Issues installing about powsimr HOT 6 CLOSED

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.

from powsimr.

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)

• installing source package ‘powsimR’ ...
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** preparing package for lazy loading
  Warning: replacing previous import ‘DECENT::lrTest’ by ‘MAST::lrTest’ when loading ‘powsimR’
  Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/nloptr/libs/nloptr.so':
  `maximal number of DLLs reached...
  ERROR: lazy loading failed for package ‘powsimR’
• removing ‘/Users/lawlon/Library/R/3.4/library/powsimR’
  Warning in install.packages :
  installation of package ‘Downloads/powsimR-master/’ had non-zero exit status`

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

from powsimr.

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

from powsimr.

Hi bvieth,

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

Thanks,
Nathan

from powsimr.

Dear Nathan,

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

Beate

from powsimr.

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

• installing source package ‘powsimR’ ...
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  Warning: no function found corresponding to methods exports from ‘IRanges’ for: ‘concatenateObjects’, ‘pos’
  Error : object ‘logsumexp’ is not exported by 'namespace:limma'
  ERROR: lazy loading failed for package ‘powsimR’
• removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/powsimR’
  Installation failed: Command failed (1)

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