problem with installation

[nsabath]

Dear Xuran,

I first tried to install the package in the suggested way without success:

devtools::install_github('xuranw/MuSiC') Error in read.dcf(path) : Found continuation line starting ' plyr, ...' at begin of record.

Next I have managed to manually download the package and install it: install.packages("C:/Users/nivs/Downloads/MuSiC-master.zip", repos = NULL, type = "win.binary")

following the suggestion from other issues, I have tried to also update the dependencies: setwd("C:/Rpackages/MuSiC-master/")

devtools::check() Updating MuSiC documentation Writing NAMESPACE Loading MuSiC Loading required package: nnls Loading required package: ggplot2 Writing NAMESPACE -- Building ----------------------------------------------------------- MuSiC -- Setting env vars:

• CFLAGS : -Wall -pedantic
• CXXFLAGS : -Wall -pedantic

• CXX11FLAGS: -Wall -pedantic

  √ checking for file 'C:\Rpackages\MuSiC-master/DESCRIPTION' (553ms)

• preparing 'MuSiC': (1.1s) √ checking DESCRIPTION meta-information ...
• installing the package to build vignettes (676ms) E creating vignettes (34.2s) Quitting from lines 136-156 (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: Could not find CIBERSORT source code at '\offline.il.cgen.biz/home/nivs/Documents/R-data/bseqsc'. Please ensure you correctly configured bseqsc. See ?bseqsc_config. Execution halted Error in processx::run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), : System command error

it seems that there are some issues with the vignette

finally, I was able to load the package, but ran into another problem:

library(MuSiC)

Download EMTAB single cell dataset from Github

Mousesub.eset = readRDS("C:/Rpackages/MuSiC-master/vignettes/data/Mousesubeset.rds") Mousesub.basis = music_basis(Mousesub.eset, clusters = 'cellType', samples = 'sampleID', select.ct = c("Endo", "Podo", "PT", "LOH", "DCT", "CD-PC", "CD-IC", "Fib", "Macro", "Neutro","B lymph", "T lymph", "NK")) Error in sampleNames(x) : could not find function "sampleNames"

Any idea?

Thanks,

Niv

[xuranw]

Hi Niv,

Thanks for using MuSiC!

Have you tried to do install package xbioc? Hope that helps.

Best, Xuran

[lila167]

Hi, I also get a similar error: "Error: Failed to install 'MuSiC' from GitHub: Failed to install 'xbioc' from GitHub: (converted from warning) installation of package '/tmp/Rtmp6Qovba/file14c3605315eb/xbioc_0.1.17.tar.gz' had non-zero exit status"

It is not possible to install xbioc. Any idea? Thanks

[stephen-siecinski]

Also had this issue but it resolved itself after updating R to 4.0.3.

[lila167]

I changed my R version and then it worked

[bieniu777]

Hi,

I have a similar issue. Can't install the MuSiC nor the xbioc package.

I can't install MuSiC without xbioc apparently, and this is the error I get when trying to install MuSiC using remotes or devtools:

> remotes::install_github("xuranw/MuSiC")
Downloading GitHub repo xuranw/MuSiC@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

 1: All                                            
 2: CRAN packages only                             
 3: None                                           
 4: RcppArmad... (0.9.900.3.0 -> 0.10.5.0.0) [CRAN]
 5: matrixStats  (0.56.0      -> 0.59.0    ) [CRAN]
 6: MatrixModels (0.4-1       -> 0.5-0     ) [CRAN]
 7: SparseM      (1.78        -> 1.81      ) [CRAN]
 8: utf8         (1.1.4       -> 1.2.1     ) [CRAN]
 9: pillar       (1.6.0       -> 1.6.1     ) [CRAN]
10: fansi        (0.4.1       -> 0.5.0     ) [CRAN]
11: ellipsis     (0.3.1       -> 0.3.2     ) [CRAN]
12: colorspace   (1.4-1       -> 2.0-1     ) [CRAN]
13: viridisLite  (0.3.0       -> 0.4.0     ) [CRAN]
14: R6           (2.4.1       -> 2.5.0     ) [CRAN]
15: labeling     (0.3         -> 0.4.2     ) [CRAN]
16: farver       (2.0.3       -> 2.1.0     ) [CRAN]
17: quantreg     (5.67        -> 5.86      ) [CRAN]
18: tibble       (3.1.1       -> 3.1.2     ) [CRAN]
19: isoband      (0.2.2       -> 0.2.4     ) [CRAN]
20: digest       (0.6.25      -> 0.6.27    ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:3
Downloading GitHub repo renozao/xbioc@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

 1: All                                            
 2: CRAN packages only                             
 3: None                                           
 4: pkgmaker     (0.31.1  -> 481851326...) [GitHub]
 5: stringi      (1.5.3   -> 1.6.2       ) [CRAN]  
 6: BiocGenerics (0.36.0  -> 0.36.1      ) [CRAN]  
 7: ellipsis     (0.3.1   -> 0.3.2       ) [CRAN]  
 8: fastmap      (1.0.1   -> 1.1.0       ) [CRAN]  
 9: cachem       (1.0.3   -> 1.0.5       ) [CRAN]  
10: memoise      (1.1.0   -> 2.0.0       ) [CRAN]  
11: backports    (1.1.10  -> 1.2.1       ) [CRAN]  
12: digest       (0.6.25  -> 0.6.27      ) [CRAN]  
13: RSQLite      (2.2.1   -> 2.2.7       ) [CRAN]  
14: Biobase      (2.48.0  -> 2.50.0      ) [CRAN]  
15: BiocManager  (1.30.10 -> 1.30.15     ) [CRAN]  

Enter one or more numbers, or an empty line to skip updates:3
√  checking for file 'C:\Users\kjb2g19\AppData\Local\Temp\RtmpYPufcL\remotes39c8792c54dc\renozao-xbioc-1354168/DESCRIPTION' (6.7s)
-  preparing 'xbioc': (527ms)
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts (336ms)
-  checking for empty or unneeded directories
-  looking to see if a 'data/datalist' file should be added
-  building 'xbioc_0.1.19.tar.gz'

Installing package into ‘C:/Apps/Rlibraries’
(as ‘lib’ is unspecified)
'\\filestore.soton.ac.uk\users\kjb2g19\mydocuments'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'xbioc' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package 'BiocGenerics' was built under R version 4.0.3
Execution halted
**ERROR: lazy loading failed for package 'xbioc'
* removing 'C:/Apps/Rlibraries/xbioc'
Error: Failed to install 'MuSiC' from GitHub:
  Failed to install 'xbioc' from GitHub:
  (converted from warning) installation of package ‘C:/Users/kjb2g19/AppData/Local/Temp/RtmpYPufcL/file39c84aea58f3/xbioc_0.1.19.tar.gz’ had non-zero exit status**

I don't update any packages. When I did, it somehow messed up my Rcpp package and I had to remove it manually, install it again, otherwise I couldn't even load packages such as seurat or tidyverse anymore.

Then, trying to install xbioc:

devtools::install_github("renozao/xbioc")
remotes::install_github("renozao/xbioc")

**Error: Failed to install 'xbioc' from GitHub:
  (converted from warning) installation of package ‘C:/Users/kjb2g19/AppData/Local/Temp/RtmpYPufcL/file39c82c4c32c6/xbioc_0.1.19.tar.gz’ had non-zero exit status**

Trying simple "install.packages" doesn't work either:

Warning in install.packages :
  package ‘xbioc’ is not available (for R version 4.0.2)

I would appreciate any help

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)