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immunogenomics / presto

Fast Wilcoxon and auROC
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ERROR: installing package indices failed #5

Open I-Hao opened 4 years ago

I-Hao commented 4 years ago

Hi,

I just upgraded R to 4.0.0 and try to install this package, but there is an error I couldn't resolve:

installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-presto/00new/presto/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
sh: line 1: 22981 Killed: 9               R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/kd/yfy7p1qj79sbw5v77fjcvrc80000gn/T//RtmpUKfnVU/file59b032f1b353'
ERROR: installing package indices failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/presto’
Error: Failed to install 'presto' from GitHub:
  (converted from warning) installation of package ‘/var/folders/kd/yfy7p1qj79sbw5v77fjcvrc80000gn/T//Rtmp1tG6e7/file584627334eb4/presto_1.0.0.tar.gz’ had non-zero exit status

Could you help me? Thank you in advance!

I-Hao

slowkow commented 4 years ago

  1. Could you please share the full command that you executed as well as the full output that includes the error?

  2. Also, could I please ask if you might consider sharing the output of this command?

sessionInfo()
  1. Have you tried closing R, starting a fresh R, and then running:
devtools::install_github("immunogenomics/presto")

Thanks! This might help us to help you.

I-Hao commented 4 years ago

Hi,

answer to question 1 & 3 The command I used is:

devtools::install_github("immunogenomics/presto")

output:

Downloading GitHub repo immunogenomics/presto@master
Skipping 1 packages not available: DESeq2
✓  checking for file ‘/private/var/folders/kd/yfy7p1qj79sbw5v77fjcvrc80000gn/T/Rtmpd8Dg6u/remotes6b4368ee436e/immunogenomics-presto-7f63f96/DESCRIPTION’ ...
─  preparing ‘presto’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  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 ‘presto_1.0.0.tar.gz’

* installing *source* package ‘presto’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fast_wilcox.cpp -o fast_wilcox.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o presto.so RcppExports.o fast_wilcox.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-presto/00new/presto/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
sh: line 1: 27806 Killed: 9               R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/kd/yfy7p1qj79sbw5v77fjcvrc80000gn/T//RtmpDb2Mv8/file6c8911c5f8b0'
ERROR: installing package indices failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/presto’
Error: Failed to install 'presto' from GitHub:
  (converted from warning) installation of package ‘/var/folders/kd/yfy7p1qj79sbw5v77fjcvrc80000gn/T//Rtmpd8Dg6u/file6b43728d2093/presto_1.0.0.tar.gz’ had non-zero exit status

Answer for question 2:

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4

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

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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   base     

other attached packages:
 [1] DESeq2_1.28.0               SummarizedExperiment_1.18.1 DelayedArray_0.14.0        
 [4] matrixStats_0.56.0          Biobase_2.48.0              GenomicRanges_1.40.0       
 [7] GenomeInfoDb_1.24.0         IRanges_2.22.1              S4Vectors_0.26.0           
[10] BiocGenerics_0.34.0        

loaded via a namespace (and not attached):
 [1] pkgload_1.0.2          bit64_0.9-7            splines_4.0.0          assertthat_0.2.1      
 [5] BiocManager_1.30.10    blob_1.2.1             GenomeInfoDbData_1.2.3 remotes_2.1.1         
 [9] sessioninfo_1.1.1      pillar_1.4.4           RSQLite_2.2.0          backports_1.1.6       
[13] lattice_0.20-41        glue_1.4.0             digest_0.6.25          RColorBrewer_1.1-2    
[17] XVector_0.28.0         colorspace_1.4-1       Matrix_1.2-18          XML_3.99-0.3          
[21] pkgconfig_2.0.3        devtools_2.3.0         genefilter_1.70.0      zlibbioc_1.34.0       
[25] purrr_0.3.4            xtable_1.8-4           scales_1.1.0           processx_3.4.2        
[29] BiocParallel_1.22.0    tibble_3.0.1           annotate_1.66.0        ggplot2_3.3.0         
[33] usethis_1.6.1          ellipsis_0.3.0         withr_2.2.0            cli_2.0.2             
[37] survival_3.1-12        magrittr_1.5           crayon_1.3.4           memoise_1.1.0         
[41] ps_1.3.2               fs_1.4.1               fansi_0.4.1            pkgbuild_1.0.7        
[45] tools_4.0.0            prettyunits_1.1.1      lifecycle_0.2.0        locfit_1.5-9.4        
[49] munsell_0.5.0          AnnotationDbi_1.50.0   callr_3.4.3            compiler_4.0.0        
[53] rlang_0.4.6            grid_4.0.0             RCurl_1.98-1.2         rstudioapi_0.11       
[57] bitops_1.0-6           testthat_2.3.2         gtable_0.3.0           DBI_1.1.0             
[61] curl_4.3               R6_2.4.1               dplyr_0.8.5            bit_1.1-15.2          
[65] rprojroot_1.3-2        desc_1.2.0             Rcpp_1.0.4.6           vctrs_0.2.4           
[69] geneplotter_1.66.0     tidyselect_1.0.0

Thanks! I-Hao

slowkow commented 4 years ago

This line is curious:

sh: line 1: 27806 Killed: 9

Why would the shell script be killed with SIGKILL?

I found related issues in other repos:

Googling around leads to some questions:

  1. How much RAM is on your machine? Are you running this command in a virtual machine with insufficient RAM?

  2. Is there any chance that you might have software that killed the process? For example, do you use an antivirus or similar software that might kill processes running on your machine?

By the way, please use the formatting features of GitHub Markdown to make your posts easier to read.

slowkow commented 4 years ago

You might also consider re-installing XCode to see if that helps.

I-Hao commented 4 years ago

Hi,

  1. I'm running this command with my desktop which has 64G of RAM.
  2. I don't have such kind of software I think.
  3. I re-installed the Xcode and the package, but I got the same error:
> install_github('immunogenomics/presto')
Downloading GitHub repo immunogenomics/presto@master
Skipping 1 packages not available: DESeq2
Skipping 1 packages ahead of CRAN: data.table
✓  checking for file ‘/private/var/folders/kd/yfy7p1qj79sbw5v77fjcvrc80000gn/T/RtmpzDtAxE/remotes81267203ece2/immunogenomics-presto-7f63f96/DESCRIPTION’ ...
─  preparing ‘presto’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  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 ‘presto_1.0.0.tar.gz’

* installing *source* package ‘presto’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fast_wilcox.cpp -o fast_wilcox.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o presto.so RcppExports.o fast_wilcox.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-presto/00new/presto/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
sh: line 1: 33197 Killed: 9               R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/kd/yfy7p1qj79sbw5v77fjcvrc80000gn/T//RtmpdeOSXA/file8198373cd30a'
ERROR: installing package indices failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/presto’
Error: Failed to install 'presto' from GitHub:
  (converted from warning) installation of package ‘/var/folders/kd/yfy7p1qj79sbw5v77fjcvrc80000gn/T//RtmpzDtAxE/file81266d48856e/presto_1.0.0.tar.gz’ had non-zero exit status
I-Hao commented 4 years ago

Hi,

I found this might be a R version-specific problem, I can install the package in R/3.6.3. Thank you!

ilonliu commented 4 years ago

@slowkow @I-Hao I experience the same installation problem after upgrading to R/4.0.0, when running:

devtools::install_github("immunogenomics/presto")
Downloading GitHub repo immunogenomics/presto@master
Skipping 1 packages not available: DESeq2
✓  checking for file ‘/private/var/folders/gw/fht9stfj07xgnyfjcd5lj3g1zjt397/T/RtmpyE34O3/remotes1268d14f65302/immunogenomics-presto-7f63f96/DESCRIPTION’ ...
─  preparing ‘presto’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  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 ‘presto_1.0.0.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'

* installing *source* package ‘presto’ ...
** using staged installation
** libs
/usr/local/clang4/bin/clang++ -fopenmp -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
/usr/local/clang4/bin/clang++ -fopenmp -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fast_wilcox.cpp -o fast_wilcox.o
/usr/local/clang4/bin/clang++ -fopenmp -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o presto.so RcppExports.o fast_wilcox.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-presto/00new/presto/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
sh: line 1: 92009 Killed: 9               R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/gw/fht9stfj07xgnyfjcd5lj3g1zjt397/T//RtmpRnxcOY/file167544e72a946'
ERROR: installing package indices failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/presto’
installation of package ‘/var/folders/gw/fht9stfj07xgnyfjcd5lj3g1zjt397/T//RtmpyE34O3/file1268d112078bc/presto_1.0.0.tar.gz’ had non-zero exit status

A similar issue seems to be occurring for the harmony package, where users report installation problems with devtools::install("immunogenomics/harmony") after upgrading to R/4.0.0:

Any help is much appreciated, thank you!

slowkow commented 4 years ago

Thank you for pointing out this issue. I might need to install R 4.0.0 on my own Mac in order to start figuring this out.

aayushraman commented 4 years ago

Hello @slowkow

I hope you are doing well. I am having a similar problem installing presto on my mac laptop. I am using R version 3.6.3. I used the following command devtools::install_github("immunogenomics/presto") and here is the error message that I am getting: 

installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-presto/00new/presto/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 83302 Done                    echo 'tools:::.install_packages()'
     83303 Killed: 9               | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
Error: Failed to install 'presto' from GitHub:
  (converted from warning) installation of package ‘/var/folders/38/9pc122kx0f31yf6pxg8n_nymd16sh4/T//RtmpZF0sjY/file1450d5d3003ad/presto_1.0.0.tar.gz’ had non-zero exit status

Here is the sessionInfo: 

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (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/3.6/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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DESeq2_1.26.0               SummarizedExperiment_1.16.1 DelayedArray_0.12.3        
 [4] BiocParallel_1.20.1         matrixStats_0.56.0          Biobase_2.46.0             
 [7] GenomicRanges_1.38.0        GenomeInfoDb_1.22.1         IRanges_2.20.2             
[10] S4Vectors_0.24.4            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] fs_1.4.1               bitops_1.0-6           usethis_1.6.1         
 [4] devtools_2.3.0         bit64_0.9-7            RColorBrewer_1.1-2    
 [7] rprojroot_1.3-2        tools_3.6.3            backports_1.1.8       
[10] R6_2.4.1               rpart_4.1-15           Hmisc_4.4-0           
[13] DBI_1.1.0              colorspace_1.4-1       nnet_7.3-14           
[16] withr_2.2.0            tidyselect_1.1.0       gridExtra_2.3         
[19] prettyunits_1.1.1      processx_3.4.2         curl_4.3              
[22] bit_1.1-15.2           compiler_3.6.3         cli_2.0.2             
[25] htmlTable_2.0.0        desc_1.2.0             scales_1.1.1          
[28] checkmate_2.0.0        genefilter_1.68.0      callr_3.4.3           
[31] stringr_1.4.0          digest_0.6.25          foreign_0.8-75        
[34] XVector_0.26.0         base64enc_0.1-3        jpeg_0.1-8.1          
[37] pkgconfig_2.0.3        htmltools_0.5.0        sessioninfo_1.1.1     
[40] htmlwidgets_1.5.1      rlang_0.4.6            rstudioapi_0.11       
[43] RSQLite_2.2.0          generics_0.0.2         acepack_1.4.1         
[46] dplyr_1.0.0            RCurl_1.98-1.2         magrittr_1.5          
[49] GenomeInfoDbData_1.2.2 Formula_1.2-3          Matrix_1.2-18         
[52] Rcpp_1.0.4.6           munsell_0.5.0          fansi_0.4.1           
[55] lifecycle_0.2.0        stringi_1.4.6          zlibbioc_1.32.0       
[58] pkgbuild_1.0.8         grid_3.6.3             blob_1.2.1            
[61] crayon_1.3.4           lattice_0.20-41        splines_3.6.3         
[64] annotate_1.64.0        locfit_1.5-9.4         knitr_1.29            
[67] ps_1.3.3               pillar_1.4.4           geneplotter_1.64.0    
[70] pkgload_1.1.0          XML_3.99-0.3           glue_1.4.1            
[73] latticeExtra_0.6-29    data.table_1.12.8      remotes_2.1.1         
[76] png_0.1-7              vctrs_0.3.1            testthat_2.3.2        
[79] gtable_0.3.0           purrr_0.3.4            assertthat_0.2.1      
[82] ggplot2_3.3.2          xfun_0.15              xtable_1.8-4          
[85] survival_3.2-3         tibble_3.0.1           AnnotationDbi_1.48.0  
[88] memoise_1.1.0          cluster_2.1.0          ellipsis_0.3.1

Some of the comments based on the above discussions:

  1. I have installed the most recent version of XCode.
  2. I have about 16 GB of RAM. I am not running this command in a virtual machine.
  3. I am not running any software that would kill the process or installation of this package. I tried installing other packages and I didn't face any problems. For example, I was able to install Harmony.

Any advice/help would be helpful. Thanks a lot!

-Ar

GhobrialMoheb commented 3 years ago

Having similar issues

slowkow commented 3 years ago

We had a discussion about this issue in this thread: https://github.com/immunogenomics/harmony/issues/90#issuecomment-657058816

In the end, multiple users reported that they solved the problem by following the instructions here:

http://thecoatlessprofessor.com/programming/r/uninstalling-the-r-development-toolchain-on-macos/

This post in this link explains that you may need to remove the gfortran and clang programs that you previously installed.

@Mohebg1234 Please consider sharing information with us. What did you try? What errors did you see? The more you share, the easier it will be for others to help. Have you followed the instructions in the link above?

hugokitano commented 3 years ago

Any update on this problem? Having it right now.

slowkow commented 3 years ago

@hugokitano Could I please ask if you could try these steps? Please share your commands and output so we can try to help.

git clone git@github.com:immunogenomics/presto.git
cd presto
rm -f data/*
R CMD INSTALL .

This is inspired by this comment: https://github.com/immunogenomics/presto/issues/11#issuecomment-685094666

hugokitano commented 3 years ago

Hi Kamil, I'm running into an error with the clone. I'm about 90% sure I have my credentials set up since I've used git on the command line before and I followed the instructions for doing so again.

Cloning into 'presto'...
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
slowkow commented 3 years ago

Try using this instead: git clone https://github.com/immunogenomics/presto.git

If you'd like to resolve the Permission denied error, see the GitHub documentation: https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/error-permission-denied-publickey

hugokitano commented 3 years ago

I think this works. Thank you!

Hugo

Sanaz01 commented 2 months ago

Hi, here is the output of my sessionInfo()

> sessionInfo()
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
 [1] sctransform_0.4.1  lubridate_1.9.3    forcats_1.0.0      stringr_1.5.1      dplyr_1.1.4       
 [6] purrr_1.0.2        readr_2.1.5        tidyr_1.3.1        tibble_3.2.1       ggplot2_3.5.0     
[11] tidyverse_2.0.0    Seurat_5.0.3       SeuratObject_5.0.1 sp_2.1-3          

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          rstudioapi_0.16.0           jsonlite_1.8.8             
  [4] magrittr_2.0.3              spatstat.utils_3.0-4        farver_2.1.1               
  [7] zlibbioc_1.48.2             vctrs_0.6.5                 ROCR_1.0-11                
 [10] DelayedMatrixStats_1.24.0   spatstat.explore_3.2-7      RCurl_1.98-1.14            
 [13] S4Arrays_1.2.1              htmltools_0.5.8.1           SparseArray_1.2.4          
 [16] parallelly_1.37.1           KernSmooth_2.23-22          htmlwidgets_1.6.4          
 [19] ica_1.0-3                   plyr_1.8.9                  plotly_4.10.4              
 [22] zoo_1.8-12                  igraph_2.0.3                mime_0.12                  
 [25] lifecycle_1.0.4             pkgconfig_2.0.3             Matrix_1.6-5               
 [28] R6_2.5.1                    fastmap_1.1.1               GenomeInfoDbData_1.2.11    
 [31] MatrixGenerics_1.14.0       fitdistrplus_1.1-11         future_1.33.2              
 [34] shiny_1.8.1.1               digest_0.6.35               colorspace_2.1-0           
 [37] patchwork_1.2.0             S4Vectors_0.40.2            tensor_1.5                 
 [40] RSpectra_0.16-1             irlba_2.3.5.1               GenomicRanges_1.54.1       
 [43] labeling_0.4.3              progressr_0.14.0            fansi_1.0.6                
 [46] spatstat.sparse_3.0-3       timechange_0.3.0            httr_1.4.7                 
 [49] polyclip_1.10-6             abind_1.4-5                 compiler_4.3.3             
 [52] bit64_4.0.5                 withr_3.0.0                 fastDummies_1.7.3          
 [55] MASS_7.3-60.0.1             DelayedArray_0.28.0         tools_4.3.3                
 [58] lmtest_0.9-40               httpuv_1.6.15               future.apply_1.11.2        
 [61] goftest_1.2-3               glmGamPoi_1.14.3            glue_1.7.0                 
 [64] nlme_3.1-164                promises_1.3.0              grid_4.3.3                 
 [67] Rtsne_0.17                  cluster_2.1.6               reshape2_1.4.4             
 [70] generics_0.1.3              hdf5r_1.3.10                gtable_0.3.4               
 [73] spatstat.data_3.0-4         tzdb_0.4.0                  data.table_1.15.4          
 [76] hms_1.1.3                   XVector_0.42.0              utf8_1.2.4                 
 [79] BiocGenerics_0.48.1         spatstat.geom_3.2-9         RcppAnnoy_0.0.22           
 [82] ggrepel_0.9.5               RANN_2.6.1                  pillar_1.9.0               
 [85] spam_2.10-0                 RcppHNSW_0.6.0              later_1.3.2                
 [88] splines_4.3.3               lattice_0.22-5              survival_3.5-8             
 [91] bit_4.0.5                   deldir_2.0-4                tidyselect_1.2.1           
 [94] miniUI_0.1.1.1              pbapply_1.7-2               gridExtra_2.3              
 [97] IRanges_2.36.0              SummarizedExperiment_1.32.0 scattermore_1.2            
[100] stats4_4.3.3                Biobase_2.62.0              matrixStats_1.3.0          
[103] stringi_1.8.3               lazyeval_0.2.2              codetools_0.2-19           
[106] BiocManager_1.30.22         cli_3.6.2                   uwot_0.2.1                 
[109] xtable_1.8-4                reticulate_1.36.0           munsell_0.5.1              
[112] GenomeInfoDb_1.38.8         Rcpp_1.0.12                 globals_0.16.3             
[115] spatstat.random_3.2-3       png_0.1-8                   parallel_4.3.3             
[118] dotCall64_1.1-1             sparseMatrixStats_1.14.0    bitops_1.0-7               
[121] listenv_0.9.1               viridisLite_0.4.2           scales_1.3.0               
[124] ggridges_0.5.6              crayon_1.5.2                leiden_0.4.3.1             
[127] rlang_1.1.3                 cowplot_1.1.3

and here is the error:

> devtools::install_github('immunogenomics/presto')
Downloading GitHub repo immunogenomics/presto@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  cannot open URL 'https://api.github.com/repos/immunogenomics/presto/tarball/HEAD'

Thanks for your help in advance!

slowkow commented 2 months ago

@Sanaz01

It seems your utils::download.file() is not happy with the URL. I don't know why, but it might be something to do with your network or system.

You might try downloading the source by yourself and then installing it with R CMD INSTALL like this (copied from one of my previous comments above):

git clone git@github.com:immunogenomics/presto.git
cd presto
rm -f data/*
R CMD INSTALL .

Or you can try to troubleshoot your error message by trying if this works for you:

source_url <- "https://api.github.com/repos/immunogenomics/presto/tarball/HEAD"
capabilities("libcurl")
# libcurl 
#    TRUE 
utils::download.file(source_url, destfile="presto.tar.gz", method="libcurl")
Sanaz01 commented 2 months ago

@slowkow I was able to resolve the issue. It appears that when I restart R session and switch my network from work to home, it appears to be installed and run smoothly. Thanks a lot for your help!