egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Installation issue: Java #49

Closed zinagood closed 4 years ago

zinagood commented 4 years ago

Describe the bug Dear Ege,

My apologies for not checking the R version previously. I updated R, R Studio, and installed all dependencies, including Java 14, for the pathfindR. However, I still have installation issues. I attempted to use CRAN, pak, or GitHub, or source install, as described on your website. However, this failed each time. This time the issue appears to be with parsing the Java version (error: Java version detected but couldn't parse version from: java version "14" 2020-03-17; details below). Perhaps the issue is with 'check_java_version()' function? Please, let me know how to proceed.

Thanks! Zina

To Reproduce Steps to reproduce the behavior:

  1. install.packages("pathfindR")

installing the source package ‘pathfindR’

trying URL 'https://cran.rstudio.com/src/contrib/pathfindR_1.5.0.tar.gz' Content type 'application/x-gzip' length 3355703 bytes (3.2 MB)

downloaded 3.2 MB

The downloaded source packages are in ‘/private/var/folders/fn/mhn7pp8s3yj7cng14ywkzyx40000gn/T/Rtmp9Cdbk7/downloaded_packages’

Expected behavior Package installed successfully.

Desktop (please complete the following information):

R Session Information: R version 4.0.1 (2020-06-06) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached): [1] prettyunits_1.1.1 pak_0.1.2 ps_1.3.3 fansi_0.4.1
[5] digest_0.6.25 crayon_1.3.4 assertthat_0.2.1 rappdirs_0.3.1
[9] R6_2.4.1 lifecycle_0.2.0 magrittr_1.5 pillar_1.4.4
[13] rlang_0.4.6 cli_2.0.2 uuid_0.1-4 curl_4.3
[17] rstudioapi_0.11 callr_3.4.3 vctrs_0.3.1 ellipsis_0.3.1
[21] filelock_1.0.2 pkgcache_1.0.7 tools_4.0.1 glue_1.4.1
[25] compiler_4.0.1 processx_3.4.2 pkgconfig_2.0.3 BiocManager_1.30.10 [29] tibble_3.0.1

Additional context (base) Zinaidas-MacBook-Pro:~ zinaida$ java --version java 14 2020-03-17 Java(TM) SE Runtime Environment (build 14+36-1461) Java HotSpot(TM) 64-Bit Server VM (build 14+36-1461, mixed mode, sharing)

egeulgen commented 4 years ago

Dear @zinagood,

We had trouble parsing the version for java "14", which I fixed. Please try to install the latest development version:

install.packages("devtools") # if you have not installed "devtools"
devtools::install_github("egeulgen/pathfindR")