Incompatibility new release R 4.1.0
Closed this issue · 6 comments
I recently upgraded from R 4.0.3 to the new (May 2021) release R 4.1.0
and the streamMetabolizer package is not functioning any more.
I think because of a change in the exists() function that requires argument of length 1
In older R release, it was not checked (even if only the 1st element was considered)
in the new R release it is checked
and the function is called with argument of length 3 is called in several functions of metab.
exists(c('date',"warnings','errors"), fit)
Below the code and console output
library(streamMetabolizer)
library(dplyr)
dat <- data_metab(num_days='3', res='15', day_start=4, day_end=28, attach.units=TRUE)
classic_specs <- specs( mm_name('mle', GPP_fun='linlight', ER_fun='constant') )
(I here get the classical dplyr deprecated messages)
mm_classic <- streamMetabolizer::metab(classic_specs, data=dat)
Erreur dans exists(c("date", "warnings", "errors"), fit) :
first argument is of length > 1
devtools::session_info()
setting value
version R version 4.1.0 (2021-05-18)
os Ubuntu 18.04.5 LTS
system x86_64, linux-gnu
ui RStudio
language fr_FR
collate fr_FR.UTF-8
ctype fr_FR.UTF-8
tz Europe/Paris
date 2021-06-23
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
cachem 1.0.5 2021-05-15 [1] CRAN (R 4.1.0)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
cli 2.5.0 2021-04-26 [1] CRAN (R 4.1.0)
codetools 0.2-18 2020-11-04 [4] CRAN (R 4.0.3)
colorspace 2.0-1 2021-05-04 [1] CRAN (R 4.1.0)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.1.0)
curl 4.3.1 2021-04-30 [1] CRAN (R 4.1.0)
data.table 1.14.0 2021-02-21 [1] CRAN (R 4.1.0)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.0)
desc 1.3.0 2021-03-05 [1] CRAN (R 4.1.0)
deSolve 1.28 2020-03-08 [1] CRAN (R 4.1.0)
devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.0)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.1.0)
dplyr * 1.0.6 2021-05-05 [1] CRAN (R 4.1.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0)
generics 0.1.0 2020-10-31 [1] CRAN (R 4.1.0)
ggplot2 * 3.3.4 2021-06-16 [1] CRAN (R 4.1.0)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0)
htmlwidgets 1.5.3 2020-12-10 [1] CRAN (R 4.1.0)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0)
hydrogeo * 0.6-1 2017-03-12 [1] CRAN (R 4.1.0)
inline 0.3.19 2021-05-31 [1] CRAN (R 4.1.0)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0)
LakeMetabolizer 1.5.3 2021-05-25 [1] Github (GLEON/LakeMetabolizer@5e42781)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.1.0)
loo 2.4.1 2020-12-09 [1] CRAN (R 4.1.0)
lubridate 1.7.10 2021-02-26 [1] CRAN (R 4.1.0)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0)
matrixStats 0.59.0 2021-06-01 [1] CRAN (R 4.1.0)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.0)
misc3d 0.9-0 2020-09-06 [1] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
openxlsx * 4.2.4 2021-06-16 [1] CRAN (R 4.1.0)
pillar 1.6.1 2021-05-16 [1] CRAN (R 4.1.0)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.1.0)
plotly * 4.9.4 2021-06-08 [1] CRAN (R 4.1.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0)
ptinpoly 2.8 2020-06-02 [1] CRAN (R 4.1.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.1.0)
Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.1.0)
RcppParallel 5.1.4 2021-05-04 [1] CRAN (R 4.1.0)
remotes 2.4.0 2021-06-02 [1] CRAN (R 4.1.0)
rLakeAnalyzer 1.11.4.1 2019-06-09 [1] CRAN (R 4.1.0)
rlang 0.4.11 2021-04-30 [1] CRAN (R 4.1.0)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0)
rstan 2.21.2 2020-07-27 [1] CRAN (R 4.1.0)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0)
StanHeaders 2.21.0-7 2020-12-17 [1] CRAN (R 4.1.0)
streamMetabolizer * 0.11.4 2021-05-25 [1] Github (USGS-R/streamMetabolizer@4a7ba9c)
stringi 1.6.2 2021-05-17 [1] CRAN (R 4.1.0)
testthat 3.0.2 2021-02-14 [1] CRAN (R 4.1.0)
tibble 3.1.2 2021-05-16 [1] CRAN (R 4.1.0)
tidyr 1.1.3 2021-03-03 [1] CRAN (R 4.1.0)
tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0)
unitted 0.2.9 2021-05-25 [1] Github (appling/unitted@d1f1172)
usethis 2.0.1 2021-02-10 [1] CRAN (R 4.1.0)
utf8 1.2.1 2021-03-12 [1] CRAN (R 4.1.0)
V8 3.4.2 2021-05-01 [1] CRAN (R 4.1.0)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0)
viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.0)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0)
zip 2.2.0 2021-05-31 [1] CRAN (R 4.1.0)
[1] /home/sguillon/R/x86_64-pc-linux-gnu-library/4.1
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library
Thanks! Should be fixed with version 0.12.0 - please let me know if you still have trouble.
Many thanks for the new version.
I don't get the error any more, metab calculations (classic MLE and bayesian) run ok.
But I now have trouble with all the "plot" commands (plot_metab_preds(), plot_DO_preds())
They systematically lead to "R session abort".
Hi Sophie, thanks for the feedback. So far I'm unable to replicate the issues you're reporting for the plot commands - could you share a code script for which it's breaking?
Hi Alison,
My issue is when I want to do
plot_DO_preds(mm_classic)
(the last command in the Quickstart for the package, using the 3 days dataset
I get no error message in the terminal, but a windows opens "R session aborted". See attached screenshot
But I don't have any problem when I use R in a terminal (I am running on Linux) instead of Rstudio.
So I guess I will have to fix somehow my Rstudio...
Hi again,
My apologies , I updated Rstudio to the latest version and everything is working fine now.
I close the comment and thank you very much for the the update of the package.
Great, glad you found a solution, and thanks for following up!