Installation error: non-zero exit status for package 'Rvsearch'

[APepey]

I have installed the HaplotypR package to work on MiSeq data. When calling the function mergeAmpliconReads(), the following error appears:

Error in loadNamespace(x) : there is no package called ‘Rvsearch’

I tried to install Rvsearch with both devtools and remotes packages, but the following errors appear:

with devtools:

> devtools::install_github("lerch-a/Rvsearch")
Downloading GitHub repo lerch-a/Rvsearch@HEAD
"C:\Users\apepey\AppData\Local\Programs\Git\cmd\git.exe" clone --depth 1 --no-hardlinks --recurse-submodules git://github.com/torognes/vsearch.git C:\Users\apepey\AppData\Local\Temp\RtmpMTkQJL\remotes3c74a9b4dca/lerch-a-Rvsearch-28d10d6/src/vsearch
√  checking for file 'C:\Users\apepey\AppData\Local\Temp\RtmpMTkQJL\remotes3c74a9b4dca\lerch-a-Rvsearch-28d10d6/DESCRIPTION' (980ms)
-  preparing 'Rvsearch': (482ms)
√  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 (714ms)
-  building 'Rvsearch_0.99.1.tar.gz'
   
* installing *source* package 'Rvsearch' ...
** using staged installation
** libs

*** arch - i386
no DLL was created
ERROR: compilation failed for package 'Rvsearch'
* removing 'C:/Users/apepey/Documents/R/R-4.1.2/library/Rvsearch'
Warning in i.p(...) :
  installation of package ‘C:/Users/apepey/AppData/Local/Temp/RtmpMTkQJL/file3c74166346d1/Rvsearch_0.99.1.tar.gz’ had non-zero exit status

with remotes:

> remotes::install_github("lerch-a/Rvsearch")
  Downloading GitHub repo lerch-a/Rvsearch@HEAD
Warning in untar2(tarfile, files, list, exdir) :
  skipping pax global extended headers
Warning in untar2(tarfile, files, list, exdir) :
  skipping pax global extended headers
"C:\Users\apepey\AppData\Local\Programs\Git\cmd\git.exe" clone --depth 1 --no-hardlinks --recurse-submodules git://github.com/torognes/vsearch.git C:\Users\apepey\AppData\Local\Temp\RtmpMTkQJL\remotes3c7461c5b16/lerch-a-Rvsearch-28d10d6/src/vsearch
√  checking for file 'C:\Users\apepey\AppData\Local\Temp\RtmpMTkQJL\remotes3c7461c5b16\lerch-a-Rvsearch-28d10d6/DESCRIPTION' (862ms)
-  preparing 'Rvsearch': (439ms)
√  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 (590ms)
-  building 'Rvsearch_0.99.1.tar.gz'
   
* installing *source* package 'Rvsearch' ...
** using staged installation
** libs

*** arch - i386
no DLL was created
ERROR: compilation failed for package 'Rvsearch'
* removing 'C:/Users/apepey/Documents/R/R-4.1.2/library/Rvsearch'
Warning in i.p(...) :
  installation of package ‘C:/Users/apepey/AppData/Local/Temp/RtmpMTkQJL/file3c7439195336/Rvsearch_0.99.1.tar.gz’ had non-zero exit status

I have tried to add 'dependencies = TRUE' and 'type = "source"', as seen for similar issues on github and stackoverflow, but the error messages are the same respectively for the devtools and the remotes packages.

Is this way of installing incorrect? I could not find a solution so far on any platform. What could I try next to install successfully Rvsearch?

Here is my session info:

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.6.0        Biobase_2.54.0              pkgload_1.2.4               RcppParallel_5.1.5          assertthat_0.2.1           
 [6] stats4_4.1.2                latticeExtra_0.6-29         GenomeInfoDbData_1.2.7      Rsamtools_2.10.0            remotes_2.4.2              
[11] sessioninfo_1.2.2           pillar_1.6.4                lattice_0.20-45             glue_1.6.0                  digest_0.6.29              
[16] GenomicRanges_1.46.1        RColorBrewer_1.1-2          XVector_0.34.0              colorspace_2.0-2            cowplot_1.1.1              
[21] htmltools_0.5.2             Matrix_1.4-0                plyr_1.8.6                  pkgconfig_2.0.3             devtools_2.4.3             
[26] ShortRead_1.52.0            zlibbioc_1.40.0             purrr_0.3.4                 scales_1.1.1                processx_3.5.2             
[31] jpeg_0.1-9                  BiocParallel_1.28.3         tibble_3.1.6                generics_0.1.1              IRanges_2.28.0             
[36] ggplot2_3.3.5               usethis_2.1.5               ellipsis_0.3.2              cachem_1.0.6                withr_2.4.3                
[41] SummarizedExperiment_1.24.0 BiocGenerics_0.40.0         cli_3.1.0                   magrittr_2.0.1              crayon_1.4.2               
[46] memoise_2.0.1               ps_1.6.0                    dada2_1.21.0                fs_1.5.2                    fansi_0.5.0                
[51] hwriter_1.3.2               pkgbuild_1.3.1              tools_4.1.2                 prettyunits_1.1.1           lifecycle_1.0.1            
[56] matrixStats_0.61.0          stringr_1.4.0               S4Vectors_0.32.3            munsell_0.5.0               DelayedArray_0.20.0        
[61] callr_3.7.0                 Biostrings_2.62.0           compiler_4.1.2              GenomeInfoDb_1.30.0         rlang_0.4.12               
[66] grid_4.1.2                  RCurl_1.98-1.5              rstudioapi_0.13             bitops_1.0-7                testthat_3.1.1             
[71] gtable_0.3.0                curl_4.3.2                  DBI_1.1.2                   reshape2_1.4.4              R6_2.5.1                   
[76] GenomicAlignments_1.30.0    knitr_1.37                  dplyr_1.0.7                 fastmap_1.1.0               utf8_1.2.2                 
[81] rprojroot_2.0.2             desc_1.4.0                  stringi_1.7.6               parallel_4.1.2              Rcpp_1.0.7                 
[86] vctrs_0.3.8                 png_0.1-7                   dbplyr_2.1.1                tidyselect_1.1.1            xfun_0.29

[lerch-a]

It is very challenging to compile Rvsearch on a Windows computer.
Go to the release page of Rvsearch (https://github.com/lerch-a/Rvsearch/releases) and download the precompiled R package.
Install the package with
install.packages("PathToPackage/Rvsearch_0.99.1-win_R-v3.6.zip", repos = NULL)
Let me know if this does not work for you.

[APepey]

Thank you so much for your help!

I was getting the following issue:

>install.packages("C:/Users/apepey/Downloads/Rvsearch_0.99.1-win_R-v4.1.zip", repos = NULL)
Error in install.packages : type == "both" cannot be used with 'repos = NULL'

I used type = "win.binary" and it successfully installed the package:

>install.packages("C:/Users/apepey/Downloads/Rvsearch_0.99.1-win_R-v4.1.zip", type = "win.binary", repos = NULL)
package ‘Rvsearch’ successfully unpacked and MD5 sums checked