Is presto not compatible with the latest version of R (4.0)?

[coreyscipione]

I recently updated my R to the most recent version. I noticed my computing time has gone up significantly, and determined that Presto will not launch in this version.

Loading required package: presto
Error: package or namespace load failed for �presto�:
 package �presto� was installed before R 4.0.0: please re-install it

I tried:

devtools::install_github("immunogenomics/presto")

and still it won't launch the presto.

Any ideas?

[slowkow]

Thanks for opening the issue. This might be a duplicate of #5.

Please consider sharing the full output when you run

devtools::install_github("immunogenomics/presto")

and also the full output of sessionInfo()

[slowkow]

I just tried installing presto on a machine with R 4.0.2 and it worked just fine:

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> devtools::install_github("immunogenomics/presto")
Downloading GitHub repo immunogenomics/presto@master
Skipping 1 packages not available: DESeq2
✔  checking for file ‘/tmp/Rtmpmw4rJy/remotesf8fb3e91683c/immunogenomics-presto-7f63f96/DESCRIPTION’ ...
─  preparing ‘presto’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘presto_1.0.0.tar.gz’

Installing package into ‘/home/ks38/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘presto’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fast_wilcox.cpp -o fast_wilcox.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o presto.so RcppExports.o fast_wilcox.o -L/usr/lib/R/lib -lR
installing to /home/ks38/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-presto/00new/presto/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (presto)
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] ps_1.3.3          fansi_0.4.1       prettyunits_1.1.1 rprojroot_1.3-2
 [5] withr_2.2.0       digest_0.6.25     crayon_1.3.4      assertthat_0.2.1
 [9] R6_2.4.1          backports_1.1.8   magrittr_1.5      rlang_0.4.6
[13] cli_2.0.2         curl_4.3          fs_1.4.2          remotes_2.1.1
[17] testthat_2.3.2    callr_3.4.3       ellipsis_0.3.1    desc_1.2.0
[21] devtools_2.3.0    tools_4.0.2       glue_1.4.1        pkgload_1.1.0
[25] compiler_4.0.2    processx_3.4.2    pkgbuild_1.0.8    sessioninfo_1.1.1
[29] memoise_1.1.0     usethis_1.6.1
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