Problem installed DeepCC

CityUHK-CompBio / DeepCC

DeepCC: a novel deep learning-based framework for cancer molecular subtype classification

https://CityUHK-CompBio.github.io/DeepCC/

MIT License

20 stars 16 forks source link

Problem installed DeepCC #2

Closed amphun closed 4 years ago

amphun commented 4 years ago

Hi I got this error while installed DeepCC any suggestions?

devtools::install_github("CityUHK-CompBio/DeepCC") mxnet (NA -> 1.3.0 ) [CRAN] dplyr (0.8.4 -> 0.8.5 ) [CRAN] igraph (1.1.2 -> 1.2.4.2) [CRAN] lifecycle (0.1.0 -> 0.2.0 ) [CRAN] ggplot2 (3.2.1 -> 3.3.0 ) [CRAN] isoband (NA -> 0.2.0 ) [CRAN] Installing 6 packages: mxnet, dplyr, igraph, lifecycle, ggplot2, isoband Error: Failed to install 'DeepCC' from GitHub: (converted from warning) unable to access index for repository https://s3-us-west-2.amazonaws.com/apache-mxnet/R/CRAN/bin/macosx/mavericks/contrib/3.3: cannot download all files

Many thanks

amphun commented 4 years ago

Here is additional error: devtools::install_github("CityUHK-CompBio/DeepCC") Downloading GitHub repo CityUHK-CompBio/DeepCC@master Skipping 1 packages not available: mxnet Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) : unknown timezone 'zone/tz/2019c.1.0/zoneinfo/Asia/Bangkok' ERROR: dependency ‘mxnet’ is not available for package ‘DeepCC’

removing ‘/Users/amphun/.RLibrary/DeepCC’ Error: Failed to install 'DeepCC' from GitHub: (converted from warning) installation of package ‘/var/folders/r9/qb4kx9zx0gz_sp7v7pgrmkrh0000gn/T//RtmpAUdEUr/filec1c42b2bec05/DeepCC_0.3.0.9000.tar.gz’ had non-zero exit status In addition: Warning message: In pkgbuild::with_build_tools({ : bytecode version mismatch; using eval

gaofeng21cn commented 4 years ago

Hi,

I think it's something wrong with mxnet's prebuilt R package. I checked it today and found they only have a prebuilt R package for Windows/macOS. For Linux or other situation like downloading issue, I think you can manually install it following their guide. https://mxnet.apache.org/get_started?platform=linux&language=r&processor=cpu&

Anyway, we will change the deep learning backend to keras to get better R compatibility.