Difficulty with install

[mosscoder]

Thank you for putting this package together. I am having trouble installing waddR.

BiocManager::install("waddR")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'waddR'
trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/waddR_1.2.0.tgz'
Content type 'application/x-gzip' length 197731 bytes (193 KB)
==================================================
downloaded 193 KB


The downloaded binary packages are in
	/var/folders/fw/ng_3gb5x467903z58bc8nwfm0000gn/T//Rtmp34Hw08/downloaded_packages

library(waddR)
Error: package or namespace load failed for ‘waddR’:
 .onLoad failed in loadNamespace() for 'waddR', details:
  call: gzfile(file)
  error: invalid 'description' argument


sessionInfo()
R version 4.0.0 (2020-04-24)
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] SummarizedExperiment_1.18.1 statmod_1.4.34              tinytex_0.23                tidyselect_1.1.0            xfun_0.14                  
 [6] purrr_0.3.4                 splines_4.0.0               lattice_0.20-41             vctrs_0.3.1                 generics_0.0.2             
[11] stats4_4.0.0                BiocFileCache_1.12.0        blob_1.2.1                  rlang_0.4.6                 nloptr_1.2.2.1             
[16] pillar_1.4.4                glue_1.4.1                  DBI_1.1.0                   BiocParallel_1.22.0         rappdirs_0.3.1             
[21] SingleCellExperiment_1.10.1 BiocGenerics_0.34.0         sp_1.4-2                    bit64_0.9-7                 dbplyr_1.4.4               
[26] matrixStats_0.56.0          GenomeInfoDbData_1.2.3      lifecycle_0.2.0             zlibbioc_1.34.0             rgeos_0.5-3                
[31] coda_0.19-3                 memoise_1.1.0               Biobase_2.48.0              IRanges_2.22.2              GenomeInfoDb_1.24.0        
[36] curl_4.3                    parallel_4.0.0              Rcpp_1.0.4.6                arm_1.11-1                  BiocManager_1.30.10        
[41] DelayedArray_0.14.0         S4Vectors_0.26.1            XVector_0.28.0              abind_1.4-5                 lme4_1.1-23                
[46] bit_1.1-15.2                digest_0.6.25               dplyr_1.0.0                 GenomicRanges_1.40.0        grid_4.0.0                 
[51] tools_4.0.0                 bitops_1.0-6                magrittr_1.5                RCurl_1.98-1.2              tibble_3.0.1               
[56] RSQLite_2.2.0               crayon_1.3.4                pkgconfig_2.0.3             MASS_7.3-51.6               ellipsis_0.3.1             
[61] Matrix_1.2-18               minqa_1.2.4                 assertthat_0.2.1            httr_1.4.1                  rstudioapi_0.11            
[66] boot_1.3-25                 R6_2.4.1                    nlme_3.1-148                compiler_4.0.0         

I have also attempted to install_github directly from this repository with the same result.

[mosscoder]

After exploring further on the Bioconductor website I tried the following without success:

BiocManager::install('waddR', type = "source", checkBuilt = TRUE)
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'waddR'
trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/waddR_1.2.0.tar.gz'
Content type 'application/x-gzip' length 69611 bytes (67 KB)
==================================================
downloaded 67 KB

* installing *source* package ‘waddR’ ...
** 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 wasserstein.cpp -o wasserstein.o
wasserstein.cpp:386:27: warning: unused variable 'out_it_end' [-Wunused-variable]
        vector<double>::iterator out_it_end = out.end();
                                 ^
wasserstein.cpp:501:4: warning: unused variable 'max_x' [-Wunused-variable]
        T max_x = x_sorted[n-1];
          ^
wasserstein.cpp:1168:8: note: in instantiation of function template specialization 'quantile<double>' requested here
        res = quantile(x, q, type);
              ^
2 warnings generated.
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 waddR.so RcppExports.o wasserstein.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-waddR/00new/waddR/libs
** R
** inst
** 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
Error: package or namespace load failed for ‘waddR’:
 .onLoad failed in loadNamespace() for 'waddR', details:
  call: gzfile(file)
  error: invalid 'description' argument
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/waddR’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/waddR’

The downloaded source packages are in
	‘/private/var/folders/fw/ng_3gb5x467903z58bc8nwfm0000gn/T/RtmpZBBcnt/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘waddR’ had non-zero exit status

[JulianFlesch]

Hey @mosscoder, thanks for using our package! I was unable to reproduce the errors you describe on this system:

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.9.0
LAPACK: /usr/lib/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] waddR_1.2.0

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.18.1 statmod_1.4.34             
 [3] tidyselect_1.1.0            purrr_0.3.4                
 [5] splines_4.0.0               lattice_0.20-41            
 [7] vctrs_0.3.1                 generics_0.0.2             
 [9] stats4_4.0.0                BiocFileCache_1.12.0       
[11] blob_1.2.1                  rlang_0.4.6                
[13] pillar_1.4.4                nloptr_1.2.2.1             
[15] glue_1.4.1                  DBI_1.1.0                  
[17] BiocParallel_1.22.0         rappdirs_0.3.1             
[19] SingleCellExperiment_1.10.1 BiocGenerics_0.34.0        
[21] bit64_0.9-7                 dbplyr_1.4.4               
[23] matrixStats_0.56.0          GenomeInfoDbData_1.2.3     
[25] lifecycle_0.2.0             zlibbioc_1.34.0            
[27] coda_0.19-3                 memoise_1.1.0              
[29] Biobase_2.48.0              IRanges_2.22.2             
[31] GenomeInfoDb_1.24.0         parallel_4.0.0             
[33] curl_4.3                    Rcpp_1.0.4.6               
[35] arm_1.11-1                  BiocManager_1.30.10        
[37] DelayedArray_0.14.0         S4Vectors_0.26.1           
[39] XVector_0.28.0              abind_1.4-5                
[41] bit_1.1-15.2                lme4_1.1-23                
[43] digest_0.6.25               dplyr_1.0.0                
[45] GenomicRanges_1.40.0        grid_4.0.0                 
[47] tools_4.0.0                 bitops_1.0-6               
[49] magrittr_1.5                RCurl_1.98-1.2             
[51] tibble_3.0.1                RSQLite_2.2.0              
[53] crayon_1.3.4                pkgconfig_2.0.3            
[55] ellipsis_0.3.1              MASS_7.3-51.6              
[57] Matrix_1.2-18               assertthat_0.2.1           
[59] minqa_1.2.4                 httr_1.4.1                 
[61] R6_2.4.1                    boot_1.3-25                
[63] nlme_3.1-147                compiler_4.0.0             

You could try installing right from our github with the command below. Please note, however, that the current github version is developmental and outputs are likely to differ from the Bioconductor versions (1.2.0 and 1.3.0).

devtools::install_github("https://github.com/goncalves-lab/waddR/")

Best,
Julian

[mosscoder]

I was able to get the wasserstein_metric() operational by cloning this repository and running Rcpp::sourceCpp('/path/to/waddR/src/wasserstein.cpp')

It is quite a bit faster than transport package, thank you!

Trying to go the official installation route with biocmanager or install_github, I still run into problems. Digging into the installation logs it reports that the description file author and maintainer are malformed. Hope this helps.

[JulianFlesch]

Digging into the installation logs it reports that the description file author and maintainer are malformed.

Could you post that log here, so I can investigate this further?

It is quite a bit faster than transport package, thank you!

Glad you find our package useful :)

[lijxug]

I have problem installing it too. The installation process strangely paused a long time right after the line "** testing if installed package can be loaded from temporary location".

Then the error log looks like this:

[1] "Downloading Reference Distribution: \n"
Warning: download failed
  web resource path: ‘https://github.com/goncalves-lab/waddR-data/blob/master/data/empcdf_ref.RData?raw=true’
  local file path: ‘~/.cache/BiocFileCache/13b8ac1a800fac_empcdf_ref.RData%3Fraw%3Dtrue’
  reason: Empty reply from server
Warning: bfcadd() failed; resource removed
  rid: BFC3
  fpath: ‘https://github.com/goncalves-lab/waddR-data/blob/master/data/empcdf_ref.RData?raw=true’
  reason: download failed
Error: package or namespace load failed for ‘waddR’:
 .onLoad failed in loadNamespace() for 'waddR', details:
  call: .util_download(x, rid[i], proxy, config, "bfcadd()", ...)
  error: bfcadd() failed; see warnings()
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/data1/jason/tools/softwares/R_library/4.0.5/waddR’

It seems that you have somehow included a data-loading command during the installation. Since the communication between my computer and github is not that well, the system finally popped out the timeout error.

[lijxug]

I think it might help if you deposit your demo data elsewhere..
It is really annoying when I cloned the repository to local through mirror and still have to download dataset from github.

[wangshun1121]

Similar problem after installation from Bioconductor. After library("waddR"), I got following error info:

Error: package or namespace load failed for ‘waddR’:
 .onLoad failed in loadNamespace() for 'waddR', details:
  call: UseMethod("filter_")
  error: no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
In addition: Warning message:
package ‘waddR’ was built under R version 3.6.3 

I tried R 3.6.2 on my MacBook, macOS Monterey 12.0.1