gversmee / dbgap2x Goto Github PK
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License: Apache License 2.0
library(devtools)
library(BiocInstaller)
biocLite("XML")
install.packages("data.table")
install.packages("htmlTable")```
Need to add an option for datatables.dict and variables.dict to choose the number of cores used.
This function is important to the tool, but only returns the URL of the dbgap page listing the studies. Would prefer to return a structured summary of those studies, so that it can be used in combination with other queries.
see if we can remove "-u root" from code
Hi! I observed the weird format of output from parent.study()
function.
parent.study("phs000090")
[1] " 'phs000280.v6.p1" ""
(space) '
in the first element and the empty string in the second element.
Do you know why I got this? Thanks.
> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dbgap2x_1.0 dplyr_0.8.5
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 pillar_1.4.3 compiler_3.6.2 bitops_1.0-6 prettyunits_1.1.1 remotes_2.1.1
[7] tools_3.6.2 testthat_2.3.2 digest_0.6.25 pkgbuild_1.0.6 pkgload_1.0.2 jsonlite_1.6.1
[13] memoise_1.1.0 tibble_2.1.3 pkgconfig_2.0.3 rlang_0.4.5 cli_2.0.2 parallel_3.6.2
[19] curl_4.3 yaml_2.2.1 xfun_0.12 httr_1.4.1 withr_2.1.2 stringr_1.4.0
[25] knitr_1.28 vctrs_0.2.4 desc_1.2.0 fs_1.3.2 devtools_2.2.2 rprojroot_1.3-2
[31] tidyselect_1.0.0 data.table_1.12.8 glue_1.3.1 R6_2.4.1 processx_3.4.2 fansi_0.4.1
[37] XML_3.99-0.3 sessioninfo_1.1.1 callr_3.4.2 purrr_0.3.3 magrittr_1.5 backports_1.1.5
[43] ps_1.3.2 ellipsis_0.3.0 usethis_1.5.1 assertthat_0.2.1 utf8_1.1.4 stringi_1.4.6
[49] RCurl_1.98-1.1 crayon_1.3.4
On the Jupyter/mybinder, http request error.
Error in curl::curl_fetch_memory(url, handle = handle): Error in the HTTP2 framing layer Tracebak
In the tutorial (chunk 1), the name of the github repository is not in accordance with the paper's
browse.dbgap, browse.study, search.dbgap
change for "open.browser"
10Gb is way too much
The Docker image took 40 min to download, and after checking, docker image is 10Gb. My understanding is that dbGaP2x only requires a jupyter server, a few dev libraries and a R environment. The image should be much less than 1Gb.
Hi Authors!!
I am trying to use this package. When I run the exemplary command in R i.e. search.dbgap("Jackson")
it throws the following error:
Error in parallel::mclapply(mc.cores = getOption("mc.cores", parallel::detectCores()), :
'mc.cores' > 1 is not supported on Windows
Please help me understand how to deal with this?
dbgap2x password provided in the documentation doesn't work.
It looks like htmlTable package needs to be manually installed before installing the package via devtools
Original size: 762Mb.
Change #1: Size decreased to 369Mb.
Other ways to decrease the size:
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