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neurogenomics / MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics
https://neurogenomics.github.io/MAGMA_Celltyping
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Installation #6

Closed alexandruioanvoda closed 5 years ago

alexandruioanvoda commented 5 years ago

Hi! I was installing the latest version on a node, and this error came out (using either devtools::install_github and remotes::install_github):

remotes::install_github("nathanskene/MAGMA_Celltyping") Downloading GitHub repo nathanskene/MAGMA_Celltyping@master These packages have more recent versions available. Which would you like to update? 1: colorspace (1.4-0 -> 1.4-1 ) [CRAN] 2: XML (3.98-1.16 -> 3.98-1.19) [CRAN] 3: CRAN packages only 4: All 5: None Enter one or more numbers separated by spaces, or an empty line to cancel 1: 5 ✔ checking for file ‘/tmp/RtmpTMiZNJ/remotes14476b11eefb/NathanSkene-MAGMA_Celltyping-bdab1fa/DESCRIPTION’ ... ─ preparing ‘MAGMA.Celltyping’: ✔ checking DESCRIPTION meta-information ... Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:31: unexpected section header '\value' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:34: unexpected section header '\description' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:37: unexpected section header '\examples' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:45: unexpected END_OF_INPUT ' ' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/load.magma.results.file.Rd:13: unknown macro '\item' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/load.magma.results.file.Rd:15: unknown macro '\item' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/load.magma.results.file.Rd:17: unknown macro '\item' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/load.magma.results.file.Rd:19: unknown macro '\item' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/load.magma.results.file.Rd:21: unexpected section header '\value' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/load.magma.results.file.Rd:24: unexpected section header '\description' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/load.magma.results.file.Rd:27: unexpected section header '\examples' Warning: /tmp/Rtmpm8tgPq/Rbuild188917afa83d/MAGMA.Celltyping/man/load.magma.results.file.Rd:31: unexpected END_OF_INPUT ' ' ─ 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 Warning: file ‘ctd_AIBS.rda’ has magic number 'versi' Use of save versions prior to 2 is deprecated unable to create a ‘datalist’ file: may need the package to be installed ─ building ‘MAGMA.Celltyping_0.99.0.tar.gz’ Warning: invalid uid value replaced by that for user 'nobody' Installing package into ‘/gfs/devel/avoda/R/x86_64-pc-linux-gnu-library/3.5’ (as ‘lib’ is unspecified) installing source* package ‘MAGMA.Celltyping’ ... R data ** moving datasets to lazyload DB Warning: file ‘ctd_AIBS.rda’ has magic number 'versi' Use of save versions prior to 2 is deprecated Error in load(zfile, envir = envir) : bad restore file magic number (file may be corrupted) -- no data loaded ERROR: lazydata failed for package ‘MAGMA.Celltyping’ removing ‘/gfs/devel/avoda/R/x86_64-pc-linux-gnu-library/3.5/MAGMA.Celltyping’ Error in i.p(...) : (converted from warning) installation of package ‘/tmp/RtmpTMiZNJ/file144722b7defb/MAGMA.Celltyping_0.99.0.tar.gz’ had non-zero exit status

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alexandruioanvoda commented 5 years ago

And it seems to be specific to this version, as my old fork installs just fine:

remotes::install_github("alexandruioanvoda/MAGMA_Celltyping-1") Downloading GitHub repo alexandruioanvoda/MAGMA_Celltyping-1@master These packages have more recent versions available. Which would you like to update?

1: colorspace (1.4-0 -> 1.4-1 ) [CRAN] 2: XML (3.98-1.16 -> 3.98-1.19) [CRAN] 3: CRAN packages only 4: All 5: None

Enter one or more numbers separated by spaces, or an empty line to cancel 1: 5 ✔ checking for file ‘/tmp/RtmpTMiZNJ/remotes14474bf47e93/alexandruioanvoda-MAGMA_Celltyping-1-017081b/DESCRIPTION’ ... ─ preparing ‘MAGMA.Celltyping’: ✔ checking DESCRIPTION meta-information ... Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:31: unexpected section header '\value' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:34: unexpected section header '\description' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:37: unexpected section header '\examples' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:45: unexpected END_OF_INPUT ' ' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/load.magma.results.file.Rd:13: unknown macro '\item' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/load.magma.results.file.Rd:15: unknown macro '\item' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/load.magma.results.file.Rd:17: unknown macro '\item' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/load.magma.results.file.Rd:19: unknown macro '\item' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/load.magma.results.file.Rd:21: unexpected section header '\value' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/load.magma.results.file.Rd:24: unexpected section header '\description' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/load.magma.results.file.Rd:27: unexpected section header '\examples' Warning: /tmp/RtmpSsM4pX/Rbuild1cf625af0c8/MAGMA.Celltyping/man/load.magma.results.file.Rd:31: unexpected END_OF_INPUT ' ' ─ 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 ‘MAGMA.Celltyping_0.99.0.tar.gz’ (3.4s) Warning: invalid uid value replaced by that for user 'nobody'

Installing package into ‘/gfs/devel/avoda/R/x86_64-pc-linux-gnu-library/3.5’ (as ‘lib’ is unspecified)

Exiting MAGMA. Goodbye.

alexandruioanvoda commented 5 years ago

It looks as if ctd_AIBS.rda is saved in a wrong format. See https://stackoverflow.com/a/21505731

NathanSkene commented 5 years ago

Hi Alex,

Thanks for letting me know about this. I had tried moving the data files to LFS but apparently install_github is not compatible with repositories which use LFS. I think it's fixed now (works on my computer at least).

Let me know if you've still got any issues.

Nathan