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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 BEclear
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* checking for file ‘BEclear/DESCRIPTION’ ... OK
* preparing ‘BEclear’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
Loading required namespace: BEclear
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘BEclear.Rmd’ using rmarkdown
BiocParallelParam-class package:BiocParallel R Documentation
_B_i_o_c_P_a_r_a_l_l_e_l_P_a_r_a_m _o_b_j_e_c_t_s
_D_e_s_c_r_i_p_t_i_o_n:
The 'BiocParallelParam' virtual class stores configuration
parameters for parallel execution. Concrete subclasses include
'SnowParam', 'MulticoreParam', 'BatchtoolsParam', and 'DoparParam'
and 'SerialParam'.
_D_e_t_a_i_l_s:
'BiocParallelParam' is the virtual base class on which other
parameter objects build. There are 5 concrete subclasses:
'SnowParam': distributed memory computing
'MulticoreParam': shared memory computing
'BatchtoolsParam': scheduled cluster computing
'DoparParam': foreach computing
'SerialParam': non-parallel execution
The parameter objects hold configuration parameters related to the
method of parallel execution such as shared memory, independent
memory or computing with a cluster scheduler.
_C_o_n_s_t_r_u_c_t_i_o_n:
The 'BiocParallelParam' class is virtual and has no constructor.
Instances of the subclasses can be created with the following:
• 'SnowParam()'
• 'MulticoreParam()'
• 'BatchtoolsParam()'
• 'DoparParam()'
• 'SerialParam()'
_A_c_c_e_s_s_o_r_s:
_B_a_c_k-_e_n_d _c_o_n_t_r_o_l:
In the code below 'BPPARAM' is a 'BiocParallelParam' object.
'bpworkers(x)', 'bpworkers(x, ...)': 'integer(1)' or
'character()'. Gets the number or names of the back-end
workers. The setter is supported for SnowParam and
MulticoreParam only.
'bpnworkers(x)': 'integer(1)'. Gets the number of the back-end
workers.
'bptasks(x)', 'bptasks(x) <- value': 'integer(1)'. Get or set
the number of tasks for a job. 'value' can be a scalar
integer > 0L, or integer 0L for matching the worker number,
or 'NA' for representing an infinite task number.
'DoparParam' and 'BatchtoolsParam' have their own approach
to dividing a job among workers.
We define a job as a single call to a function such as
'bplapply', 'bpmapply' etc. A task is the division of the
'X' argument into chunks. When 'tasks == 0' (default), 'X'
is divided by the number of workers. This approach
distributes 'X' in (approximately) equal chunks.
A 'tasks' value of > 0 dictates the total number of tasks.
Values can range from 1 (all of 'X' to a single worker) to
the length of 'X' (each element of 'X' to a different
worker); values greater than 'length(X)' (e.g.,
'.Machine$integer.max') are rounded to 'length(X)'.
When the length of 'X' is less than the number of workers
each element of 'X' is sent to a worker and 'tasks' is
ignored. Another case where the 'tasks' value is ignored is
when using the 'bpiterate' function; the number of tasks are
defined by the number of data chunks returned by the 'ITER'
function.
'bpstart(x)': 'logical(1)'. Starts the back-end, if necessary.
'bpstop(x)': 'logical(1)'. Stops the back-end, if necessary and
possible.
'bpisup(x)': 'logical(1)'. Tests whether the back-end is
available for processing, returning a scalar logical value.
'bp*' functions such as 'bplapply' automatically start the
back-end if necessary.
'bpbackend(x)', 'bpbackend(x) <- value': Gets or sets the
parallel 'bpbackend'. Not all back-ends can be retrieved;
see 'methods("bpbackend")'.
'bplog(x)', 'bplog(x) <- value': Get or enable logging, if
available. 'value' must be a 'logical(1)'.
'bpthreshold(x)', 'bpthreshold(x) <- value': Get or set the
logging threshold. 'value' must be a 'character(1)' string
of one of the levels defined in the 'futile.logger' package:
"TRACE", "DEBUG", "INFO", "WARN", "ERROR", or "FATAL".
'bplogdir(x)', 'bplogdir(x) <- value': Get or set an optional
directory for saving log files. The directory must already
exist with read / write ability.
'bpresultdir(x)', 'bpresultdir(x) <- value': Get or set an
optional directory for saving results as 'rda' files. The
directory must already exist with read / write ability.
'bptimeout(x)', 'bptimeout(x) <- value': 'numeric(1)' Time (in
seconds) allowed for worker to complete a task. This value
is passed to base::setTimeLimit() as both the 'cpu' and
'elapsed' arguments. If the computation exceeds 'timeout' an
error is thrown with message 'reached elapsed time limit'.
'bpexportglobals(x)', 'bpexportglobals(x) <- value':
'logical(1)' Export 'base::options()' from manager to
workers? Default 'TRUE'.
'bpexportvariables(x)', 'bpexportvariables(x) <- value':
'logical(1)' Automatically export the variables which are
defined in the global environment and used by the function
from manager to workers. Default 'TRUE'.
'bpprogressbar(x)', 'bpprogressbar(x) <- value': Get or set the
value to enable text progress bar. 'value' must be a
'logical(1)'.
'bpRNGseed(x)', 'bpRNGseed(x) <- value': Get or set the seed for
random number generaton. 'value' must be a 'numeric(1)' or
'NULL'.
'bpjobname(x)', 'bpjobname(x) <- value': Get or set the job
name.
'bpforceGC(x)', 'bpforceGC(x) <- value': Get or set whether
'garbage collection' should be invoked at the end of each
call to 'FUN'.
'bpfallback(x)', 'bpfallback(x) <- value': Get or set whether
the fallback 'SerialParam' should be used (e.g., for
efficiency when starting a cluster) when the current
'BPPARAM' has not been started and the worker number is less
than or equal to 1.
_E_r_r_o_r _H_a_n_d_l_i_n_g:
In the code below 'BPPARAM' is a 'BiocParallelParam' object.
'bpstopOnError(x)', 'bpstopOnError(x) <- value': 'logical()'.
Controls if the job stops when an error is hit.
'stop.on.error' controls whether the job stops after an
error is thrown. When 'TRUE', the output contains all
successfully completed results up to and including the
error. When 'stop.on.error == TRUE' all computations stop
once the error is hit. When 'FALSE', the job runs to
completion and successful results are returned along with
any error messages.
_M_e_t_h_o_d_s:
_E_v_a_l_u_a_t_i_o_n:
In the code below 'BPPARAM' is a 'BiocParallelParam' object.
Full documentation for these functions are on separate man
pages: see ?'bpmapply', ?'bplapply', ?'bpvec', ?'bpiterate' and
?'bpaggregate'.
• 'bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE,
USE.NAMES=TRUE, BPPARAM=bpparam())'
• 'bplapply(X, FUN, ..., BPPARAM=bpparam())'
• 'bpvec(X, FUN, ..., AGGREGATE=c, BPPARAM=bpparam())'
• 'bpiterate(ITER, FUN, ..., BPPARAM=bpparam())'
• 'bpaggregate(x, data, FUN, ..., BPPARAM=bpparam())'
_O_t_h_e_r:
In the code below 'BPPARAM' is a 'BiocParallelParam' object.
• 'show(x)'
_A_u_t_h_o_r(_s):
Martin Morgan and Valerie Obenchain.
_S_e_e _A_l_s_o:
• 'SnowParam' for computing in distributed memory
• 'MulticoreParam' for computing in shared memory
• 'BatchtoolsParam' for computing with cluster schedulers
• 'DoparParam' for computing with foreach
• 'SerialParam' for non-parallel execution
_E_x_a_m_p_l_e_s:
getClass("BiocParallelParam")
## For examples see ?SnowParam, ?MulticoreParam, ?BatchtoolsParam
## and ?SerialParam.
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: processing vignette 'BEclear.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building ‘BEclear.Rmd’
SUMMARY: processing the following file failed:
‘BEclear.Rmd’
Error: Vignette re-building failed.
Execution halted