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colewunderlich robinotn sgblanch olaris justinzzw jun-lizst huipan1973 zzzsssyyy1995 saisaitianctsgetr's Issues
Error in to %in% valid_to() : argument "to" is missing, with no default
Dear Developer,
I'm trying to execute the CTSgetR like the example but receiving the above error.
> CTSgetR::CTSgetR(id=c("C15973","C00026","C05381"), from=c("KEGG"), to = c("PubChem CID")) Error in to %in% valid_to() : argument "to" is missing, with no default
my session info:
- Session info -----------------------------------------------------------------------------------------------
setting value
version R version 4.0.4 (2021-02-15)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz Asia/Jerusalem
date 2021-03-07
- Packages ---------------------------------------------------------------------------------------------------
! package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0)
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.3)
bit 4.0.4 2020-08-04 [1] CRAN (R 4.0.4)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.4)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.2)
cachem 1.0.4 2021-02-13 [1] CRAN (R 4.0.4)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.3)
caret 6.0-86 2020-03-20 [1] CRAN (R 4.0.3)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2)
class 7.3-18 2021-01-24 [2] CRAN (R 4.0.4)
cli 2.3.1 2021-02-23 [1] CRAN (R 4.0.4)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.0.4)
colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.3)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.2)
CTSgetR * 1.3 2021-03-07 [1] Github (dgrapov/CTSgetR@61bd64d)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.2)
data.table 1.13.6 2020-12-30 [1] CRAN (R 4.0.3)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.0.3)
desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.4)
devtools * 2.3.2 2020-09-18 [1] CRAN (R 4.0.3)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3)
doParallel 1.0.16 2020-10-16 [1] CRAN (R 4.0.3)
dplyr * 1.0.4 2021-02-02 [1] CRAN (R 4.0.3)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
fansi 0.4.2 2021-01-15 [1] CRAN (R 4.0.3)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.4)
fingerprint 3.5.7 2018-01-07 [1] CRAN (R 4.0.3)
foreach 1.5.1 2020-10-15 [1] CRAN (R 4.0.3)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.3)
ggplot2 3.3.3 2020-12-30 [1] CRAN (R 4.0.3)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3)
gower 0.2.2 2020-06-23 [1] CRAN (R 4.0.3)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.3)
httpuv 1.5.5 2021-01-13 [1] CRAN (R 4.0.3)
httr * 1.4.2 2020-07-20 [1] CRAN (R 4.0.2)
ipred 0.9-9 2019-04-28 [1] CRAN (R 4.0.3)
iterators 1.0.13 2020-10-15 [1] CRAN (R 4.0.3)
itertools 0.1-3 2014-03-12 [1] CRAN (R 4.0.3)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.3)
keras 2.3.0.0.9000 2021-02-21 [1] Github (rstudio/keras@419e2ab)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.3)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.4)
lava 1.6.8.1 2020-11-04 [1] CRAN (R 4.0.3)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.4)
lubridate 1.7.9.2 2020-11-13 [1] CRAN (R 4.0.3)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.3)
MASS 7.3-53 2020-09-09 [2] CRAN (R 4.0.4)
Matrix 1.3-2 2021-01-06 [2] CRAN (R 4.0.4)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.0.3)
mime 0.10 2021-02-13 [1] CRAN (R 4.0.4)
ModelMetrics 1.2.2.2 2020-03-17 [1] CRAN (R 4.0.3)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
nlme 3.1-152 2021-02-04 [2] CRAN (R 4.0.4)
nnet 7.3-15 2021-01-24 [2] CRAN (R 4.0.4)
pillar 1.5.1 2021-03-05 [1] CRAN (R 4.0.4)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2)
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.3)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
pROC 1.17.0.1 2021-01-13 [1] CRAN (R 4.0.3)
processx 3.4.5 2020-11-30 [1] CRAN (R 4.0.3)
prodlim 2019.11.13 2019-11-17 [1] CRAN (R 4.0.3)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.0.3)
ps 1.5.0 2020-12-05 [1] CRAN (R 4.0.3)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3)
rcdk 3.5.0 2020-03-11 [1] CRAN (R 4.0.3)
rcdklibs 2.3 2020-03-08 [1] CRAN (R 4.0.3)
Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.0.3)
readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.2)
recipes 0.1.15 2020-11-11 [1] CRAN (R 4.0.3)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.3)
reshape2 * 1.4.4 2020-04-09 [1] CRAN (R 4.0.3)
reticulate 1.18-9007 2021-02-21 [1] Github (rstudio/reticulate@e4a9aa2)
Retip 0.5.4 2021-02-11 [1] Github (Paolobnn/Retip@8c23eda)
D rJava 0.9-13 2020-07-06 [1] CRAN (R 4.0.3)
rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.3)
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.0.4)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.3)
RSQLite * 2.2.3 2021-01-24 [1] CRAN (R 4.0.4)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.3)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.3)
shiny 1.6.0 2021-01-25 [1] CRAN (R 4.0.3)
stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.3)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
survival 3.2-7 2020-09-28 [2] CRAN (R 4.0.4)
tensorflow 2.2.0.9000 2021-02-21 [1] Github (rstudio/tensorflow@8f9ddd9)
testthat 3.0.2 2021-02-14 [1] CRAN (R 4.0.4)
tfruns 1.5.0 2021-02-26 [1] CRAN (R 4.0.4)
tibble 3.0.6 2021-01-29 [1] CRAN (R 4.0.3)
tidyr * 1.1.3 2021-03-03 [1] CRAN (R 4.0.4)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
timeDate 3043.102 2018-02-21 [1] CRAN (R 4.0.3)
usethis * 2.0.1 2021-02-10 [1] CRAN (R 4.0.3)
utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.2)
vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.3)
whisker 0.4 2019-08-28 [1] CRAN (R 4.0.2)
withr 2.4.1 2021-01-26 [1] CRAN (R 4.0.3)
xgboost 1.3.2.1 2021-01-18 [1] CRAN (R 4.0.3)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.3)
zeallot 0.1.0 2018-01-28 [1] CRAN (R 4.0.3)
[1] D:/BCDD/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.4/library
D -- DLL MD5 mismatch, broken installation.```
Any hint, idea, or assistance will be helpful,
Regards,
Tal
Is there an option to convert inchikey values to smiles ?
Dear developers,
I want to ask if there's an option to convert Inchikey values to Smiles ?
Best regards,
Tal
errors
Caused by error in curl::curl_fetch_memory():
! Recv failure: Connection was aborted
this error raised in code:
keggid=CTSgetR(com_name,from = "Chemical Name",to="KEGG")
seems connection aborted, how can I solve this
Broken?
I cannot make this output anything now. All I get is "error". Even with the examples the help. I have been using this heavily so it must be something recent.
CTSgetR() does not return the scores
Hi, when converting from names to PubChem, the web interface
has scores which are reasonably good to assess the ID confidence.
It would be cool to have that accessible from R as well.
5-Methyltetrahydrofolic acid
444412 -> 1.0
146 -> 0.1921
9825434 -> 0.3353
439234 -> 0.0703
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