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immunogenomics / singlecellmethods

Collection of useful methods for single cell analysis
GNU General Public License v3.0
14 stars 5 forks source link

Trouble with downloading the R Package #1

Open ghost opened 4 years ago

ghost commented 4 years ago

Hey,

I'm having trouble with downloading the R package. Whenever I run the code devtools::install_github('immunogenomics/singlecellmethods') I get the following error message:

Downloading GitHub repo immunogenomics/singlecellmethods@master
√  checking for file 'C:\Users\Anne Fleur\AppData\Local\Temp\RtmpaSLVZP\remotes235d476ee30ee\immunogenomics-singlecellmethods-6f3a00d/DESCRIPTION' (356ms)
-  preparing 'singlecellmethods':
√  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
-  building 'singlecellmethods_0.1.0.tar.gz'

Installing package into ‘C:/Users/Anne Fleur/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package 'singlecellmethods' ...
** using staged installation
** libs

*** arch - i386
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG  -I"C:/Users/Anne Fleur/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/Anne Fleur/Documents/R/win-library/3.6/RcppArmadillo/include"        -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG  -I"C:/Users/Anne Fleur/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/Anne Fleur/Documents/R/win-library/3.6/RcppArmadillo/include"        -O2 -Wall  -mtune=generic -c methods.cpp -o methods.o
methods.cpp: In function 'arma::mat merge_redundant_clusters(const mat&, float)':
methods.cpp:409:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < R_new.n_rows; i++) {
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG  -I"C:/Users/Anne Fleur/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/Anne Fleur/Documents/R/win-library/3.6/RcppArmadillo/include"        -O2 -Wall  -mtune=generic -c temp.cpp -o temp.o
temp.cpp: In function 'Rcpp::List soft_kmeans_weighted_cpp(arma::mat, arma::mat, const rowvec&, unsigned int, float, float)':
temp.cpp:39:11: warning: unused variable 's0' [-Wunused-variable]
     float s0, s1;
           ^
temp.cpp:39:15: warning: unused variable 's1' [-Wunused-variable]
     float s0, s1;
               ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o singlecellmethods.dll tmp.def RcppExports.o methods.o temp.o -LC:/PROGRA~1/R/R-36~1.2/bin/i386 -lR
methods.o:methods.cpp:(.text$_ZN4arma6op_dot10direct_dotIdEENS_14arma_real_onlyIT_E6resultEjPKS3_S7_[__ZN4arma6op_dot10direct_dotIdEENS_14arma_real_onlyIT_E6resultEjPKS3_S7_]+0x9d): undefined reference to `ddot_'
methods.o:methods.cpp:(.text$_ZN4arma16op_normalise_mat5applyIdEEvRNS_3MatIT_EERKS4_jj[__ZN4arma16op_normalise_mat5applyIdEEvRNS_3MatIT_EERKS4_jj]+0x5f6): undefined reference to `dnrm2_'
methods.o:methods.cpp:(.text$_ZN4arma16op_normalise_mat5applyIdEEvRNS_3MatIT_EERKS4_jj[__ZN4arma16op_normalise_mat5applyIdEEvRNS_3MatIT_EERKS4_jj]+0x6cc): undefined reference to `dasum_'
methods.o:methods.cpp:(.text$_ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_[__ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_]+0x17a): undefined reference to `dgemm_'
methods.o:methods.cpp:(.text$_ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_[__ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_]+0x358): undefined reference to `dgemv_'
methods.o:methods.cpp:(.text$_ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_[__ZN4arma10glue_times5applyIdLb1ELb0ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_]+0x499): undefined reference to `dsyrk_'
methods.o:methods.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE]+0x1a1): undefined reference to `dgemm_'
methods.o:methods.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE]+0x3c6): undefined reference to `dgemm_'
methods.o:methods.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE]+0x6fe): undefined reference to `dgemv_'
methods.o:methods.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE]+0x7d8): undefined reference to `dgemv_'
methods.o:methods.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE]+0x8ae): undefined reference to `dgemv_'
methods.o:methods.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE]+0x96d): undefined reference to `dsyrk_'
methods.o:methods.cpp:(.text$_ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE[__ZN4arma27glue_times_redirect2_helperILb0EE5applyINS_3MatIdEENS_2OpIS4_NS_9op_htransEEEEEvRNS3_INT_9elem_typeEEERKNS_4GlueIS8_T0_NS_10glue_timesEEE]+0xc67): undefined reference to `dsyrk_'
methods.o:methods.cpp:(.text$_ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3ColIdEES3_EEvRNS_3MatIT_EERKT3_RKT4_S5_[__ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3ColIdEES3_EEvRNS_3MatIT_EERKT3_RKT4_S5_]+0x18b): undefined reference to `dgemm_'
methods.o:methods.cpp:(.text$_ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3ColIdEES3_EEvRNS_3MatIT_EERKT3_RKT4_S5_[__ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3ColIdEES3_EEvRNS_3MatIT_EERKT3_RKT4_S5_]+0x28e): undefined reference to `dgemv_'
methods.o:methods.cpp:(.text$_ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3ColIdEES3_EEvRNS_3MatIT_EERKT3_RKT4_S5_[__ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3ColIdEES3_EEvRNS_3MatIT_EERKT3_RKT4_S5_]+0x3f4): undefined reference to `dsyrk_'
temp.o:temp.cpp:(.text+0x10d1): undefined reference to `ddot_'
temp.o:temp.cpp:(.text$_ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_[__ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_]+0x32e): undefined reference to `dgemm_'
temp.o:temp.cpp:(.text$_ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_[__ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_]+0x61f): undefined reference to `dsyrk_'
temp.o:temp.cpp:(.text$_ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_[__ZN4arma10glue_times5applyIdLb0ELb1ELb0ENS_3MatIdEES3_EEvRNS2_IT_EERKT3_RKT4_S4_]+0x7a2): undefined reference to `dgemv_'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'singlecellmethods'
* removing 'C:/Users/Anne Fleur/Documents/R/win-library/3.6/singlecellmethods'
Error: Failed to install 'singlecellmethods' from GitHub:
  (converted from warning) installation of package ‘C:/Users/ANNEFL~1/AppData/Local/Temp/RtmpaSLVZP/file235d461051e6/singlecellmethods_0.1.0.tar.gz’ had non-zero exit status

So I'm not sure if you want to help me, but I really appreciate it if you will.

Thanks in advance,

Anne Fleur

tenglongli commented 4 years ago

I have the same issue, please fix this if you can.

Thank you so much!

Best Tenglong Li

Yale73 commented 3 years ago

Run the sample issue, and will appreciate it if you can fix it.

Thanks, Yale

RenLinMed commented 2 years ago

I have the same issue, and will appreciate if you can six it

Thanks, Ren

miltargid commented 2 years ago

Hi,

Different issue for me; Will be a great if this is solved.

> devtools::install_github("immunogenomics/singlecellmethods")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo immunogenomics/singlecellmethods@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: tibble (3.1.2 -> 3.1.7) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
Error: Failed to install 'singlecellmethods' from GitHub:immunogenomics-singlecellmethods-ae5e58d/DESCRIPTION’ ...
  lazy-load database '/home/luna.kuleuven.be/u0119129/R/x86_64-pc-linux-gnu-library/3.6/cli/R/cli.rdb' is corrupt
In addition: Warning messages:
1: In (function ()  : restarting interrupted promise evaluation
2: In (function ()  : internal error -3 in R_decompress1
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SeuratDisk_0.0.0.9012       SingleR_1.1.7               SummarizedExperiment_1.16.1
 [4] DelayedArray_0.12.3         BiocParallel_1.20.1         matrixStats_0.59.0         
 [7] Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.1        
[10] IRanges_2.20.2              Seurat_3.2.2                S4Vectors_0.24.4           
[13] BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
  [1] AnnotationHub_2.18.0          BiocFileCache_1.10.2          plyr_1.8.6                   
  [4] igraph_1.2.7                  lazyeval_0.2.2                splines_3.6.3                
  [7] listenv_0.8.0                 usethis_2.1.0                 ggplot2_3.3.5                
 [10] digest_0.6.28                 htmltools_0.5.2               viridis_0.6.2                
 [13] fansi_1.0.3                   magrittr_2.0.3                memoise_2.0.0                
 [16] tensor_1.5                    cluster_2.1.2                 ROCR_1.0-11                  
 [19] remotes_2.4.1                 globals_0.14.0                prettyunits_1.1.1            
 [22] colorspace_2.0-2              blob_1.2.2                    rappdirs_0.3.3               
 [25] ggrepel_0.9.1                 dplyr_1.0.9                   callr_3.7.0                  
 [28] crayon_1.5.1                  RCurl_1.98-1.5                jsonlite_1.7.2               
 [31] spatstat_1.64-1               spatstat.data_2.1-0           survival_3.2-13              
 [34] zoo_1.8-9                     glue_1.6.2                    polyclip_1.10-0              
 [37] gtable_0.3.0                  zlibbioc_1.32.0               XVector_0.26.0               
 [40] leiden_0.3.8                  pkgbuild_1.2.0                future.apply_1.8.1           
 [43] abind_1.4-5                   scales_1.1.1                  pheatmap_1.0.12              
 [46] DBI_1.1.1                     miniUI_0.1.1.1                Rcpp_1.0.8.3                 
 [49] viridisLite_0.4.0             xtable_1.8-4                  reticulate_1.20              
 [52] bit_4.0.4                     rsvd_1.0.3                    htmlwidgets_1.5.4            
 [55] httr_1.4.2                    RColorBrewer_1.1-2            ellipsis_0.3.2               
 [58] ica_1.0-2                     pkgconfig_2.0.3               farver_2.1.0                 
 [61] uwot_0.1.10                   dbplyr_2.1.1                  deldir_1.0-5                 
 [64] utf8_1.2.2                    tidyselect_1.1.2              rlang_1.0.2                  
 [67] reshape2_1.4.4                later_1.3.0                   AnnotationDbi_1.48.0         
 [70] munsell_0.5.0                 BiocVersion_3.10.1            tools_3.6.3                  
 [73] cachem_1.0.6                  cli_3.3.0                     generics_0.1.2               
 [76] RSQLite_2.2.8                 ExperimentHub_1.12.0          devtools_2.4.2               
 [79] ggridges_0.5.3                stringr_1.4.0                 fastmap_1.1.0                
 [82] yaml_2.2.1                    goftest_1.2-3                 processx_3.5.2               
 [85] fs_1.5.0                      bit64_4.0.5                   fitdistrplus_1.1-5           
 [88] purrr_0.3.4                   RANN_2.6.1                    pbapply_1.5-0                
 [91] future_1.21.0                 nlme_3.1-152                  mime_0.12                    
 [94] rstudioapi_0.13               hdf5r_1.3.4                   compiler_3.6.3               
 [97] plotly_4.10.0                 curl_4.3.2                    png_0.1-7                    
[100] interactiveDisplayBase_1.24.0 testthat_3.1.0                spatstat.utils_2.2-0         
[103] tibble_3.1.2                  stringi_1.7.5                 ps_1.6.0                     
[106] desc_1.4.0                    lattice_0.20-44               Matrix_1.3-2                 
[109] vctrs_0.4.1                   pillar_1.7.0                  lifecycle_1.0.1              
[112] BiocManager_1.30.15           lmtest_0.9-38                 RcppAnnoy_0.0.19             
[115] BiocNeighbors_1.4.2           data.table_1.14.2             cowplot_1.1.1                
[118] bitops_1.0-7                  irlba_2.3.3                   httpuv_1.6.3                 
[121] patchwork_1.1.1               R6_2.5.1                      promises_1.2.0.1             
[124] KernSmooth_2.23-20            gridExtra_2.3                 parallelly_1.25.0            
[127] sessioninfo_1.1.1             codetools_0.2-18              pkgload_1.2.3                
[130] MASS_7.3-54                   assertthat_0.2.1              rprojroot_2.0.2              
[133] withr_2.4.2                   sctransform_0.3.2             GenomeInfoDbData_1.2.2       
[136] mgcv_1.8-36                   grid_3.6.3                    rpart_4.1-15                 
[139] tidyr_1.2.0                   DelayedMatrixStats_1.8.0      Rtsne_0.15                   
[142] shiny_1.7.1