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Non parametric differential abundance tests for microbiome data
Hi @barakbri,
thanks for your package for differential abundance analysis. I was wondering whether you could adjust the output for estimated effect sizes by adding a sign to denote the direction of the effect size and not by providing a string describing the ordering of mean ranks? This way it would be easier to integrate your method in a general workflow.
Many thanks,
Axel
When I'm trying to install the lib I've got thу following error without desciption of its origin.
Downloading GitHub repo barakbri/dacomp@master
Skipping 1 packages not available: phyloseq
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_TIME failed, using "C"
3: Setting LC_MESSAGES failed, using "C"
4: Setting LC_MONETARY failed, using "C"
5: Setting LC_PAPER failed, using "C"
6: Setting LC_MEASUREMENT failed, using "C"
v checking for file '/tmp/RtmpgAmLHA/remotes798920fc2aef/barakbri-dacomp-ce225d4/DESCRIPTION' ...
- preparing 'dacomp':
v checking DESCRIPTION meta-information ...
- cleaning src
Warning: /tmp/RtmpZXtpzN/Rbuild176e5a0d0da9/dacomp/man/dacomp.select_references.Rd:16: unknown macro '\core'
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'dacomp_1.0.tar.gz'
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
Error in i.p(...): (converted from warning) installation of package '/tmp/RtmpgAmLHA/file79891f373e43/dacomp_1.0.tar.gz' had non-zero exit status
Traceback:
1. devtools::install_github("barakbri/dacomp")
2. install_remotes(remotes, auth_token = auth_token, host = host,
. dependencies = dependencies, upgrade = upgrade, force = force,
. quiet = quiet, build = build, build_opts = build_opts, repos = repos,
. type = type, ...)
3. vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
4. FUN(X[[i]], ...)
5. install(source, dependencies = dependencies, upgrade = upgrade,
. force = force, quiet = quiet, build = build, build_opts = build_opts,
. repos = repos, type = type, ...)
6. safe_install_packages(pkgdir, repos = NULL, quiet = quiet, type = "source",
. ...)
7. with_envvar(c(R_LIBS = lib, R_LIBS_USER = lib, R_LIBS_SITE = lib,
. RGL_USE_NULL = "TRUE"), if (should_error_for_warnings()) {
. with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
. i.p(...)))
. } else {
. i.p(...)
. })
8. force(code)
9. with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
. i.p(...)))
10. force(code)
11. with_rprofile_user("options(warn = 2)", i.p(...))
12. with_envvar(c(R_PROFILE_USER = temp_rprofile), {
. force(code)
. })
13. force(code)
14. force(code)
15. i.p(...)
16. warning(gettextf("installation of package %s had non-zero exit status",
. sQuote(update[i, 1L])), domain = NA)
17. .signalSimpleWarning("installation of package '/tmp/RtmpgAmLHA/file79891f373e43/dacomp_1.0.tar.gz' had non-zero exit status",
. quote(i.p(...)))
18. withRestarts({
. .Internal(.signalCondition(simpleWarning(msg, call), msg,
. call))
. .Internal(.dfltWarn(msg, call))
. }, muffleWarning = function() NULL)
19. withOneRestart(expr, restarts[[1L]])
20. doWithOneRestart(return(expr), restart)
Hi developer,
Thank for creating this package. I have successfully installed it on my mac. But I can not install it on Linux cluster. Would you mind to give me some suggestions?
Here is the error message:
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (vegan)
* installing *source* package ‘HHG’ ...
** package ‘HHG’ successfully unpacked and MD5 sums checked
checking whether the C++ compiler works... no
configure: error: in `/tmp/Rtmpfvw0Bp/R.INSTALL188a57b2d2c2d/HHG':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘HHG’
* removing ‘/R/HHG’
Error: Failed to install 'dacomp' from GitHub:
(converted from warning) installation of package ‘HHG’ had non-zero exit status
Hi Barak,
Does dacomp supports covariate adjustment, such as age, sex?
Thanks.
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