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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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Sample ctd datasets not linked #5

Closed rbutleriii closed 5 years ago

rbutleriii commented 5 years ago

Hello, I was trying to load the ctd_AIBS dataset, but instead it loads ctd (with the 24 level 1 and 149 level 2 of the original ctd). Related, when trying to build (Ubuntu 18.04, R3.5.2, 64bit) I get the following pertinent error:

Warning: objects ‘ctd’, ‘ctd’, ‘ctd’ are created by more than one data call

Here is the full build log, which looks like it may encounter another issue with calculate.celltype.associtations that perhaps supersedes this one:

> install_github('nathanskene/MAGMA_Celltyping', force = TRUE)
Downloading GitHub repo nathanskene/MAGMA_Celltyping@master
✔  checking for file ‘/tmp/RtmptlCvgD/remotes17616eeb5fc7/NathanSkene-MAGMA_Celltyping-6bb417d/DESCRIPTION’ ...
─  preparing ‘MAGMA.Celltyping’:
✔  checking DESCRIPTION meta-information ...
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:31: unexpected section header '\value'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:34: unexpected section header '\description'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:37: unexpected section header '\examples'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:45: unexpected END_OF_INPUT '
   '
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/load.magma.results.file.Rd:13: unknown macro '\item'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/load.magma.results.file.Rd:15: unknown macro '\item'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/load.magma.results.file.Rd:17: unknown macro '\item'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/load.magma.results.file.Rd:19: unknown macro '\item'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/load.magma.results.file.Rd:21: unexpected section header '\value'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/load.magma.results.file.Rd:24: unexpected section header '\description'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/MAGMA.Celltyping/man/load.magma.results.file.Rd:27: unexpected section header '\examples'
   Warning: /tmp/Rtmpiyr4Zp/Rbuild17a44f57a477/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’ (4.9s)

Installing package into ‘/home/dragon951/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: objects ‘ctd’, ‘ctd’, ‘ctd’ are created by more than one data call
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘MAGMA.Celltyping’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘MAGMA.Celltyping’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘MAGMA.Celltyping’
Warning: replacing previous import ‘cowplot::ggsave’ by ‘ggplot2::ggsave’ when loading ‘MAGMA.Celltyping’
Warning: replacing previous import ‘dplyr::combine’ by ‘gridExtra::combine’ when loading ‘MAGMA.Celltyping’
** help
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:31: unexpected section header '\value'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:34: unexpected section header '\description'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:37: unexpected section header '\examples'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/calculate_celltype_associations.Rd:45: unexpected END_OF_INPUT '
'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/load.magma.results.file.Rd:13: unknown macro '\item'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/load.magma.results.file.Rd:15: unknown macro '\item'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/load.magma.results.file.Rd:17: unknown macro '\item'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/load.magma.results.file.Rd:19: unknown macro '\item'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/load.magma.results.file.Rd:21: unexpected section header '\value'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/load.magma.results.file.Rd:24: unexpected section header '\description'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/load.magma.results.file.Rd:27: unexpected section header '\examples'
Warning: /tmp/RtmpDY2W3Z/R.INSTALL17b147322cb2/MAGMA.Celltyping/man/load.magma.results.file.Rd:31: unexpected END_OF_INPUT '
'
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘MAGMA.Celltyping’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘MAGMA.Celltyping’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘MAGMA.Celltyping’
Warning: replacing previous import ‘cowplot::ggsave’ by ‘ggplot2::ggsave’ when loading ‘MAGMA.Celltyping’
Warning: replacing previous import ‘dplyr::combine’ by ‘gridExtra::combine’ when loading ‘MAGMA.Celltyping’
No arguments specified. Please consult manual for usage instructions.

Exiting MAGMA. Goodbye.
Warning in system2("magma", "--v", stdout = TRUE, stderr = TRUE) :
  running command ''magma' --v 2>&1' had status 2
* DONE (MAGMA.Celltyping)
>
rbutleriii commented 5 years ago

FYI they just have the same name. you can fix with:

> load('Downloads/MAGMA_Celltyping-master/data/ctd_AIBS.rda')
> ctd_AIBS <- ctd
> save(ctd_AIBS, file = 'Downloads/MAGMA_Celltyping-master/data/ctd_AIBS.rda')
> load('Downloads/MAGMA_Celltyping-master/data/ctd_DRONC_human.rda')
> ctd_DRONC_human <- ctd
> save(ctd_DRONC_human, file = 'Downloads/MAGMA_Celltyping-master/data/ctd_DRONC_human.rda')
> load('Downloads/MAGMA_Celltyping-master/data/ctd_DRONC_mouse.rda')
> ctd_DRONC_mouse <- ctd
> save(ctd_DRONC_mouse, file = 'Downloads/MAGMA_Celltyping-master/data/ctd_DRONC_mouse.rda')
NathanSkene commented 5 years ago

Hi Rob, I've fixed this now. Thanks for letting me know about it!