Objects listed as exports, but not present in namespace:

[montenegrina]

Hello,

I installed your software via:

devtools::install_github("variani/finemapr")

When I loaded it I got this:

library(finemapr) Warning message: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘finemapr’

When I tried to do:

load_all("~/R/x86_64-pc-linux-gnu-library/3.6/finemapr")

Loading finemapr Skipping missing files: package.R, names.R, sumstats.R, abf.R, cojo.R, utils.R, read.R, datasets.R, files.R, plots.R, finemap.R, caviar.R, paintor.R, classMethods.R, classFinemaprPaintor.R, classFinemaprFinemap.R, classFinemaprCaviar.R, finemapr.R, ld.R, zzz.R Warning messages: 1: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘finemapr’ 2: S3 methods ‘collect_results.FinemaprFinemap’, ‘collect_results.FinemaprPaintor’, ‘extract_credible_set.Finemapr’, ‘filename_annot.FinemaprPaintor’, ‘filename_config.FinemaprFinemap’, ‘filename_k.FinemaprFinemap’, ‘filename_ld.FinemaprFinemap’, ‘filename_ld.FinemaprPaintor’, ‘filename_log.FinemaprFinemap’, ‘filename_master.FinemaprFinemap’, ‘filename_master.FinemaprPaintor’, ‘filename_snp.FinemaprFinemap’, ‘filename_snp.FinemaprPaintor’, ‘filename_zscore.FinemaprFinemap’, ‘filename_zscore.FinemaprPaintor’, ‘plot.Finemapr’, ‘plot.FinemaprCaviar’, ‘plot.FinemaprFinemap’, ‘plot_config.FinemaprFinemap’, ‘plot_ncausal.FinemaprFinemap’, ‘plot_snp.Finemapr’, ‘plot_snp.FinemaprCaviar’, ‘plot_snp.FinemaprFinemap’, ‘plot_zscore.Finemapr’, ‘process_annot.FinemaprPaintor’, ‘process_ld.Finemapr’, ‘process_tab.Finemapr’, ‘run_tool.FinemaprFinemap’, ‘run_tool.FinemaprPaintor’, ‘write_f [... truncated] 3: In setup_ns_exports(path, export_all, export_imports) : Objects listed as exports, but not present in namespace: cojo, collect_results, example_finemap, extract_credible_set, filename_annot, filename_config, filename_k, filename_ld, filename_log, filename_master, filename_snp, filename_zscore, finemapr, plot_config, plot_ncausal, plot_snp, plot_zscore, print.Finemapr, print.FinemaprCaviar, print.FinemaprFinemap, print.FinemaprPaintor, process_annot, process_ld, process_n, process_tab, proxysnps_ref_ld, proxysnps_ref_vcf, read_ld, read_zscore, ref_bed, ref_ld, ref_pop, run_caviar, run_finemap, run_paintor, run_tool, sumstats_bmi, write_files

And following your example here:

file1_z <- system.file("extdata/region1.z", package = "finemapr") file1_ld <- system.file("extdata/region1.ld", package = "finemapr")

z1 <- read_zscore(file1_z) Error in read_zscore(file1_z) : could not find function "read_zscore"

Can you please advise, Thanks Ana

[montenegrina]

Hi @variani,

can you please get back to me about this issue?

Thanks Ana

[variani]

@montenegrina, your last example should work now.

[variani]

Unfortunately, I don't have much time to support this package from now on. I would suggest you to build your analysis around original fine-mapping tools, e.g., FINEMAP. This package is merely a wrapper around system calls.

[montenegrina]

Thank you so much for getting back to me. Can you please tell me which find mapping tools do you prefer from all that are available?

Sent from my iPhone

On 9 Dec 2020, at 20:40, Andrey Ziyatdinov notifications@github.com wrote:

 Unfortunately, I don't have much time to support this package from now on. I would suggest you to build your analysis around original fine-mapping tools, e.g., FINEMAP. This package is merely a wrapper around system calls.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[variani]

That depends on the problem you are trying to solve. I would suggest to check the literature or talk to your collaborators/colleges. Sorry I couldn't be of more help.