cannot install scCATCH #18

skim245 · 2020-06-11T22:10:17Z

Dear ZJUFanLab

I cannot install scCATCH with an error message below

install.packages(pkgs = 'scCATCH_2.0.tar.gz')

##Warning in install.packages :

package ‘scCATCH_2.0.tar.gz’ is not available (for R version 3.6.3)

and with second install codes

install devtools and install scCATCH

install.packages(pkgs = 'devtools')
devtools::install_github('ZJUFanLab/scCATCH')

Error: Failed to install 'scCATCH' from GitHub:
System command 'R' failed, exit status: 137, stdout + stderr:
E> * checking for file ‘/private/var/folders/g0/w9p16d056l1d15r38h9r2y8m0000gn/T/Rtmp4o8efy/remotes1c4a4db10501/ZJUFanLab-scCATCH-5637658/DESCRIPTION’ ... OK
E> * preparing ‘scCATCH’:
E> * checking DESCRIPTION meta-information ... OK
E> * checking for LF line-endings in source and make files and shell scripts
E> * checking for empty or unneeded directories
E> * looking to see if a ‘data/datalist’ file should be added
E> /Library/Frameworks/R.framework/Resources/bin/build: line 10: 7505 Done echo 'tools:::.build_packages()'
E> 7506 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" --no-restore --slave --args ${args}

Thank you in advance!

ZJUFanLab · 2020-06-12T02:03:05Z

Hello, I'm very sorry that I can't help you with it because installation of scCATCH on our different devices works today, including windows and linux, R (3.6.1) and R (3.6.3.), installation via devtools and source package (tar.gz). I don't know why you can't install it. Maybe you could try installing other github R package to check.

dmitroi · 2020-06-17T21:22:25Z

I have the same problem as skim245. I tried many approaches and different R versions. Other github R packages are working, like garnett, harmony, seurat, etc. Only scCATCH doesn't want to install. Thanks.

multitalk · 2020-06-18T01:58:00Z

Hello, sorry for the failure of scCATCH installation. I have no idea why scCATCH doesn't want to install in your devices. Here are my attempts.

Time: 2020.06.18

[1] Windows 10, R 3.6.1, by source package --working

> install.packages("D:/github_repo/scCATCH_2.0.tar.gz", repos = NULL, type = "source")
* installing *source* package 'scCATCH' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
** help
*** installing help indices
  converting help for package 'scCATCH'
    finding HTML links ... 好了
    findmarkergenes                         html  
    mouse_kidney_203_Seurat                 html  
    scCATCH                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
*** arch - x64
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
** testing if installed package can be loaded from final location
*** arch - i386
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
*** arch - x64
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)
Making 'packages.html' ... 好了

[2] Windows 10, R 3.6.1, by devtools --working

> devtools::install_github('ZJUFanLab/scCATCH')
Downloading GitHub repo ZJUFanLab/scCATCH@master
These packages have more recent versions available.
Which would you like to update?

 1: All                                         
 2: CRAN packages only                          
 3: None                                        
 4: Seurat       (3.1.0     -> 3.1.5    ) [CRAN]
 5: data.table   (1.12.2    -> 1.12.8   ) [CRAN]
 6: ape          (5.3       -> 5.4      ) [CRAN]
 7: fitdistrplus (1.0-14    -> 1.1-1    ) [CRAN]
 8: future       (1.14.0    -> 1.17.0   ) [CRAN]
 9: future.apply (1.3.0     -> 1.5.0    ) [CRAN]
10: ggplot2      (3.2.0     -> 3.3.1    ) [CRAN]
11: ggrepel      (0.8.1     -> 0.8.2    ) [CRAN]
12: ggridges     (0.5.1     -> 0.5.2    ) [CRAN]
13: igraph       (1.2.4.1   -> 1.2.5    ) [CRAN]
14: leiden       (0.3.1     -> 0.3.3    ) [CRAN]
15: pbapply      (1.4-1     -> 1.4-2    ) [CRAN]
16: plotly       (4.9.0     -> 4.9.2.1  ) [CRAN]
17: Rcpp         (1.0.2     -> 1.0.4.6  ) [CRAN]
18: RcppAnnoy    (0.0.12    -> 0.0.16   ) [CRAN]
19: reticulate   (1.13      -> 1.16     ) [CRAN]
20: rlang        (0.4.0     -> 0.4.6    ) [CRAN]
21: ROCR         (1.0-7     -> 1.0-11   ) [CRAN]
22: rsvd         (1.0.2     -> 1.0.3    ) [CRAN]
23: scales       (1.0.0     -> 1.1.1    ) [CRAN]
24: sctransform  (0.2.0     -> 0.2.1    ) [CRAN]
25: uwot         (0.1.3     -> 0.1.8    ) [CRAN]
26: RcppEigen    (0.3.3.5.0 -> 0.3.3.7.0) [CRAN]
27: RcppProgress (0.4.1     -> 0.4.2    ) [CRAN]
28: digest       (0.6.20    -> 0.6.25   ) [CRAN]
29: glue         (1.3.1     -> 1.4.1    ) [CRAN]
30: isoband      (0.2.0     -> 0.2.1    ) [CRAN]
31: tibble       (2.1.3     -> 3.0.1    ) [CRAN]
32: withr        (2.1.2     -> 2.2.0    ) [CRAN]
33: farver       (2.0.1     -> 2.0.3    ) [CRAN]
34: R6           (2.4.0     -> 2.4.1    ) [CRAN]
35: testthat     (2.2.1     -> 2.3.2    ) [CRAN]
36: cli          (1.1.0     -> 2.0.2    ) [CRAN]
37: ellipsis     (0.2.0.1   -> 0.3.1    ) [CRAN]
38: fansi        (0.4.0     -> 0.4.1    ) [CRAN]
39: pillar       (1.4.2     -> 1.4.4    ) [CRAN]
40: pkgconfig    (2.0.2     -> 2.0.3    ) [CRAN]
41: vctrs        (0.2.0     -> 0.3.1    ) [CRAN]
42: pkgload      (1.0.2     -> 1.1.0    ) [CRAN]
43: pkgbuild     (1.0.4     -> 1.0.8    ) [CRAN]
44: rstudioapi   (0.10      -> 0.11     ) [CRAN]
45: callr        (3.3.1     -> 3.4.3    ) [CRAN]
46: prettyunits  (1.0.2     -> 1.1.1    ) [CRAN]
47: backports    (1.1.4     -> 1.1.8    ) [CRAN]
48: processx     (3.4.1     -> 3.4.2    ) [CRAN]
49: ps           (1.3.0     -> 1.3.3    ) [CRAN]
50: globals      (0.12.4    -> 0.12.5   ) [CRAN]
51: listenv      (0.7.0     -> 0.8.0    ) [CRAN]
52: plyr         (1.8.4     -> 1.8.6    ) [CRAN]
53: curl         (4.0       -> 4.3      ) [CRAN]
54: jsonlite     (1.6       -> 1.6.1    ) [CRAN]
55: mime         (0.7       -> 0.9      ) [CRAN]
56: sys          (3.2       -> 3.3      ) [CRAN]
57: zoo          (1.8-6     -> 1.8-8    ) [CRAN]
58: htmltools    (0.3.6     -> 0.5.0    ) [CRAN]
59: htmlwidgets  (1.3       -> 1.5.1    ) [CRAN]
60: tidyr        (0.8.3     -> 1.1.0    ) [CRAN]
61: hexbin       (1.27.3    -> 1.28.1   ) [CRAN]
62: dplyr        (0.8.3     -> 1.0.0    ) [CRAN]
63: crosstalk    (1.0.0     -> 1.1.0.1  ) [CRAN]
64: purrr        (0.3.2     -> 0.3.4    ) [CRAN]
65: promises     (1.0.1     -> 1.1.1    ) [CRAN]
66: tidyselect   (0.2.5     -> 1.1.0    ) [CRAN]
67: yaml         (2.2.0     -> 2.2.1    ) [CRAN]
68: later        (0.8.0     -> 1.1.0.1  ) [CRAN]
69: stringi      (1.4.3     -> 1.4.6    ) [CRAN]
70: BH           (1.69.0-1  -> 1.72.0-3 ) [CRAN]
71: gplots       (3.0.1.1   -> 3.0.3    ) [CRAN]
72: gtools       (3.8.1     -> 3.8.2    ) [CRAN]
73: caTools      (1.17.1.2  -> 1.18.0   ) [CRAN]
74: reshape2     (1.4.3     -> 1.4.4    ) [CRAN]
75: RSpectra     (0.15-0    -> 0.16-0   ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
3
√  checking for file 'C:\Users\Syed\AppData\Local\Temp\RtmpwtKzm6\remotes2cf82a9f58fc\ZJUFanLab-scCATCH-5637658/DESCRIPTION' ...
-  preparing 'scCATCH':
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  looking to see if a 'data/datalist' file should be added
-  building 'scCATCH_2.0.tar.gz' (6.5s)
   
* installing *source* package 'scCATCH' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
** help
*** installing help indices
  converting help for package 'scCATCH'
    finding HTML links ... 好了
    findmarkergenes                         html  
    mouse_kidney_203_Seurat                 html  
    scCATCH                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
*** arch - x64
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
** testing if installed package can be loaded from final location
*** arch - i386
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
*** arch - x64
Warning: replacing previous import 'Matrix::cov2cor' by 'stats::cov2cor' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::toeplitz' by 'stats::toeplitz' when loading 'scCATCH'
Warning: replacing previous import 'Matrix::update' by 'stats::update' when loading 'scCATCH'
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)
Making 'packages.html' ... 好了

[3] Linux (Ubuntu 18.04), R 3.6.3, by source package --working

> install.packages("~/scCATCH_2.0.tar.gz", repos = NULL, type = "source")
Installing package into ‘/home/shaoxin/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘scCATCH’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘scCATCH’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘scCATCH’
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

[4] Linux (Ubuntu 18.04), R 3.6.3, by devtools --working

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> devtools::install_github('ZJUFanLab/scCATCH')
Downloading GitHub repo ZJUFanLab/scCATCH@master
✓  checking for file ‘/tmp/RtmpuKJCHS/remotesa5c542145da7/ZJUFanLab-scCATCH-5637658/DESCRIPTION’ ...
─  preparing ‘scCATCH’:
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘scCATCH_2.0.tar.gz’ (2.9s)
   
Installing package into ‘/home/shaoxin/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘scCATCH’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘scCATCH’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘scCATCH’
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

multitalk · 2020-06-18T02:11:34Z

Dear ZJUFanLab

I cannot install scCATCH with an error message below

install.packages(pkgs = 'scCATCH_2.0.tar.gz')

##Warning in install.packages :

package ‘scCATCH_2.0.tar.gz’ is not available (for R version 3.6.3)

and with second install codes

install devtools and install scCATCH

install.packages(pkgs = 'devtools')
devtools::install_github('ZJUFanLab/scCATCH')

Error: Failed to install 'scCATCH' from GitHub:
System command 'R' failed, exit status: 137, stdout + stderr:
E> * checking for file ‘/private/var/folders/g0/w9p16d056l1d15r38h9r2y8m0000gn/T/Rtmp4o8efy/remotes1c4a4db10501/ZJUFanLab-scCATCH-5637658/DESCRIPTION’ ... OK
E> * preparing ‘scCATCH’:
E> * checking DESCRIPTION meta-information ... OK
E> * checking for LF line-endings in source and make files and shell scripts
E> * checking for empty or unneeded directories
E> * looking to see if a ‘data/datalist’ file should be added
E> /Library/Frameworks/R.framework/Resources/bin/build: line 10: 7505 Done echo 'tools:::.build_packages()'
E> 7506 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" --no-restore --slave --args ${args}

Thank you in advance!

You should add `epos = NULL, type = "source"` by installing scCATCH via source package! Ensure the right directory for scCATCH_2.0.tar.gz!

dmitroi · 2020-06-18T21:11:35Z

I tried your suggestion but it still gives me the same error (please see below). I see that you replied several installation reports but none for macOS. Could you try to see how it goes on a macOS system?
Thanks.

install.packages ("/Users/danielm/Downloads/scCATCH_2.0.tar.gz", repos=NULL, type="source")

installing source package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 10033 Done echo 'tools:::.install_packages()'
10034 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
Warning in install.packages :
installation of package ‘/Users/danielm/Downloads/scCATCH_2.0.tar.gz’ had non-zero exit status

multitalk · 2020-06-19T02:16:30Z

[5] MacOS Mojave 10.14.6 (18G103), R 3.6.1, by source package --working

> install.packages("~/Desktop/scCATCH_2.0.tar.gz", repos = NULL, type = "source")
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘scCATCH’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘scCATCH’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘scCATCH’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘scCATCH’
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

skim245 · 2020-06-19T09:27:21Z

dmitroi , I finally got scCATCH installed on my mac by several alternative ways of installing, but i am not sure which one got it through so I will just list them up!

I tried manual installation
#manually downloaded the tar.gz file on my "Desktop" and indicated in R studio to install the package manually from desktop

install.packages("~/Desktop/scCATCH_2.0.tar.gz", repos = NULL, type = "source")

this one throw me a warning
Warning in install.packages : scCATCH_2.0.tar.gz’ had non-zero exit status

and also tried by:

R studio/Tools/Install Packages/Install from: Packages Archive File(.tgz; tar.gz) and browse the file where I had the "scCATCH_2.0.tar.gz" downloaded.

hope this helps!

ankushs0128 · 2020-07-08T21:39:56Z

scCATCH_2.0.tar.gz

Installation of scCATCH_2.1.tar.gz gives an error message on installing using these commands
install.packages("~/Downloads/scCATCH-2.1.tar.gz",` repos = NULL, type = "source", dependencies = TRUE, INSTALL_opts = '--no-lock')
&
devtools::install_github('ZJUFanLab/scCATCH')

Warning in untar2(tarfile, files, list, exdir, restore_times) :
skipping pax global extended headers

installing source package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 70029 Done echo 'tools:::.install_packages()'
70030 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Warning in install.packages :
installation of package ‘/Users/ankushs/Downloads/scCATCH-2.1.tar.gz’ had non-zero exit status

Sessioninfo

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5                  lattice_0.20-41             tidyr_1.1.0                 prettyunits_1.1.1          
 [5] ps_1.3.3                    assertthat_0.2.1            rprojroot_1.3-2             digest_0.6.25              
 [9] R6_2.4.1                    GenomeInfoDb_1.24.2         plyr_1.8.6                  backports_1.1.8            
[13] stats4_4.0.2                dynparam_1.0.1              pillar_1.4.4                zlibbioc_1.34.0            
[17] rlang_0.4.6                 rstudioapi_0.11             callr_3.4.3                 S4Vectors_0.26.1           
[21] Matrix_1.2-18               desc_1.2.0                  devtools_2.3.0              readr_1.3.1                
[25] stringr_1.4.0               igraph_1.2.5                RCurl_1.98-1.2              DelayedArray_0.14.0        
[29] compiler_4.0.2              carrier_0.1.0               pkgconfig_2.0.3             BiocGenerics_0.34.0        
[33] pkgbuild_1.0.8              SummarizedExperiment_1.18.1 tidyselect_1.1.0            tibble_3.0.2               
[37] GenomeInfoDbData_1.2.3      matrixStats_0.56.0          IRanges_2.22.2              fansi_0.4.1                
[41] crayon_1.3.4                dplyr_1.0.0                 withr_2.2.0                 bitops_1.0-6               
[45] grid_4.0.2                  lifecycle_0.2.0             magrittr_1.5                RcppParallel_5.0.2         
[49] cli_2.0.2                   stringi_1.4.6               XVector_0.28.0              reshape2_1.4.4             
[53] fs_1.4.2                    remotes_2.1.1               dynwrap_1.2.1               testthat_2.3.2             
[57] ellipsis_0.3.1              generics_0.0.2              vctrs_0.3.1                 Rhdf5lib_1.10.0            
[61] tools_4.0.2                 Biobase_2.48.0              glue_1.4.1                  purrr_0.3.4                
[65] hms_0.5.3                   proxyC_0.1.5                processx_3.4.3              pkgload_1.1.0              
[69] parallel_4.0.2              yaml_2.2.1                  colorspace_1.4-1            rhdf5_2.32.2               
[73] babelwhale_1.0.1            BiocManager_1.30.10         ArchR_0.9.5                 GenomicRanges_1.40.0       
[77] sessioninfo_1.1.1           dynutils_1.0.5              memoise_1.1.0               usethis_1.6.1

Thank you in advance for your help!

dmitroi · 2020-07-09T04:15:37Z

I succeeded to install scCATCH_2.1 in R version 3.6.0 on my MacBook Pro.

ankushs0128 · 2020-07-09T08:27:58Z

I succeeded to install scCATCH_2.1 in R version 3.6.0 on my MacBook Pro.

How about R version 4.0.2?

multitalk · 2020-07-10T02:17:31Z

Hello, scCATCH is not available for R >= 4.0 now. We will make it work in future version.

lyuguol · 2020-09-10T14:58:58Z

Hello, scCATCH is not available for R >= 4.0 now. We will make it work in future version.

Hello Xin,
When will the scCATCH be available for R >= 4.0?
I am working on an unstudied tissue. The other packages for cell type identification did not annotate my cells well.
So, I look very much forward to trying the scCATCH.
Thank you very much.
Best,
Guoliang

multitalk · 2020-09-11T07:40:07Z

Hello, scCATCH is available for R > 4.0 now. You can have a try. Good luck.

lyuguol · 2020-09-11T13:21:24Z

Hello, scCATCH is available for R > 4.0 now. You can have a try. Good luck.

Excellent!!
I will give it a try then.

All the best,
Guoliang

lyuguol · 2020-09-11T19:44:28Z

I have the same problem as skim245. I tried many approaches and different R versions. Other github R packages are working, like garnett, harmony, seurat, etc. Only scCATCH doesn't want to install. Thanks.

Hello Daniel,

May I ask how you manage to install the package in your laptop?

Thank you.

Best,
Guoliang

multitalk · 2020-09-12T01:01:25Z

Hello, scCATCH is available for R > 4.0 now. You can have a try. Good luck.

Excellent!!
I will give it a try then.

All the best,
Guoliang

Ensure the depend packages have been installed. Seurat, data.table, progress, stats, Matrix
For windows, ensure the install of Rtools to install R source package. Besides, we have uploaded a binary package in the Release page for windows.

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> install.packages("~/workspace/R/scCATCH_2.1.R-4.0.tar.gz", repos = NULL, type = "source")
Installing package into ‘/home/shaoxin/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

lyuguol · 2020-09-12T04:55:56Z

Hello, scCATCH is available for R > 4.0 now. You can have a try. Good luck.

Excellent!!
I will give it a try then.
All the best,
Guoliang

Ensure the depend packages have been installed. Seurat, data.table, progress, stats, Matrix

For windows, ensure the install of Rtools to install R source package. Besides, we have uploaded a binary package in the Release page for windows.
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> install.packages("~/workspace/R/scCATCH_2.1.R-4.0.tar.gz", repos = NULL, type = "source")
Installing package into ‘/home/shaoxin/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

Hello Xin, Many thanks for the quick reply!!

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

packageVersion("Seurat")
[1] ‘3.2.1’
packageVersion("data.table")
[1] ‘1.13.0’
packageVersion("progress")
[1] ‘1.2.2’
packageVersion("stats")
[1] ‘4.0.2’
packageVersion("Matrix")
[1] ‘1.2.18’

After having tried to re-install R and Rstudio, I am still repeatedly encountering the following error, which is similar to skim's and ankus's:

installing source package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 792 Done echo 'tools:::.install_packages()'
793 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Warning in install.packages :
installation of package ‘/Users/guolianglyu/Downloads/scCATCH_2.1.R-4.0.tar.gz’ had non-zero exit status

Thank you very much!

All the best,
Guoliang

xxyyll-1999 · 2020-09-15T03:33:28Z

Hello, scCATCH is available for R > 4.0 now. You can have a try. Good luck.

Excellent!!
I will give it a try then.
All the best,
Guoliang

Ensure the depend packages have been installed. Seurat, data.table, progress, stats, Matrix

For windows, ensure the install of Rtools to install R source package. Besides, we have uploaded a binary package in the Release page for windows.
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> install.packages("~/workspace/R/scCATCH_2.1.R-4.0.tar.gz", repos = NULL, type = "source")
Installing package into ‘/home/shaoxin/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)
Hello Xin, Many thanks for the quick reply!!

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

packageVersion("Seurat")
[1] ‘3.2.1’
packageVersion("data.table")
[1] ‘1.13.0’
packageVersion("progress")
[1] ‘1.2.2’
packageVersion("stats")
[1] ‘4.0.2’
packageVersion("Matrix")
[1] ‘1.2.18’

After having tried to re-install R and Rstudio, I am still repeatedly encountering the following error, which is similar to skim's and ankus's:

installing source package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 792 Done echo 'tools:::.install_packages()'
793 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Warning in install.packages :
installation of package ‘/Users/guolianglyu/Downloads/scCATCH_2.1.R-4.0.tar.gz’ had non-zero exit status

Thank you very much!

All the best,
Guoliang

Hello Guoliang, I have successfully installed scCATCH on my MacBook(macOS Catalina 10.15.5). For macOs, you can try this alternative way to install.

install.packages('devtools')

--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
1: 0-Cloud [https]
2: Australia (Canberra) [https]
3: Australia (Melbourne 1) [https]
4: Australia (Melbourne 2) [https]
5: Australia (Perth) [https]
6: Austria [https]
7: Belgium (Ghent) [https]
8: Brazil (BA) [https]
9: Brazil (PR) [https]
10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]
12: Brazil (SP 2) [https]
13: Bulgaria [https]
14: China (Beijing 1) [https]
15: China (Beijing 2) [https]
16: China (Hong Kong) [https]
17: China (Guangzhou) [https]
18: China (Lanzhou) [https]
19: China (Nanjing) [https]
20: China (Shanghai 1) [https]
21: Colombia (Cali) [https]
22: Costa Rica [https]
23: Denmark [https]
24: East Asia [https]
25: Ecuador (Cuenca) [https]
26: Ecuador (Quito) [https]
27: France (Lyon 1) [https]
28: France (Lyon 2) [https]
29: France (Marseille) [https]
30: Germany (Erlangen) [https]
31: Germany (Münster) [https]
32: Germany (Regensburg) [https]
33: Greece [https]
34: Hungary [https]
35: Iceland [https]
36: India [https]
37: Indonesia (Jakarta) [https]
38: Italy (Padua) [https]
39: Japan (Tokyo) [https]
40: Korea (Gyeongsan-si) [https]
41: Korea (Ulsan) [https]
42: Malaysia [https]
43: Mexico (Mexico City) [https]
44: Morocco [https]
45: Netherlands [https]
46: Norway [https]
47: Philippines [https]
48: Russia (Moscow) [https]
49: South Africa (Johannesburg) [https]
50: Spain (A Coruña) [https]
51: Sweden [https]
52: Switzerland [https]
53: Taiwan (Taipei) [https]
54: Turkey (Mersin) [https]
55: UK (Bristol) [https]
56: UK (London 1) [https]
57: USA (IA) [https]
58: USA (KS) [https]
59: USA (MI) [https]
60: USA (OH) [https]
61: USA (OR) [https]
62: USA (TN) [https]
63: USA (TX 1) [https]
64: Uruguay [https]
65: (other mirrors)

select suitable mirror in your country.
download devtools.

devtools::install_github('ZJUFanLab/scCATCH')

Downloading GitHub repo ZJUFanLab/scCATCH@HEAD

installing source package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

DONE (scCATCH)

In this step, it may probably ask you 'do you want to update these packages', you can select the number which you want.

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: deldir (0.1-28 -> 0.1-29) [CRAN]
5: data.table (1.12.8 -> 1.13.0) [CRAN]
6: lmtest (0.9-37 -> 0.9-38) [CRAN]
7: cowplot (1.0.0 -> 1.1.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:

Then the packages and dependencies which you need will be downloaded automatically. It is important to install from the source package which doesn't need compilation!

Hope this helps!

All the best,
Yulin

lyuguol · 2020-09-15T16:43:39Z

Hello, scCATCH is available for R > 4.0 now. You can have a try. Good luck.

Excellent!!
I will give it a try then.
All the best,
Guoliang

Ensure the depend packages have been installed. Seurat, data.table, progress, stats, Matrix

For windows, ensure the install of Rtools to install R source package. Besides, we have uploaded a binary package in the Release page for windows.
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> install.packages("~/workspace/R/scCATCH_2.1.R-4.0.tar.gz", repos = NULL, type = "source")
Installing package into ‘/home/shaoxin/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)
Hello Xin, Many thanks for the quick reply!!

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

packageVersion("Seurat")
[1] ‘3.2.1’
packageVersion("data.table")
[1] ‘1.13.0’
packageVersion("progress")
[1] ‘1.2.2’
packageVersion("stats")
[1] ‘4.0.2’
packageVersion("Matrix")
[1] ‘1.2.18’

After having tried to re-install R and Rstudio, I am still repeatedly encountering the following error, which is similar to skim's and ankus's:

installing source package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 792 Done echo 'tools:::.install_packages()'
793 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Warning in install.packages :
installation of package ‘/Users/guolianglyu/Downloads/scCATCH_2.1.R-4.0.tar.gz’ had non-zero exit status

Thank you very much!
All the best,
Guoliang
Hello Guoliang, I have successfully installed scCATCH on my MacBook(macOS Catalina 10.15.5). For macOs, you can try this alternative way to install.

install.packages('devtools')

--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
1: 0-Cloud [https]
2: Australia (Canberra) [https]
3: Australia (Melbourne 1) [https]
4: Australia (Melbourne 2) [https]
5: Australia (Perth) [https]
6: Austria [https]
7: Belgium (Ghent) [https]
8: Brazil (BA) [https]
9: Brazil (PR) [https]
10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]
12: Brazil (SP 2) [https]
13: Bulgaria [https]
14: China (Beijing 1) [https]
15: China (Beijing 2) [https]
16: China (Hong Kong) [https]
17: China (Guangzhou) [https]
18: China (Lanzhou) [https]
19: China (Nanjing) [https]
20: China (Shanghai 1) [https]
21: Colombia (Cali) [https]
22: Costa Rica [https]
23: Denmark [https]
24: East Asia [https]
25: Ecuador (Cuenca) [https]
26: Ecuador (Quito) [https]
27: France (Lyon 1) [https]
28: France (Lyon 2) [https]
29: France (Marseille) [https]
30: Germany (Erlangen) [https]
31: Germany (Münster) [https]
32: Germany (Regensburg) [https]
33: Greece [https]
34: Hungary [https]
35: Iceland [https]
36: India [https]
37: Indonesia (Jakarta) [https]
38: Italy (Padua) [https]
39: Japan (Tokyo) [https]
40: Korea (Gyeongsan-si) [https]
41: Korea (Ulsan) [https]
42: Malaysia [https]
43: Mexico (Mexico City) [https]
44: Morocco [https]
45: Netherlands [https]
46: Norway [https]
47: Philippines [https]
48: Russia (Moscow) [https]
49: South Africa (Johannesburg) [https]
50: Spain (A Coruña) [https]
51: Sweden [https]
52: Switzerland [https]
53: Taiwan (Taipei) [https]
54: Turkey (Mersin) [https]
55: UK (Bristol) [https]
56: UK (London 1) [https]
57: USA (IA) [https]
58: USA (KS) [https]
59: USA (MI) [https]
60: USA (OH) [https]
61: USA (OR) [https]
62: USA (TN) [https]
63: USA (TX 1) [https]
64: Uruguay [https]
65: (other mirrors)

select suitable mirror in your country.
download devtools.

devtools::install_github('ZJUFanLab/scCATCH')

Downloading GitHub repo ZJUFanLab/scCATCH@HEAD

installing source package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

DONE (scCATCH)

In this step, it may probably ask you 'do you want to update these packages', you can select the number which you want.

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: deldir (0.1-28 -> 0.1-29) [CRAN]
5: data.table (1.12.8 -> 1.13.0) [CRAN]
6: lmtest (0.9-37 -> 0.9-38) [CRAN]
7: cowplot (1.0.0 -> 1.1.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:

Then the packages and dependencies which you need will be downloaded automatically. It is important to install from the source package which doesn't need compilation!

Hope this helps!

All the best,
Yulin

Dear Yulin,

Many thanks for the detailed information!!

Unfortunately, still did not work for me.

Maybe some of the parameters/settings of my own Mac lead to the failure of scCATCH installation.. I am working on proving this 'hypothesis'.

Thank you very much again.

All the best,
Guoliang

xxyyll-1999 · 2020-09-17T14:55:24Z

[1] MacOS Catalina 10.15.5 , R 4.0.2, by source package --working

First download scCATCH_2.1.R-4.0.tar.gz. Then open r studio, click package and install as shown blow. Select the right install source from Package Archive File. Then browse scCATCH_2.1.R-4.0.tar.gz and install it.

>install.packages("~/Desktop/scCATCH_2.1.R-4.0.tar.gz", repos = NULL, type = "source")
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

[2] MacOS Catalina 10.15.5 , R 4.0.2, by devtools --working

> install.packages('devtools')
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors 

 1: 0-Cloud [https]
 2: Australia (Canberra) [https]
 3: Australia (Melbourne 1) [https]
 4: Australia (Melbourne 2) [https]
 5: Australia (Perth) [https]
 6: Austria [https]
 7: Belgium (Ghent) [https]
 8: Brazil (BA) [https]
 9: Brazil (PR) [https]
10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]
12: Brazil (SP 2) [https]
13: Bulgaria [https]
14: China (Beijing 1) [https]
15: China (Beijing 2) [https]
16: China (Hong Kong) [https]
17: China (Guangzhou) [https]
18: China (Lanzhou) [https]
19: China (Nanjing) [https]
20: China (Shanghai 1) [https]
21: Colombia (Cali) [https]
22: Costa Rica [https]
23: Denmark [https]
24: East Asia [https]
25: Ecuador (Cuenca) [https]
26: Ecuador (Quito) [https]
27: France (Lyon 1) [https]
28: France (Lyon 2) [https]
29: France (Marseille) [https]
30: Germany (Erlangen) [https]
31: Germany (Münster) [https]
32: Germany (Regensburg) [https]
33: Greece [https]
34: Hungary [https]
35: Iceland [https]
36: India [https]
37: Indonesia (Jakarta) [https]
38: Italy (Padua) [https]
39: Japan (Tokyo) [https]
40: Korea (Gyeongsan-si) [https]
41: Korea (Ulsan) [https]
42: Malaysia [https]
43: Mexico (Mexico City) [https]
44: Morocco [https]
45: Netherlands [https]
46: Norway [https]
47: Philippines [https]
48: Russia (Moscow) [https]
49: South Africa (Johannesburg) [https]
50: Spain (A Coruña) [https]
51: Sweden [https]
52: Switzerland [https]
53: Taiwan (Taipei) [https]
54: Turkey (Mersin) [https]
55: UK (Bristol) [https]
56: UK (London 1) [https]
57: USA (IA) [https]
58: USA (KS) [https]
59: USA (MI) [https]
60: USA (OH) [https]
61: USA (OR) [https]
62: USA (TN) [https]
63: USA (TX 1) [https]
64: Uruguay [https]
65: (other mirrors)

Selection: 14
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/el-capitan/contrib/3.6/devtools_2.3.1.tgz'
Content type 'application/octet-stream' length 338088 bytes (330 KB)
==================================================
downloaded 330 KB


The downloaded binary packages are in
	/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T//Rtmp0r6YJt/downloaded_packages
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
  unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
  dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/modules/R_X11.so
  Reason: image not found

> packageVersion('devtools')
[1] ‘2.3.1’

> devtools::install_github('ZJUFanLab/scCATCH')
Downloading GitHub repo ZJUFanLab/scCATCH@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: deldir    (0.1-28 -> 0.1-29) [CRAN]
5: backports (1.1.9  -> 1.1.10) [CRAN]
6: stringi   (1.4.6  -> 1.5.3 ) [CRAN]
7: lmtest    (0.9-37 -> 0.9-38) [CRAN]
8: cowplot   (1.0.0  -> 1.1.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
Installing 1 packages: Seurat
trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/Seurat_3.2.1.tgz'
Content type 'application/x-gzip' length 3540821 bytes (3.4 MB)
==================================================
downloaded 3.4 MB


The downloaded binary packages are in
	/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T//RtmpUquRmV/downloaded_packages
   checking for file ‘/private/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T/R✔  checking for file ‘/private/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T/RtmpUquRmV/remotes1c331725bce4/ZJUFanLab-scCATCH-05e9441/DESCRIPTION’ (521ms)
─  preparing ‘scCATCH’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘scCATCH_2.1.tar.gz’
   
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

lyuguol · 2020-09-18T05:47:28Z

[1] MacOS Catalina 10.15.5 , R 4.0.2, by source package --working

First download scCATCH_2.1.R-4.0.tar.gz. Then open r studio, click package and install as shown blow. Select the right install source from Package Archive File. Then browse scCATCH_2.1.R-4.0.tar.gz and install it.

>install.packages("~/Desktop/scCATCH_2.1.R-4.0.tar.gz", repos = NULL, type = "source")
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

[2] MacOS Catalina 10.15.5 , R 4.0.2, by devtools --working

> install.packages('devtools')
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors 

 1: 0-Cloud [https]
 2: Australia (Canberra) [https]
 3: Australia (Melbourne 1) [https]
 4: Australia (Melbourne 2) [https]
 5: Australia (Perth) [https]
 6: Austria [https]
 7: Belgium (Ghent) [https]
 8: Brazil (BA) [https]
 9: Brazil (PR) [https]
10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]
12: Brazil (SP 2) [https]
13: Bulgaria [https]
14: China (Beijing 1) [https]
15: China (Beijing 2) [https]
16: China (Hong Kong) [https]
17: China (Guangzhou) [https]
18: China (Lanzhou) [https]
19: China (Nanjing) [https]
20: China (Shanghai 1) [https]
21: Colombia (Cali) [https]
22: Costa Rica [https]
23: Denmark [https]
24: East Asia [https]
25: Ecuador (Cuenca) [https]
26: Ecuador (Quito) [https]
27: France (Lyon 1) [https]
28: France (Lyon 2) [https]
29: France (Marseille) [https]
30: Germany (Erlangen) [https]
31: Germany (Münster) [https]
32: Germany (Regensburg) [https]
33: Greece [https]
34: Hungary [https]
35: Iceland [https]
36: India [https]
37: Indonesia (Jakarta) [https]
38: Italy (Padua) [https]
39: Japan (Tokyo) [https]
40: Korea (Gyeongsan-si) [https]
41: Korea (Ulsan) [https]
42: Malaysia [https]
43: Mexico (Mexico City) [https]
44: Morocco [https]
45: Netherlands [https]
46: Norway [https]
47: Philippines [https]
48: Russia (Moscow) [https]
49: South Africa (Johannesburg) [https]
50: Spain (A Coruña) [https]
51: Sweden [https]
52: Switzerland [https]
53: Taiwan (Taipei) [https]
54: Turkey (Mersin) [https]
55: UK (Bristol) [https]
56: UK (London 1) [https]
57: USA (IA) [https]
58: USA (KS) [https]
59: USA (MI) [https]
60: USA (OH) [https]
61: USA (OR) [https]
62: USA (TN) [https]
63: USA (TX 1) [https]
64: Uruguay [https]
65: (other mirrors)

Selection: 14
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/el-capitan/contrib/3.6/devtools_2.3.1.tgz'
Content type 'application/octet-stream' length 338088 bytes (330 KB)
==================================================
downloaded 330 KB


The downloaded binary packages are in
	/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T//Rtmp0r6YJt/downloaded_packages
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
  unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
  dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/modules/R_X11.so
  Reason: image not found

> packageVersion('devtools')
[1] ‘2.3.1’

> devtools::install_github('ZJUFanLab/scCATCH')
Downloading GitHub repo ZJUFanLab/scCATCH@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: deldir    (0.1-28 -> 0.1-29) [CRAN]
5: backports (1.1.9  -> 1.1.10) [CRAN]
6: stringi   (1.4.6  -> 1.5.3 ) [CRAN]
7: lmtest    (0.9-37 -> 0.9-38) [CRAN]
8: cowplot   (1.0.0  -> 1.1.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
Installing 1 packages: Seurat
trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/Seurat_3.2.1.tgz'
Content type 'application/x-gzip' length 3540821 bytes (3.4 MB)
==================================================
downloaded 3.4 MB


The downloaded binary packages are in
	/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T//RtmpUquRmV/downloaded_packages
   checking for file ‘/private/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T/R✔  checking for file ‘/private/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T/RtmpUquRmV/remotes1c331725bce4/ZJUFanLab-scCATCH-05e9441/DESCRIPTION’ (521ms)
─  preparing ‘scCATCH’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘scCATCH_2.1.tar.gz’
   
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

Many thanks for all of the efforts to help me!

Unfortunately, the errors are going on...
Nonetheless, I noticed a difference in downloading and installing 'devtools' between you and me:

Yours: trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/el-capitan/contrib/3.6/devtools_2.3.1.tgz'
Mine: trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/contrib/4.0/devtools_2.3.1.tgz'

'3.6 VS. 4.0', would this difference lead to the continuous error of mine?

Thank you very much.

All the best,
Guoliang

xxyyll-1999 · 2020-09-18T13:17:11Z

Many thanks for all of the efforts to help me!

Unfortunately, the errors are going on...
Nonetheless, I noticed a difference in downloading and installing 'devtools' between you and me:

Yours: trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/el-capitan/contrib/3.6/devtools_2.3.1.tgz'
Mine: trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/contrib/4.0/devtools_2.3.1.tgz'

'3.6 VS. 4.0', would this difference lead to the continuous error of mine?

Thank you very much.

All the best,
Guoliang

Hello, Guoliang. I have tried to install 'devtools' from URL 4.0. It's still working. I don't think this difference lead to the error of yours. Maybe you can send me the accurate bug you've met in code.

> install.packages("devtools")
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors 

 1: 0-Cloud [https]
 2: Australia (Canberra) [https]
 3: Australia (Melbourne 1) [https]
 4: Australia (Melbourne 2) [https]
 5: Australia (Perth) [https]
 6: Austria [https]
 7: Belgium (Ghent) [https]
 8: Brazil (BA) [https]
 9: Brazil (PR) [https]
10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]
12: Brazil (SP 2) [https]
13: Bulgaria [https]
14: China (Beijing 1) [https]
15: China (Beijing 2) [https]
16: China (Hong Kong) [https]
17: China (Guangzhou) [https]
18: China (Lanzhou) [https]
19: China (Nanjing) [https]
20: China (Shanghai 1) [https]
21: Colombia (Cali) [https]
22: Costa Rica [https]
23: Denmark [https]
24: East Asia [https]
25: Ecuador (Cuenca) [https]
26: Ecuador (Quito) [https]
27: France (Lyon 1) [https]
28: France (Lyon 2) [https]
29: France (Marseille) [https]
30: Germany (Erlangen) [https]
31: Germany (Münster) [https]
32: Germany (Regensburg) [https]
33: Greece [https]
34: Hungary [https]
35: Iceland [https]
36: India [https]
37: Indonesia (Jakarta) [https]
38: Italy (Padua) [https]
39: Japan (Tokyo) [https]
40: Korea (Gyeongsan-si) [https]
41: Korea (Ulsan) [https]
42: Malaysia [https]
43: Mexico (Mexico City) [https]
44: Morocco [https]
45: Netherlands [https]
46: Norway [https]
47: Philippines [https]
48: Russia (Moscow) [https]
49: South Africa (Johannesburg) [https]
50: Spain (A Coruña) [https]
51: Sweden [https]
52: Switzerland [https]
53: Taiwan (Taipei) [https]
54: Turkey (Mersin) [https]
55: UK (Bristol) [https]
56: UK (London 1) [https]
57: USA (IA) [https]
58: USA (KS) [https]
59: USA (MI) [https]
60: USA (OH) [https]
61: USA (OR) [https]
62: USA (TN) [https]
63: USA (TX 1) [https]
64: Uruguay [https]
65: (other mirrors)

Selection: 15
also installing the dependencies ‘usethis’, ‘covr’

  There are binary versions available but the source versions are later:
         binary source needs_compilation
usethis   1.6.1  1.6.3             FALSE
devtools  2.3.1  2.3.2             FALSE

trying URL 'https://mirrors.bfsu.edu.cn/CRAN/bin/macosx/contrib/4.0/covr_3.5.1.tgz'
Content type 'application/octet-stream' length 289111 bytes (282 KB)
==================================================
downloaded 282 KB

The downloaded binary packages are in
	/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T//RtmplUmR25/downloaded_packages
installing the source packages ‘usethis’, ‘devtools’

trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/usethis_1.6.3.tar.gz'
Content type 'application/octet-stream' length 254833 bytes (248 KB)
==================================================
downloaded 248 KB

trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/devtools_2.3.2.tar.gz'
Content type 'application/octet-stream' length 373387 bytes (364 KB)
==================================================
downloaded 364 KB

* installing *source* package ‘usethis’ ...
** package ‘usethis’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (usethis)
* installing *source* package ‘devtools’ ...
** package ‘devtools’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (devtools)

The downloaded source packages are in
	‘/private/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T/RtmplUmR25/downloaded_packages’
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
  unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
  dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/modules/R_X11.so
  Reason: image not found
> devtools::install_github('ZJUFanLab/scCATCH')
Downloading GitHub repo ZJUFanLab/scCATCH@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: deldir    (0.1-28 -> 0.1-29) [CRAN]
5: backports (1.1.9  -> 1.1.10) [CRAN]
6: stringi   (1.4.6  -> 1.5.3 ) [CRAN]
7: globals   (0.12.5 -> 0.13.0) [CRAN]
8: lmtest    (0.9-37 -> 0.9-38) [CRAN]
9: cowplot   (1.0.0  -> 1.1.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

lyuguol · 2020-09-18T15:17:37Z

Many thanks for all of the efforts to help me!
Unfortunately, the errors are going on...
Nonetheless, I noticed a difference in downloading and installing 'devtools' between you and me:
Yours: trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/el-capitan/contrib/3.6/devtools_2.3.1.tgz'
Mine: trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/macosx/contrib/4.0/devtools_2.3.1.tgz'
'3.6 VS. 4.0', would this difference lead to the continuous error of mine?
Thank you very much.
All the best,
Guoliang

Hello, Guoliang. I have tried to install 'devtools' from URL 4.0. It's still working. I don't think this difference lead to the error of yours. Maybe you can send me the accurate bug you've met in code.

> install.packages("devtools")
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors 

 1: 0-Cloud [https]
 2: Australia (Canberra) [https]
 3: Australia (Melbourne 1) [https]
 4: Australia (Melbourne 2) [https]
 5: Australia (Perth) [https]
 6: Austria [https]
 7: Belgium (Ghent) [https]
 8: Brazil (BA) [https]
 9: Brazil (PR) [https]
10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]
12: Brazil (SP 2) [https]
13: Bulgaria [https]
14: China (Beijing 1) [https]
15: China (Beijing 2) [https]
16: China (Hong Kong) [https]
17: China (Guangzhou) [https]
18: China (Lanzhou) [https]
19: China (Nanjing) [https]
20: China (Shanghai 1) [https]
21: Colombia (Cali) [https]
22: Costa Rica [https]
23: Denmark [https]
24: East Asia [https]
25: Ecuador (Cuenca) [https]
26: Ecuador (Quito) [https]
27: France (Lyon 1) [https]
28: France (Lyon 2) [https]
29: France (Marseille) [https]
30: Germany (Erlangen) [https]
31: Germany (Münster) [https]
32: Germany (Regensburg) [https]
33: Greece [https]
34: Hungary [https]
35: Iceland [https]
36: India [https]
37: Indonesia (Jakarta) [https]
38: Italy (Padua) [https]
39: Japan (Tokyo) [https]
40: Korea (Gyeongsan-si) [https]
41: Korea (Ulsan) [https]
42: Malaysia [https]
43: Mexico (Mexico City) [https]
44: Morocco [https]
45: Netherlands [https]
46: Norway [https]
47: Philippines [https]
48: Russia (Moscow) [https]
49: South Africa (Johannesburg) [https]
50: Spain (A Coruña) [https]
51: Sweden [https]
52: Switzerland [https]
53: Taiwan (Taipei) [https]
54: Turkey (Mersin) [https]
55: UK (Bristol) [https]
56: UK (London 1) [https]
57: USA (IA) [https]
58: USA (KS) [https]
59: USA (MI) [https]
60: USA (OH) [https]
61: USA (OR) [https]
62: USA (TN) [https]
63: USA (TX 1) [https]
64: Uruguay [https]
65: (other mirrors)

Selection: 15
also installing the dependencies ‘usethis’, ‘covr’

  There are binary versions available but the source versions are later:
         binary source needs_compilation
usethis   1.6.1  1.6.3             FALSE
devtools  2.3.1  2.3.2             FALSE

trying URL 'https://mirrors.bfsu.edu.cn/CRAN/bin/macosx/contrib/4.0/covr_3.5.1.tgz'
Content type 'application/octet-stream' length 289111 bytes (282 KB)
==================================================
downloaded 282 KB

The downloaded binary packages are in
	/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T//RtmplUmR25/downloaded_packages
installing the source packages ‘usethis’, ‘devtools’

trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/usethis_1.6.3.tar.gz'
Content type 'application/octet-stream' length 254833 bytes (248 KB)
==================================================
downloaded 248 KB

trying URL 'https://mirrors.bfsu.edu.cn/CRAN/src/contrib/devtools_2.3.2.tar.gz'
Content type 'application/octet-stream' length 373387 bytes (364 KB)
==================================================
downloaded 364 KB

* installing *source* package ‘usethis’ ...
** package ‘usethis’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (usethis)
* installing *source* package ‘devtools’ ...
** package ‘devtools’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (devtools)

The downloaded source packages are in
	‘/private/var/folders/mh/mthv22w94hg6fwnqwzzywstc0000gn/T/RtmplUmR25/downloaded_packages’
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
  unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
  dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/modules/R_X11.so
  Reason: image not found
> devtools::install_github('ZJUFanLab/scCATCH')
Downloading GitHub repo ZJUFanLab/scCATCH@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: deldir    (0.1-28 -> 0.1-29) [CRAN]
5: backports (1.1.9  -> 1.1.10) [CRAN]
6: stringi   (1.4.6  -> 1.5.3 ) [CRAN]
7: globals   (0.12.5 -> 0.13.0) [CRAN]
8: lmtest    (0.9-37 -> 0.9-38) [CRAN]
9: cowplot   (1.0.0  -> 1.1.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
* installing *source* package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scCATCH)

Hello, the error is quoted as below.

devtools::install_github('ZJUFanLab/scCATCH')
Downloading GitHub repo ZJUFanLab/scCATCH@HEAD
✓ checking for file ‘/private/var/folders/w9/svz18j7x417ctrz4_gchqyhh0000gn/T/Rtmp7KD0tr/remotes47f674ad0f84/ZJUFanLab-scCATCH-05e9441/DESCRIPTION’ ...
─ preparing ‘scCATCH’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘scCATCH_2.1.tar.gz’

installing source package ‘scCATCH’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 18473 Done echo 'tools:::.install_packages()'
18474 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Error: Failed to install 'scCATCH' from GitHub:
(converted from warning) installation of package ‘/var/folders/w9/svz18j7x417ctrz4_gchqyhh0000gn/T//Rtmp7KD0tr/file47f6dd5def4/scCATCH_2.1.tar.gz’ had non-zero exit status

Many thanks!
Have a nice weekend!
All the best,
Guoliang

xxyyll-1999 · 2020-09-20T15:07:18Z

Hello, the error is quoted as below.

/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 18473 Done echo 'tools:::.install_packages()'
18474 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Error: Failed to install 'scCATCH' from GitHub:
(converted from warning) installation of package ‘/var/folders/w9/svz18j7x417ctrz4_gchqyhh0000gn/T//Rtmp7KD0tr/file47f6dd5def4/scCATCH_2.1.tar.gz’ had non-zero exit status

Many thanks!
Have a nice weekend!
All the best,
Guoliang

Hello, I'm very sorry that i don't know exactly why this error happened. But i suppose that maybe it's due to your R package. Maybe you can first try to install from source package manually. If you still meet the same error in byte-compile, it's possible that you've installed some packages which need compilation. Perhaps you can install r from brew on mac and then retry it.
Hope this helps!

lyuguol · 2020-10-26T17:09:16Z

Hello, the error is quoted as below.

/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 18473 Done echo 'tools:::.install_packages()'
18474 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Error: Failed to install 'scCATCH' from GitHub:
(converted from warning) installation of package ‘/var/folders/w9/svz18j7x417ctrz4_gchqyhh0000gn/T//Rtmp7KD0tr/file47f6dd5def4/scCATCH_2.1.tar.gz’ had non-zero exit status
Many thanks!
Have a nice weekend!
All the best,
Guoliang

Hello, I'm very sorry that i don't know exactly why this error happened. But i suppose that maybe it's due to your R package. Maybe you can first try to install from source package manually. If you still meet the same error in byte-compile, it's possible that you've installed some packages which need compilation. Perhaps you can install r from brew on mac and then retry it.
Hope this helps!

Dear Xin and the very helpful colleague,

Finally, I managed to install scCATCH (V2.1) by the following manipulations:

Clean install of Catalina
Install Xcode - open terminal, type: xcode-select --install
Install gfortran - https://github.com/fxcoudert/gfortran-for-macOS/releases
Install brew - open terminal, type: /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
In terminal, type: brew install boost
Start RStudio (4.0)
Download the source 'scCATCH-2.1.tar.gz'
In RStudio, choose: Tools >install.packages from archive; install.packages("~/Downloads/packages/scCATCH_2.1.R-4.0.tar.gz", repos = NULL, type = "source")

So, it turns out that all the failures of installation may be caused by the system settings of my own Mac.

Thank you all so much!! I am really grateful for your help!!

All the best,

Guoliang

multitalk closed this as completed Jun 13, 2020

multitalk reopened this Jun 18, 2020

multitalk closed this as completed Jun 20, 2020

multitalk added the good first issue Good for newcomers label Sep 18, 2020

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cannot install scCATCH #18

cannot install scCATCH #18

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multitalk commented Jun 18, 2020 •

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multitalk commented Jun 18, 2020

package ‘scCATCH_2.0.tar.gz’ is not available (for R version 3.6.3)

install devtools and install scCATCH

dmitroi commented Jun 18, 2020

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xxyyll-1999 commented Sep 18, 2020

lyuguol commented Sep 18, 2020

xxyyll-1999 commented Sep 20, 2020

lyuguol commented Oct 26, 2020

cannot install scCATCH #18

cannot install scCATCH #18

Comments

skim245 commented Jun 11, 2020

package ‘scCATCH_2.0.tar.gz’ is not available (for R version 3.6.3)

install devtools and install scCATCH

ZJUFanLab commented Jun 12, 2020

dmitroi commented Jun 17, 2020

multitalk commented Jun 18, 2020 • edited Loading

Time: 2020.06.18

[1] Windows 10, R 3.6.1, by source package --working

[2] Windows 10, R 3.6.1, by devtools --working

[3] Linux (Ubuntu 18.04), R 3.6.3, by source package --working

[4] Linux (Ubuntu 18.04), R 3.6.3, by devtools --working

multitalk commented Jun 18, 2020

package ‘scCATCH_2.0.tar.gz’ is not available (for R version 3.6.3)

install devtools and install scCATCH

You should add epos = NULL, type = "source" by installing scCATCH via source package! Ensure the right directory for scCATCH_2.0.tar.gz!

dmitroi commented Jun 18, 2020

multitalk commented Jun 19, 2020

[5] MacOS Mojave 10.14.6 (18G103), R 3.6.1, by source package --working

skim245 commented Jun 19, 2020

ankushs0128 commented Jul 8, 2020

dmitroi commented Jul 9, 2020

ankushs0128 commented Jul 9, 2020

multitalk commented Jul 10, 2020

lyuguol commented Sep 10, 2020

multitalk commented Sep 11, 2020

lyuguol commented Sep 11, 2020

lyuguol commented Sep 11, 2020

multitalk commented Sep 12, 2020

lyuguol commented Sep 12, 2020

xxyyll-1999 commented Sep 15, 2020

lyuguol commented Sep 15, 2020

xxyyll-1999 commented Sep 17, 2020

lyuguol commented Sep 18, 2020

xxyyll-1999 commented Sep 18, 2020

lyuguol commented Sep 18, 2020

xxyyll-1999 commented Sep 20, 2020

lyuguol commented Oct 26, 2020

multitalk commented Jun 18, 2020 •

edited

Loading

You should add `epos = NULL, type = "source"` by installing scCATCH via source package! Ensure the right directory for scCATCH_2.0.tar.gz!