Error when running init(sclvm,Y=Y,tech_noise = tech_noise)

[zji90]

Hi,
I have already installed scLVM R package and limix (from anaconda) and is trying to go through the vignette. However, I encountered the following error when running init(sclvm,Y=Y,tech_noise = tech_noise):

Loading required package: rPython
Loading required package: RJSONIO
Error in python.exec(paste(objName, " = scLVM(Y,geneID=geneID,tech_noise=tech_noise)", : name 'scLVM' is not defined

All the previous code are exactly the same as the ones in the vignette. I am wondering why this error occurs and how to fix it. Thanks!

Below is the sessioninfo:

                             R version 3.2.3 (2015-12-10)
                       Platform: x86_64-apple-darwin13.4.0 (64-bit)
                       Running under: OS X 10.11.3 (El Capitan)

                       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  
                       [9] base     

                       other attached packages:
                             [1] rPython_0.0-6             RJSONIO_1.3-0             org.Mm.eg.db_3.1.2       
                       [4] RSQLite_1.0.0             DBI_0.3.1                 AnnotationDbi_1.30.1     
                       [7] Biobase_2.28.0            scLVM_0.99.2              DESeq2_1.8.2             
                       [10] RcppArmadillo_0.6.600.4.0 Rcpp_0.12.5               GenomicRanges_1.20.8     
                       [13] GenomeInfoDb_1.4.3        IRanges_2.2.9             S4Vectors_0.6.6          
                       [16] BiocGenerics_0.14.0       gplots_3.0.1              ggplot2_2.1.0            
                       [19] statmod_1.4.24            genefilter_1.50.0        

                       loaded via a namespace (and not attached):
                             [1] RColorBrewer_1.1-2   futile.logger_1.4.1  plyr_1.8.4          
                       [4] XVector_0.8.0        bitops_1.0-6         futile.options_1.0.0
                       [7] tools_3.2.3          rpart_4.1-10         lattice_0.20-33     
                       [10] annotate_1.46.1      gtable_0.2.0         gridExtra_2.2.1     
                       [13] cluster_2.0.3        gtools_3.5.0         caTools_1.17.1      
                       [16] locfit_1.5-9.1       nnet_7.3-12          grid_3.2.3          
                       [19] XML_3.98-1.4         survival_2.38-3      BiocParallel_1.2.22 
                       [22] foreign_0.8-66       latticeExtra_0.6-28  gdata_2.17.0        
                       [25] Formula_1.2-1        geneplotter_1.46.0   lambda.r_1.1.7      
                       [28] scales_0.4.0         Hmisc_3.17-2         splines_3.2.3       
                       [31] rsconnect_0.4.2.2    xtable_1.8-2         colorspace_1.2-6    
                       [34] KernSmooth_2.23-15   acepack_1.3-3.3      munsell_0.4.3       

[emerygoossens]

I am also having this issue. Any help would be appreciated.

[flophys]

This seems to be an issue with a specific R-python combination which I couldn't reproduce. Try this workaround:

When attaching the package, this line is normally executed: python.load(system.file("pysrc","init_data.py",package="scLVM“))
It seems this doesn’t happen for you which is why it doesn’t find the scLVM function. Execute this manually after loading the package, this normally solves the problem.

[lrodda]

This work around worked well for the init function, but I got a very similar error when trying to run Ycorr = getCorrectedExpression(sclvm)

Error in python.exec(paste("Ycorr = ", objName, ".getCorrectedExpression(rand_eff_ids)", :
name 'sclvm' is not defined

Is there a similar work around?

[emerygoossens]

I had a similar problem with this. My problem went away when I correctly installed rPython. First, make sure your ~/bash_To do this, download a new rPython package and open your terminal and type these commands

python --version
export RPYTHON_PYTHON_VERSION="whatever python anaconda version such as 2.7.12"
R CMD INSTALL /Users/egoossen/Downloads/rPython_0.0-6.tar.gz

Now go into R and type

library(rPython)
python.exec("import sys; print(sys.version)")

and verify that it is the same. When you load the scLVM package more than once, it doesn't give the same error about differing versions of python between the system and rPython versions.

[BinDuan]

I have the same problem. I tried set "export RPYTHON_PYTHON_VERSION=2.7.13", and "R CMD INSTALL rPython_0.0-6.tar.gz", but when I check like this:
library(rPython)
python.exec("import sys;print(sys.version)")

I got something like:
"2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609]
"
I have several python version, and 2.7.13 is in the anaconda. Obviously, set "export" is invalid. Then, how should I do?

[BinDuan]

I'm sure that my rPython was installed correctly now, but there was something wrong with scLVM like below:

library(scLVM)
[1] "It seems python package deprecated is not installed. Try to install it using 'pip install deprecated ' If the package is installed already, make sure rPyhton is using the correct python version. If you have several versions of python installed, have a look at our installation guide on github."

And when I tried to install deprecated like below:
pip install deprecated
Collecting deprecated
Could not find a version that satisfies the requirement deprecated (from versions: )
No matching distribution found for deprecated
I don't know why, and I'll appreciate if someone can give me a hand.

[Shians]

Also having this problem with "deprecated". This is caused by the attempt to import limix.deprecated. From what I gather at some point they deprecated a whole version of LIMIX, they then deprecated that whole LIMIX package and made a new one with the same name. Now the new one does not have the deprecated version included and I assume this is the version installed by pip, so scLVM will not find limix.deprecated.

If the new version is backwards compatible then it may be possible to simply import limix rather than limix.deprecated, otherwise one would need to install the deprecated version of limix to get this software to work.

[flophys]

@BinDuan unfortunately rPython does not work with Anaconda python (also check out the rPython docs), maybe try to use the one that came with your OS? I have fixed the "deprecated" problem though which occurred due to some changes in the latest release of limix.

[BinDuan]

Thank you for your reply, I have fixed the problem by using the default python on the server. At 2017-06-21 04:46:58, "flophys" <notifications@github.com> wrote: @BinDuan unfortunately rPython does not work with Anaconda python (also check out the rPython docs), maybe try to use the one that came with your OS? I have fixed the "deprecated" problem though which occurred due to some changes in the latest release of limix. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[BinDuan]

郁逸菲： 调研了ml包里的几个算法，准备研究有什么可以用的地方。 危志庭： 第一篇文献的结果重复没问题，第二篇的重复有以下两个问题： 1.觉得文献所用的方法不是很合理； 2.文献的一些过滤条件目前不知道怎么做； 下个礼拜把已有结果整理一下，希望和老师您讨论一下。 段斌： 目前主要是sgrna敲除效率矫正和脱靶矫正问题。这两个问题之前的工作都没有做多少分析，尤其是脱靶问题。对于脱靶问题的解决方法和您已经讨论过，第一种矫正策略想了想还是没有什么好的办法，或许只能是第二种简单策略了。