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rasilab / adarnell_2018

scripts for analyzing data and generating figures in the paper
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Calculate codon-specific ribosome density error #2

Open madaojjc opened 4 years ago

madaojjc commented 4 years ago

Hi, I had met some problem when using your scripts, and I don't know whether it was due to some package update..

`> codon.ribo.density <- lapply(codons, calculateCodonDensity)

Error: Columns 1, 2, 3, 4, 5, … (and 295 more) must be named. Use .name_repair to specify repair. Call rlang::last_error() to see a backtrace `

madaojjc commented 4 years ago

Here is my session info

! package version date lib source
AnnotationDbi 1.46.0 2019-05-02 [1] Bioconductor
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
Biobase 2.44.0 2019-05-02 [1] Bioconductor
BiocGenerics 0.30.0 2019-05-02 [1] Bioconductor
BiocParallel 1.18.1 2019-08-06 [1] Bioconductor
biomaRt 2.40.3 2019-07-17 [1] Bioconductor
Biostrings 2.52.0 2019-05-02 [1] Bioconductor
bit 1.1-14 2018-05-29 [1] CRAN (R 3.6.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 3.6.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
blob 1.2.0 2019-07-09 [1] CRAN (R 3.6.0)
broom 0.5.2 2019-04-07 [1] CRAN (R 3.6.0)
BSgenome 1.52.0 2019-05-02 [1] Bioconductor
BSgenome.Hsapiens.UCSC.hg38 1.4.1 2019-08-12 [1] Bioconductor
callr 3.3.1 2019-07-18 [1] CRAN (R 3.6.0)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 3.6.1)
class 7.3-15 2019-01-01 [1] CRAN (R 3.6.0)
classInt 0.4-1 2019-08-06 [1] CRAN (R 3.6.1)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
curl 4.0 2019-07-22 [1] CRAN (R 3.6.1)
DBI 1.0.0 2018-05-02 [1] CRAN (R 3.6.0)
DelayedArray 0.10.0 2019-05-02 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
devtools 2.1.0 2019-07-06 [1] CRAN (R 3.6.0)
digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.0)
dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.0)
e1071 1.7-2 2019-06-05 [1] CRAN (R 3.6.0)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.6.0)
forcats 0.4.0 2019-02-17 [1] CRAN (R 3.6.1)
foreign 0.8-72 2019-08-02 [1] CRAN (R 3.6.1)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.0)
GenomeInfoDb 1.20.0 2019-05-02 [1] Bioconductor
GenomeInfoDbData 1.2.1 2019-05-06 [1] Bioconductor
GenomicAlignments 1.20.1 2019-06-18 [1] Bioconductor
GenomicFeatures 1.36.4 2019-07-10 [1] Bioconductor
GenomicRanges 1.36.0 2019-05-02 [1] Bioconductor
ggplot2 3.2.1 2019-08-10 [1] CRAN (R 3.6.1)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.1)
haven 2.1.1 2019-07-04 [1] CRAN (R 3.6.1)
V hms 0.5.0 2019-08-23 [1] CRAN (R 3.6.1)
httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.1)
IRanges 2.18.1 2019-05-31 [1] Bioconductor
jsonlite 1.6 2018-12-07 [1] CRAN (R 3.6.0)
KernSmooth 2.23-15 2015-06-29 [1] CRAN (R 3.6.0)
lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0)
lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.6.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
maptools 0.9-5 2019-02-18 [1] CRAN (R 3.6.1)
Matrix 1.2-17 2019-03-22 [1] CRAN (R 3.6.0)
matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.6.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
modelr 0.1.5 2019-08-08 [1] CRAN (R 3.6.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
nlme 3.1-141 2019-08-01 [1] CRAN (R 3.6.1)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0)
pkgbuild 1.0.4 2019-08-05 [1] CRAN (R 3.6.1)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 3.6.0)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
purrr 0.3.2 2019-03-15 [1] CRAN (R 3.6.0)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 3.6.0)
Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
RCurl 1.95-4.12 2019-03-04 [1] CRAN (R 3.6.0)
readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.0)
readxl 1.3.1 2019-03-13 [1] CRAN (R 3.6.1)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.0)
rgdal 1.4-4 2019-05-29 [1] CRAN (R 3.6.1)
rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
Rsamtools 2.0.0 2019-05-02 [1] Bioconductor
RSQLite 2.1.2 2019-07-24 [1] CRAN (R 3.6.1)
rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.0)
rtracklayer 1.44.2 2019-07-22 [1] Bioconductor
rvest 0.3.4 2019-05-15 [1] CRAN (R 3.6.1)
S4Vectors 0.22.0 2019-05-02 [1] Bioconductor
scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
sf 0.7-7 2019-07-24 [1] CRAN (R 3.6.1)
sp 1.3-1 2018-06-05 [1] CRAN (R 3.6.1)
stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
SummarizedExperiment 1.14.1 2019-07-31 [1] Bioconductor
testthat 2.2.1 2019-07-25 [1] CRAN (R 3.6.1)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
tidycensus 0.9.3 2019-08-26 [1] Github (walkerke/tidycensus@f7753bb) tidyr 0.8.3 2019-03-01 [1] CRAN (R 3.6.0)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0)
tidyverse 1.2.1 2017-11-14 [1] CRAN (R 3.6.1)
tigris 0.8.2 2019-06-12 [1] CRAN (R 3.6.1)
units 0.6-4 2019-08-22 [1] CRAN (R 3.6.1)
usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.0)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.0)
uuid 0.1-2 2015-07-28 [1] CRAN (R 3.6.0)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
XML 3.98-1.20 2019-06-06 [1] CRAN (R 3.6.0)
xml2 1.2.2 2019-08-09 [1] CRAN (R 3.6.1)
XVector * 0.24.0 2019-05-02 [1] Bioconductor
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.0)
zlibbioc 1.30.0 2019-05-02 [1] Bioconductor