Error in "map_snps_to_genes"

Question

Error in "map_snps_to_genes"

LDHHAHA opened this issue 2 years ago · 8 comments

1. Bug description

I had arealdy Munged GWAS data in formatted type, and an error came when i ran the following steps:
genesOutPath <- MAGMA.Celltyping::map_snps_to_genes(path_formatted = path_formatted,
genome_build = "GRCh37",
upstream_kb=10,downstream_kb=1.5,
storage_dir = "./ref/MAGMA/")

Console output

  Cannot access release data for repository neurogenomics/MAGMA_Celltyping. Check that you have provided a .token and that at least one release on your GitHub repository page.

Expected behaviour

Any help is greatly appreciated.

Answer 1 · 2022-04-07T09:26:48.000Z

Likely related to this issue #102
Root cause is piggyback, working with the developers of that package to try and get it resolved

Answer 2 · 2022-04-07T09:41:21.000Z

remotes::install_github("ropensci/piggyback@gh_token") # done
but the follwing code met another error
piggyback::pb_download(repo="cboettig/piggyback-tests")

Error in match.fun(FUN) :
lazy-load database '/share/home/zhangwl/R/x86_64-pc-linux-gnu-library/4.1/piggyback/R/piggyback.rdb' is corrupt
In addition: Warning messages:
1: In match.fun(FUN) : restarting interrupted promise evaluation
2: In match.fun(FUN) : internal error -3 in R_decompress1

Answer 3 · 2022-04-07T09:43:40.000Z

remotes::install_github("ropensci/piggyback@gh_token") # done but the follwing code met another error piggyback::pb_download(repo="cboettig/piggyback-tests")

Error in match.fun(FUN) : lazy-load database '/share/home/zhangwl/R/x86_64-pc-linux-gnu-library/4.1/piggyback/R/piggyback.rdb' is corrupt In addition: Warning messages: 1: In match.fun(FUN) : restarting interrupted promise evaluation 2: In match.fun(FUN) : internal error -3 in R_decompress1

Could you please post this Issue on the piggyback repo instead of here? I'm afraid I'm not the maintainer of that package.

Answer 4 · 2022-04-07T10:29:56.000Z

in the meantime, I've pushed some checks that give instructions on how to resolve this issue by adding GitHub PAT:
#102 (comment)

Answer 5 · 2022-04-07T11:05:42.000Z

1. Bug description

I had arealdy Munged GWAS data in formatted type, and an error came when i ran the following steps: genesOutPath <- MAGMA.Celltyping::map_snps_to_genes(path_formatted = path_formatted, genome_build = "GRCh37", upstream_kb=10,downstream_kb=1.5, storage_dir = "./ref/MAGMA/")

Console output
  Cannot access release data for repository neurogenomics/MAGMA_Celltyping. Check that you have provided a .token and that at least one release on your GitHub repository page.		
Expected behaviour

Any help is greatly appreciated.

Sorry, I am newer to use this software. I met another error when run the above steps:

Error in data.table::fread(tmp, nrows = 10, nThread = 1) :
Single column input contains invalid quotes. Self healing only effective when ncol>1

Answer 6 · 2022-04-07T12:57:30.000Z

Did you re-install MAGMA.Celltyping and follow the instructions here?
#102 (comment)

Answer 7 · 2022-04-07T13:19:05.000Z

Yes, but did not work.

Answer 8 · 2022-04-07T15:52:35.000Z

Error in data.table::fread(tmp, nrows = 10, nThread = 1) : Single column input contains invalid quotes. Self healing only effective when ncol>1

The fact that you got this error suggests you're not using the latest version. The line that this comes from was removed.
Please try re-installing and make sure to restart your R session.