cmdln: Run a command via terminal/command prompt

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Run a command via terminal/command prompt

Description

Provide the command and arguments as a vector. Also can take a lgfl to which all stdout and stderr is written. If lgfl is not provided, a list is returned of 'status', 'stdout' and 'stderr'. Else only the status is returned - 1 success, 0 failed.

Usage

cmdln(cmd, args, ps, lgfl = NULL)

Arguments

cmd	Command to be run
args	Vector of command arguments, each parameter and value must be a separate element
ps	Paramters
lgfl	File to which stdout/err will be written

Details

Note, stdout/err are returned as 'raw'. Use rawToChar() to convert to characters.

Value

status, integer or character

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_gen(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.