Error Install CaSpER

[nikou123456]

Hi,

THe CaSpER is a great package for CNV identification. I tried to install the CaSpER in R version 3.6 and 4.0, but it always shows "had non-zero exit status", could you help me?

>BiocManager::install(c('biomaRt', 'limma', 'GO.db', 'org.Hs.eg.db', 'GOstats'))
>install_github("akdess/CaSpER",lib="/cluster/home/wye/R/x86_64-pc-linux-gnu-library/4.0")
#or install_github("akdess/CaSpER")
ERROR: lazy loading failed for package ‘CaSpER’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/CaSpER’
Error: Failed to install 'CaSpER' from GitHub:
  (converted from warning) installation of package ‘/var/folders/sc/7h1ltb0d16v650rh5prytj100000gn/T//RtmpQF87ZA/file22c3db9061f/CaSpER_0.1.0.tar.gz’ had non-zero exit status

I have tried updating all dependence packages, but it still doesn't work.

>install_github("akdess/CaSpER",force=TRUE)
** R
** data
*** moving datasets to lazyload DB
Killed
Error: Failed to install 'CaSpER' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpJ7iymR/file29db728d5fc/CaSpER_0.1.0.tar.gz’ had non-zero exit status

Best, Seven

[nikou123456]

Hi, I have installed the CaSpER locally, but I got some problems when I run example data and code. Could you help me?

example code:https://github.com/akdess/CaSpER/blob/master/demo/meningioma.R

> final.objects <- runCaSpER(object, removeCentromere=T, cytoband=cytoband, method="iterative")
Performing recursive median filtering...
Performing HMM segmentation...
Error in .Call("forward_backward", kappa, A, py[, I], PACKAGE = "CaSpER") : 
  "forward_backward" not available for .Call() for package "CaSpER"
In addition: There were 15 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 37
2: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 37
3: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 37
4: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 97
5: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 37
6: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 37
7: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 37
8: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 131
9: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 117
10: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 97
11: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 97
12: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 149
13: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 119
14: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 131
15: In runmed(x, filt$n) : 'k' is bigger than 'n'!  Changing 'k' to 135

Best, Seven

[akdess]

Dear @nikou123456 , I am very sorry for my late reply. Did you resolve the issue? Please let me know if you still have the same problem.

[mjahanzaib119311]

Dear akdess I am facing this problem while installing CaSpER. this is the error I am facing.

install_github("akdess/CaSpER") Downloading GitHub repo akdess/CaSpER@master from URL https://api.github.com/repos/akdess/CaSpER/zipball/master Installing CaSpER '/home/jrcgr/anaconda3/lib/R/bin/R' --no-site-file --no-environ --no-save \ --no-restore --quiet CMD INSTALL \ '/tmp/RtmpKyZMOU/devtools7a1a3008dfff/akdess-CaSpER-a26e563' \ --library='/home/jrcgr/anaconda3/lib/R/library' --install-tests

• installing source package ‘CaSpER’ ... ** libs x86_64-conda_cos6-linux-gnu-cc -shared -L/home/jrcgr/anaconda3/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/home/jrcgr/anaconda3/lib -L/home/jrcgr/anaconda3/lib -o CaSpER.so forward_backward.o register.o viterbi.o -L/home/jrcgr/anaconda3/lib/R/lib -lR forward_backward.o: file not recognized: file format not recognized collect2: error: ld returned 1 exit status /home/jrcgr/anaconda3/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 ‘/home/jrcgr/anaconda3/lib/R/library/CaSpER’ Installation failed: Command failed (1)

[BMILAB]

Dear @nikou123456 , I am very sorry for my late reply. Did you resolve the issue? Please let me know if you still have the same problem.

Hi Akdess,

Thank you for your reply. I did not solve this problem on my macOS system even though I tried many different ways. It can be successfully installed and run example when I installed it on my Window system. In addition, it also can't be installed on my linux system, there has "non-zero exit status" issue.

Best, Seven

[mjahanzaib119311]

remotes::install_github("akdess/CaSpER")

R data *** moving datasets to lazyload DB Warning: file ‘hg38_cytoband.rda’ has magic number 'RDX3' Use of save versions prior to 2 is deprecated Error in load(zfile, envir = envir) : bad restore file magic number (file may be corrupted) -- no data loaded ERROR: lazydata failed for package ‘CaSpER’

• removing ‘/home/jrcgr/anaconda3/lib/R/library/CaSpER’ Error: Failed to install 'CaSpER' from GitHub: (converted from warning) installation of package ‘/tmp/RtmpvlQRN2/file18a374fd7ba/CaSpER_0.2.0.tar.gz’ had non-zero exit status

[akdess]

Dear @BMILAB,

I am very sorry for the late reply. Thanks a lot for letting me know about the Mac and Linux system installation issue. I will look into that.

Thanks!