error when installing v. 2.0

[andrea-ag]

Dear Harmanci,
thank you for this so useful package. I'm analyzing bulk RNA-seq with CaSpER. I successfully applied the procedure to install the package at:

https://rpubs.com/akdes/578955
require(devtools)
install_github("akdess/CaSpER")

However, I get few errors in the analysis due to dependencies lacking ("no slot of name "control.normalized.visbound.noiseRemoved" for this object of class "casper").
I noticed that package version automatically installed by github is still the beta release (v. 0.1). So, I manually downloaded the tar.gz at:
https://github.com/akdess/CaSpER/releases/tag/v2.0
but when I installed the package I get this error:

> install.packages("CaSpER-2.0.tar.gz")
inferring 'repos = NULL' from 'pkgs'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
* installing *source* package ‘CaSpER’ ...
** using staged installation
** libs
gcc -shared -L/usr/local/lib -o CaSpER.so forward_backward.o register.o viterbi.o
.......
.......
collect2: error: ld returned 1 exit status
/usr/local/R/3.6.1/lib/R/share/make/shlib.mk:6: recipe for target 'CaSpER.so' failed
make: *** [CaSpER.so] Error 1
ERROR: compilation failed for package ‘CaSpER’
* removing ‘/usr/local/R/3.6.1/lib/R/library/CaSpER’
Warning message:
In install.packages("CaSpER-2.0.tar.gz") :
  installation of package ‘CaSpER-2.0.tar.gz’ had non-zero exit status

Below my sessionInfo. Any suggestion is really appreciated.
Thank you in advance,
Andrea

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/local/R/3.6.1/lib/R/lib/libRblas.so
LAPACK: /usr/local/R/3.6.1/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] devtools_2.3.0 usethis_1.6.1 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3          magrittr_1.5        pkgload_1.0.2      
 [4] R6_2.4.1            rlang_0.4.8         fansi_0.4.1        
 [7] tools_3.6.1         pkgbuild_1.0.6      sessioninfo_1.1.1  
[10] cli_2.0.2           withr_2.1.2         ellipsis_0.3.0     
[13] remotes_2.1.1       assertthat_0.2.1    digest_0.6.25      
[16] rprojroot_1.3-2     crayon_1.3.4        processx_3.4.1     
[19] BiocManager_1.30.10 callr_3.4.3         fs_1.3.1           
[22] ps_1.3.0            curl_4.3            testthat_2.3.2     
[25] memoise_1.1.0       glue_1.4.1          compiler_3.6.1     
[28] desc_1.2.0          backports_1.1.5     prettyunits_1.1.1  

[akdess]

Dear @andrea-ag,

The code is updated for R.6.3. Can you please try again using the following commands? Hope it works.

BiocManager::install(c('biomaRt', 'limma', 'GO.db', 'org.Hs.eg.db', 'GOstats', 'GenomicRanges'))
require(devtools)
install_github("akdess/CaSpER")

[andrea-ag]

Dear Harmanci,
thanks a lot, now the installation works perfectly.

Just a couple of more questions. About the error:
"no slot of name "control.normalized.visbound.noiseRemoved" for this object of class "casper"
changing line 20 of the function "plotGEAndBAFOneSample.R" from:
_ value = [email protected][[cnv.scale]][,_
to:
_ value = [email protected][[cnv.scale]][,_
solved the problem for me. That's correct?

Thanks a lot for your support,
best,
Andrea

[andrea-ag]

Dear Harmanci,
sorry to bother you again.

The change I made in the "plotGEAndBAFOneSample.R" didn't solve the problem; the plot is generated, but the "expr.scale" graph shows a widespread noise of signal and it is unuseful. Looking at the code, it looks like that "control.normalized.visbound.noiseRemoved" in the casper object is always NULL. I also tested the yale meningioma dataset, and the same plot cannot be generated. Should I specify some parameters when generating a Casper object?

Also, a couple of suggestions. It looks like that:

• the param "log.transformed" is not used in the function "CreateCasperObject", so no log transformation is performed when using normalized data
• the param "fileName" is not used in the function "plotHeatmap", so the file name cannot be changed

Finally, please don't consider the question about the "genoMat" object, I misunderstood a part of the tutorial.

Thanks again for your help,
Andrea

[akdess]

Dear @andrea-ag

Thanks a lot for your interest! I am very sorry for my very late reply.

I forgot to update plotGEAndBAFOneSample function in the latest release of Casper. I have removed [email protected] slot. You have done the correct edit for changing it to [email protected]. I have updated the code also.

Please let me know if you still have any problems.
Best,
Akdes