrowPeaks}] a \code
{GRanges} containing all narrow pe...
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.
...
! Undefined control sequence.
l.318 \item[\code{extendingSize}] a \code
{numeric} value indicating the size...
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.321 twice the value of the \code
{extendingSize} parameter. The size of
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.322 the \code
{extendingSize} must be a positive integer. Default = 250.
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.
...
! Undefined control sequence.
l.324 \item[\code{expandToFitPeakRegion}] a \code
{logical} indicating if the...
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.325 the \code
{extendingSize} parameter is extended to include all narrow peak
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.
...
! Undefined control sequence.
l.331 \item[\code{shrinkToFitPeakRegion}] a \code
{logical} indicating if the...
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.332 by the \code
{extendingSize} parameter is shrinked to fit the narrow
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.
...
! Undefined control sequence.
l.335 \item[\code{minNbrExp}] a \code
{numeric} indicating the minimum number...
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.338 of files present in the \code
{narrowPeakFiles} parameter. Default = 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.
...
! Undefined control sequence.
l.340 \item[\code{chrList}] a \code
{Seqinfo} containing the name and the len...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
* checking PDF version of manual without index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
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Problem closing connection: No space left on device
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Problem closing connection: No space left on device
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Warning in close.connection(con) :
Problem closing connection: No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) :
Error writing to connection: No space left on device
* DONE
Status: 2 ERRORs, 1 WARNING
See
‘/home/biocbuild/bbs-3.18-bioc/meat/consensusSeekeR.Rcheck/00check.log’
for details.
consensusSeekeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL consensusSeekeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘consensusSeekeR’ ... ** using staged installation ** R ** data ** 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 (consensusSeekeR)