daniellemstevens / permissr Goto Github PK
View Code? Open in Web Editor NEWAn R package, permissR enables finding permissive, non-coding sites in bacterial genomes.
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Error in utils::txtProgressBar(min = 0, max = total, style = 3) : must have 'max' > 'min'
Have been contacted by a user regarding an error that has come up for one of their genomes. The steps that were completed and the error are listed below.
Calculating distance Between Protein-coding Genes...
-------------------------------------------------
Loading Fasta file...
Pulling out sequence of site and calculating GC content...
Ranking sites by GC content...
-------------------------------------------------
Loading IS elements file...
Reformating IS Elements....
-------------------------------------------------
Calculating GC Content accross the genome...
Calculating Shannon Entropy accross the genome...
-------------------------------------------------
Searching to check if sites have homology elsewhere in the genome...
Error in utils::txtProgressBar(min = 0, max = total, style = 3) :
must have 'max' > 'min'
In addition: Warning messages:
1: In if (file_in$FEATURES[[i]]$type == "CDS") { :
the condition has length > 1 and only the first element will be used
2: In if (file_in$FEATURES[[i]]$type == "gene") { :
the condition has length > 1 and only the first element will be used
3: In if (file_in$FEATURES[[i]]$type == "regulatory") { :
the condition has length > 1 and only the first element will be used
Output from session_info():
─ Session info ──────────────────────────────────────────────────────────────
setting value
version R version 4.1.1 (2021-08-10)
os Ubuntu 20.04.3 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Chicago
date 2021-11-22
pandoc 2.12 @ /home/swetha/anaconda3/bin/pandoc
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
ade4 1.7-18 2021-09-16 [2] CRAN (R 4.1.1)
AnnotationDbi 1.54.1 2021-06-08 [2] Bioconductor
assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.1.1)
Biobase 2.52.0 2021-05-19 [2] Bioconductor
BiocFileCache 2.0.0 2021-05-19 [2] Bioconductor
BiocGenerics 0.38.0 2021-05-19 [2] Bioconductor
BiocIO 1.2.0 2021-05-19 [2] Bioconductor
BiocParallel 1.26.2 2021-08-22 [2] Bioconductor
biomaRt 2.48.3 2021-08-15 [2] Bioconductor
Biostrings 2.60.2 2021-08-05 [2] Bioconductor
bit 4.0.4 2020-08-04 [2] CRAN (R 4.1.1)
bit64 4.0.5 2020-08-30 [2] CRAN (R 4.1.1)
bitops 1.0-7 2021-04-24 [2] CRAN (R 4.1.1)
blob 1.2.2 2021-07-23 [2] CRAN (R 4.1.1)
boot 1.3-28 2021-05-03 [4] CRAN (R 4.0.5)
BSgenome 1.60.0 2021-05-19 [2] Bioconductor
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.1)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.1)
class 7.3-19 2021-05-03 [4] CRAN (R 4.0.5)
cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.1)
colorspace 2.0-2 2021-06-24 [2] CRAN (R 4.1.1)
crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.1)
curl 4.3.2 2021-06-23 [2] CRAN (R 4.1.1)
data.table 1.14.2 2021-09-27 [2] CRAN (R 4.1.1)
DBI 1.1.1 2021-01-15 [2] CRAN (R 4.1.1)
dbplyr 2.1.1 2021-04-06 [2] CRAN (R 4.1.1)
DelayedArray 0.18.0 2021-05-19 [2] Bioconductor
desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.1)
DescTools 0.99.43 2021-09-09 [2] CRAN (R 4.1.1)
devtools * 2.4.2 2021-06-07 [1] CRAN (R 4.1.1)
digest 0.6.28 2021-09-23 [1] CRAN (R 4.1.1)
dplyr 1.0.7 2021-06-18 [2] CRAN (R 4.1.1)
e1071 1.7-9 2021-09-16 [2] CRAN (R 4.1.1)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.1)
Exact 3.0 2021-09-02 [2] CRAN (R 4.1.1)
expm 0.999-6 2021-01-13 [2] CRAN (R 4.1.1)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.1)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.1)
filelock 1.0.2 2018-10-05 [2] CRAN (R 4.1.1)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.1)
genbankr 1.20.0 2021-05-19 [2] Bioconductor
generics 0.1.1 2021-10-25 [2] CRAN (R 4.1.1)
GenomeInfoDb 1.28.4 2021-09-05 [2] Bioconductor
GenomeInfoDbData 1.2.6 2021-10-26 [2] Bioconductor
GenomicAlignments 1.28.0 2021-05-19 [2] Bioconductor
GenomicFeatures 1.44.2 2021-08-26 [2] Bioconductor
GenomicRanges 1.44.0 2021-05-19 [2] Bioconductor
ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.1.1)
gld 2.6.2 2020-01-08 [2] CRAN (R 4.1.1)
glue 1.5.0 2021-11-07 [1] CRAN (R 4.1.1)
gtable 0.3.0 2019-03-25 [2] CRAN (R 4.1.1)
hms 1.1.1 2021-09-26 [2] CRAN (R 4.1.1)
httr 1.4.2 2020-07-20 [2] CRAN (R 4.1.1)
IRanges 2.26.0 2021-05-19 [2] Bioconductor
KEGGREST 1.32.0 2021-05-19 [2] Bioconductor
lattice 0.20-45 2021-09-22 [4] CRAN (R 4.1.1)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1)
lmom 2.8 2019-03-12 [2] CRAN (R 4.1.1)
magrittr * 2.0.1 2020-11-17 [1] CRAN (R 4.1.1)
MASS 7.3-54 2021-05-03 [4] CRAN (R 4.0.5)
Matrix 1.3-4 2021-06-01 [4] CRAN (R 4.1.0)
MatrixGenerics 1.4.3 2021-08-26 [2] Bioconductor
matrixStats 0.61.0 2021-09-17 [2] CRAN (R 4.1.1)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.1)
munsell 0.5.0 2018-06-12 [2] CRAN (R 4.1.1)
mvtnorm 1.1-3 2021-10-08 [2] CRAN (R 4.1.1)
permissR 0.1.0 2021-10-26 [2] Github (DanielleMStevens/permissR@c98ce34)
pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.1)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.1)
pkgload 1.2.3 2021-10-13 [1] CRAN (R 4.1.1)
png 0.1-7 2013-12-03 [2] CRAN (R 4.1.1)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.1)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.1)
progress 1.2.2 2019-05-16 [2] CRAN (R 4.1.1)
proxy 0.4-26 2021-06-07 [2] CRAN (R 4.1.1)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.1)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.1.1)
Rcpp 1.0.7 2021-07-07 [2] CRAN (R 4.1.1)
RCurl 1.98-1.5 2021-09-17 [2] CRAN (R 4.1.1)
remotes 2.4.1 2021-09-29 [1] CRAN (R 4.1.1)
restfulr 0.0.13 2017-08-06 [2] CRAN (R 4.1.1)
rjson 0.2.20 2018-06-08 [2] CRAN (R 4.1.1)
rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.1)
rootSolve 1.8.2.3 2021-09-29 [2] CRAN (R 4.1.1)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.1)
Rsamtools 2.8.0 2021-05-19 [2] Bioconductor
RSQLite 2.2.8 2021-08-21 [2] CRAN (R 4.1.1)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.1)
rtracklayer 1.52.1 2021-08-15 [2] Bioconductor
S4Vectors 0.30.2 2021-10-03 [2] Bioconductor
scales 1.1.1 2020-05-11 [2] CRAN (R 4.1.1)
seqinr 4.2-8 2021-06-09 [2] CRAN (R 4.1.1)
sessioninfo 1.2.1 2021-11-02 [1] CRAN (R 4.1.1)
stringi 1.7.5 2021-10-04 [1] CRAN (R 4.1.1)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.1)
SummarizedExperiment 1.22.0 2021-05-19 [2] Bioconductor
testthat 3.1.0 2021-10-04 [1] CRAN (R 4.1.1)
tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.1)
tidyselect 1.1.1 2021-04-30 [2] CRAN (R 4.1.1)
usethis * 2.1.2 2021-10-25 [2] CRAN (R 4.1.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.1)
VariantAnnotation 1.38.0 2021-05-19 [2] Bioconductor
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.1)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.1)
XML 3.99-0.8 2021-09-17 [2] CRAN (R 4.1.1)
xml2 1.3.2 2020-04-23 [2] CRAN (R 4.1.1)
XVector 0.32.0 2021-05-19 [2] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.1)
zlibbioc 1.38.0 2021-05-19 [2] Bioconductor
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