Please add R and package version requirements

hunter-moseley commented 2 years ago

Please add R and package version requirements.

I cannot install the required packages with my default version of R and I am not sure which version of R to download and install to make this package work.

KatharinaSchmid commented 2 years ago

Hi Hunter,

thanks for your feedback. We have already specified the R version (at least 3.3) and the package versions of packages that we had issues with in the DESCRIPTION file (https://github.com/heiniglab/scPower/blob/master/DESCRIPTION). So far, we had no other issues with versions, but it could very well be that we missed something. Could you specify what your error is when installing the package (exact error message) and which R version you currently use?

Best regards, Katharina

hunter-moseley commented 2 years ago

Katharina,

Thanks for responding so quickly. I did not think to look in the DESCRIPTION file.

I was using R version 3.5.3 on Fedora 28. (I plan on upgrading my laptop sometime this summer after I submit my next grant proposal).

It is devtools that will not install, because of a dependency "usethis" which is failing to install. It is failing due to a requirement for a newer openssl library:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘openssl’ 1.3 is already loaded, but >= 1.4.1 is required ERROR: lazy loading failed for package ‘gert’

removing ‘/home/hunter/R/x86_64-redhat-linux-gnu-library/3.5/gert’ ERROR: dependency ‘gert’ is not available for package ‘usethis’
removing ‘/home/hunter/R/x86_64-redhat-linux-gnu-library/3.5/usethis’

The downloaded source packages are in ‘/tmp/RtmpnV45Zd/downloaded_packages’ Warning messages: 1: In install.packages("usethis") : installation of package ‘openssl’ had non-zero exit status 2: In install.packages("usethis") : installation of package ‘gert’ had non-zero exit status 3: In install.packages("usethis") : installation of package ‘usethis’ had non-zero exit status

R will not install an updated openssl package due to missing openssl header files. I think the only way to fix this is to upgrade my laptop or use another lab machine with a newer version of openssl.

Warm regards, Hunter

On Wed, May 25, 2022 at 3:24 AM KatharinaSchmid @.***> wrote:

Hi Hunter,

thanks for your feedback. We have already specified the R version (at least 3.3) and the package versions of packages that we had issues with in the DESCRIPTION file ( https://github.com/heiniglab/scPower/blob/master/DESCRIPTION). So far, we had no other issues with versions, but it could very well be that we missed something. Could you specify what your error is when installing the package (exact error message) and which R version you currently use?

Best regards, Katharina

— Reply to this email directly, view it on GitHub https://github.com/heiniglab/scPower/issues/7#issuecomment-1136885642, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEP7BZDCGDIAFH5FR5GHJ3VLXIS3ANCNFSM5W27MILA . You are receiving this because you authored the thread.Message ID: @.***>

-- Hunter Moseley, Ph.D. -- Univ. of Kentucky Associate Professor, Dept. of Molec. & Cell. Biochemistry / Markey Cancer Center / Institute for Biomedical Informatics / UK Superfund Research Center Not just a scientist, but a fencer as well. My foil is sharp, but my mind sharper still.

Email: @. (work) @. (personal) Phone: 859-218-2964 (office) 859-218-2965 (lab) 859-257-7715 (fax) Web: http://bioinformatics.cesb.uky.edu/ Address: CC434 Roach Building, 800 Rose Street, Lexington, KY 40536-0093

KatharinaSchmid commented 2 years ago

Sorry, I don’t know exactly how to solve your issue, as it is nothing that I can fix in scPower. But a few suggestions, maybe one of them is helpful:

If you don’t want to override your current R environment, I use conda to maintain multiple R versions at the same time, I can really recommend this, it might also help with installing openssl/devtools (there are of course other similar solutions, e.g. docker)
The R package is more powerful, but we host the basic functionalities of scPower also on a website. So far it contains only a small set of priors from PBMC data (we are working on extending it), but it could still be helpful for you: http://scpower.helmholtz-muenchen.de
I developed scPower on R3.5.1, it still runs there without any problems, maybe it helps to specify the devtools version I used there


> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.15.7

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] devtools_2.2.1 usethis_1.5.1 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4        magrittr_2.0.1    pkgload_1.0.2     R6_2.5.0         
 [5] rlang_0.4.11      fansi_0.4.1       tools_3.5.0       pkgbuild_1.0.8   
 [9] sessioninfo_1.1.1 cli_2.0.2         withr_2.4.2       ellipsis_0.3.2   
[13] remotes_2.1.0     assertthat_0.2.1  digest_0.6.25     rprojroot_1.3-2  
[17] crayon_1.4.1      processx_3.4.2    callr_3.4.3       fs_1.3.2         
[21] ps_1.3.3          testthat_2.3.2    memoise_1.1.0     glue_1.3.2       
[25] compiler_3.5.0    desc_1.2.0        backports_1.1.5   prettyunits_1.1.1

heiniglab / scPower

Please add R and package version requirements #7

It is devtools that will not install, because of a dependency "usethis" which is failing to install. It is failing due to a requirement for a newer openssl library:

-- Hunter Moseley, Ph.D. -- Univ. of Kentucky Associate Professor, Dept. of Molec. & Cell. Biochemistry / Markey Cancer Center / Institute for Biomedical Informatics / UK Superfund Research Center Not just a scientist, but a fencer as well. My foil is sharp, but my mind sharper still.