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bvieth / powsimR

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
https://bvieth.github.io/powsimR/
Artistic License 2.0
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Issues installing #15

Closed pelacables closed 6 years ago

pelacables commented 6 years ago

I'm trying to install the package after having installed all the depdencies. the command

devtools::install_github("bvieth/powsimR", build_vignettes = TRUE, dependencies = FALSE)

fails becasue:

Installing powsimR
svn: E175002: Unable to connect to a repository at URL 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/S4Vectors'
svn: E175002: OPTIONS of 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/S4Vectors': could not connect to server (https://hedgehog.fhcrc.org)
Installation failed: There was a problem retrieving the current SVN revision
Warning message:
running command ''/bin/svn' info --xml --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/S4Vectors' had status 1

S4Vector is installed in my system an can be loaded:

> library('S4Vectors')
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’
[....]

what is triggering the svn command?

pelacables commented 6 years ago

Finally I downloaded the code and installed like:

> install.packages('../powsimR-master.tar.gz', repos = NULL, type="source")

I also had to increase the num of DLLs:

> Sys.setenv(R_MAX_NUM_DLLS=500)

I don't know what's wrong but the Remotes in the DESCRIPTION are not ignored when install_github with dependecies =FALSE.

nlawlor commented 6 years ago

I also am having a similar installation problem, but unfortunately have not been able to resolve with the above suggestions. After installing all package dependencies first and then using the command:

devtools::install_github("bvieth/powsimR", build_vignettes = TRUE, dependencies = FALSE)

The error I get is similar:

Downloading GitHub repo bvieth/powsimR@master from URL https://api.github.com/repos/bvieth/powsimR/zipball/master Installing powsimR svn: E170013: Unable to connect to a repository at URL 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi' svn: E230001: Server SSL certificate verification failed: issuer is not trusted Installation failed: There was a problem retrieving the current SVN revision Warning message: running command ''/usr/bin/svn' info --xml --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationDbi' had status 1

The AnnotationDbi package is installed and can be loaded on my machine as well. When I try to install the package from source and increase the max number of DLLs to 153 (the maximum allowed on my macOS):

install.packages("Downloads/powsimR-master/", type = "source", repos = NULL, dependencies = F)

I get this error:

`Installing package into ‘/Users/lawlon/Library/R/3.4/library’ (as ‘lib’ is unspecified)

I'm not quite sure how to proceed from here, any feedback would be greatly appreciated!

My R session Information is below:

R version 3.4.4 (2018-03-15) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0 Biobase_2.38.0 BiocGenerics_0.24.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.16 digest_0.6.15 withr_2.1.2 R6_2.2.2 DBI_0.8 git2r_0.21.0 RSQLite_2.1.0 httr_1.3.1 curl_3.2 blob_1.1.1 devtools_1.13.5 [12] tools_3.4.4 bit64_0.9-7 bit_1.1-12 compiler_3.4.4 memoise_1.1.0

bvieth commented 6 years ago

Hello,

thanks for trying out powsimR and I am sorry that the installation is not working for you. I tried to reconstruct your first error without success. It appears to be a svn related issue that I encountered before as well for e.g. BASiCS (a package that was then available on bioconductor for installation via biocLite for the current R version but not listed in the repository). Since you have all dependencies installed successfully, might I suggest that you increase the ulimit first so that you can set the DLLs to a higher number? It should be possible on your machine. You can find a guide how to do this here.

Kind regards

nlawlor commented 6 years ago

Hi bvieth,

Thank you very much for the feedback. This suggestion worked great, I've successfully installed and loaded the package!

Thanks, Nathan

bvieth commented 6 years ago

Dear Nathan,

awesome news! If you need any further assistance, feel free to open another issue.

Beate

JingqunMa commented 5 years ago

Hi bvieth,: I have the error when installing powsimR. The error are following:

Downloading GitHub repo bvieth/powsimR@master from URL https://api.github.com/repos/bvieth/powsimR/zipball/master Installing powsimR '/Library/Frameworks/R.framework/Resources/bin/R' \ --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/private/var/folders/72/021myjvn1cx7pzcct7nx52vmw8086l/T/Rtmp5L8TCK/devtools4c8b31d279f5/bvieth-powsimR-f3e43ef' \ --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' \ --install-tests