todo.md

In croesel/Trans2Kegg: Annotate transcripts and predicted protein sequences

Subdirectory 'R' contains invalid file names: ‘annot.csv’ ‘blastResult.csv’ ‘deTrans.fa’ ‘en.utf-8.add’ ‘en.utf-8.add.spl’ ‘uniToKO.csv’ * NOTE: Avoid sapply(); use vapply() Found in files: annotateAws.R (line 89, column 16) annotateAws.R (line 93, column 15) Checking function lengths................ * NOTE: Recommended function length <= 50 lines. There are 1 functions > 50 lines. The longest 5 functions are: getPathways() (R/getPathway.R, line 13): 78 lines annotateAws() (R/annotateAws.R, line 23): 46 lines annotateNCBI() (R/annotateNCBI.R, line 19): 45 lines .tryParseResultAws() (R/annotateAws.R, line 122): 43 lines mergeAnnotations() (R/mergeAnnotations.R, line 15): 42 lines Checking man page documentation... * NOTE: Consider adding runnable examples to the following man pages which document exported objects: getKegg.Rd * NOTE: Consider multiples of 4 spaces for line indents, 23 lines(2%) are not. First 6 lines: R/annotateNCBI.R:20 refTrans <- readDNAStringSet(fasta) R/annotateNCBI.R:21 rowNum <- 0 R/annotateNCBI.R:22 accDone <- c() R/annotateNCBI.R:23 dfUniKegg <- data.frame() R/annotateNCBI.R:24 # Check if BLAST already started. If already star... R/annotateNCBI.R:25 # where you left off. See http://bioconductor.org/developers/how-to/coding-style/ See FormatR package: https://cran.r-project.org/web/packages/formatR/index.html

croesel/Trans2Kegg documentation built on May 12, 2019, 3:11 p.m.