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ChenWeiyan / LandSCENT

Landscape Single Cell Entropy
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Error: Failed to install 'LandSCENT' from GitHub: stderr is not a pipe #14

Closed Arcadi2020 closed 3 years ago

Arcadi2020 commented 3 years ago

Hi Chen,

I am trying to install LandSCENT via GitHub

My sessioninfo(): R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7

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

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

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

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

other attached packages: [1] swirl_2.4.5 igraph_1.2.6 paxtoolsr_1.22.0 XML_3.99-0.5 rJava_0.9-13

loaded via a namespace (and not attached): [1] Rcpp_1.0.5 pillar_1.4.7 compiler_4.0.3 plyr_1.8.6 R.methodsS3_1.8.1 R.utils_2.10.1
[7] bitops_1.0-6 tools_4.0.3 testthat_3.0.0 digest_0.6.27 jsonlite_1.7.1 lifecycle_0.2.0
[13] tibble_3.0.4 pkgconfig_2.0.3 rlang_0.4.8 cli_2.2.0 rstudioapi_0.13 curl_4.3
[19] yaml_2.2.1 httr_1.4.2 stringr_1.4.0 vctrs_0.3.5 hms_0.5.3 glue_1.4.2
[25] R6_2.5.0 fansi_0.4.1 readr_1.4.0 magrittr_2.0.1 ellipsis_0.3.1 assertthat_0.2.1 [31] utf8_1.1.4 stringi_1.5.3 RCurl_1.98-1.2 crayon_1.3.4 rjson_0.2.20 R.oo_1.24.0

THE ERROR MESSAGE:

devtools::install_github("ChenWeiyan/LandSCENT") Downloading GitHub repo ChenWeiyan/LandSCENT@HEAD ✓ checking for file ‘/private/var/folders/px/ncqctk414lx71h5wq13b91lcvpnkxl/T/Rtmp5ifQqs/remotes9ee28480512/ChenWeiyan-LandSCENT-ea35ec9/DESCRIPTION’ ... ─ preparing ‘LandSCENT’: ✓ checking DESCRIPTION meta-information ... ─ installing the package to process help pages Error: Failed to install 'LandSCENT' from GitHub: stderr is not a pipe.

Thank you Arcadi

ChenWeiyan commented 3 years ago

Hi Arcadi,

According to stderr is not a pipe, It seems the real error of the installation is not shown. This is something related to your operation system. Probably you need to solve it first, and then the installation error will appear?

Best, Weiyan

Arcadi2020 commented 3 years ago

Thank you for the prompt reply, Weiyan

I can install other packages from GitHub, but not this one. A colleague of mine, has the same problem.

Kind regards Arcadi

Arcadi2020 commented 3 years ago

SOLUTION TO: Failed to install 'LandSCENT' from GitHub: stderr is not a pipe

thanks to the help of a (clever) senior bioinformatician, I managed to solve the problem:

I am running R4.0.3 on macOS 10.15.7. Apparently the package has been only tested using R3.6 on Linux 3.10. There are a few breaking changes between R3.6.3 and R4.0, so this kind of problem will become increasingly common. Although macOS is very similar to Linux, there are some differences in core system libraries. Sometimes it is necessary to install additional libraries that Linux uses take for granted, but which are not included on Macs by default. In this case, I needed: https://www.xquartz.org/ After downloading, I restarted the laptop and the installation of the package was successful.

Cheers Arcadi