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tvpham / iq

An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
BSD 3-Clause "New" or "Revised" License
19 stars 9 forks source link

Eigen-related issue during installation #3

Closed Arthfael closed 2 years ago

Arthfael commented 2 years ago

Hi,

I tried to install today but got the following issue:

> devtools::install_github("tvpham/iq")
Downloading GitHub repo tvpham/iq@HEAD
√  checking for file 'C:\Users\MyUser\AppData\Local\Temp\2\Rtmpw9XlJo\remotes31f858ba7ff0\tvpham-iq-6e443ea/DESCRIPTION' ...
-  preparing 'iq':
√  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 'iq_1.9.1.tar.gz'

Installing package into ‘C:/Users/MyUser/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
* installing *source* package 'iq' ...
** using staged installation
** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-41~1.0/include" -DNDEBUG -I.      -fopenmp -DEIGEN_DONT_PARALLELIZE   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c iq.cpp -o iq.o
iq.cpp:32:10: fatal error: Eigen/Dense: No such file or directory
 #include <Eigen/Dense>
          ^~~~~~~~~~~~~
compilation terminated.
make: *** [C:/PROGRA~1/R/R-41~1.0/etc/i386/Makeconf:245: iq.o] Error 1
ERROR: compilation failed for package 'iq'
* removing 'C:/Users/MyUser/Documents/R/win-library/4.1/iq'
Warning message:
In i.p(...) :
  installation of package ‘C:/Users/MyUser/AppData/Local/Temp/2/Rtmpw9XlJo/file31f843ae32c0/iq_1.9.1.tar.gz’ had non-zero exit status

Any idea what could be the cause? Here is my sessionInfo:

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] aRmel_2.0.1.15       DEP_1.14.0           MSnbase_2.18.0       ProtGenerics_1.24.0  mzR_2.26.1          
 [6] Rcpp_1.0.8           qvalue_2.24.0        sva_3.40.0           BiocParallel_1.26.2  genefilter_1.74.1   
[11] mgcv_1.8-35          nlme_3.1-152         limma_3.48.3         UniProt.ws_2.32.0    RCurl_1.98-1.6      
[16] RSQLite_2.2.9        GO.db_3.13.0         AnnotationDbi_1.54.1 IRanges_2.26.0       S4Vectors_0.30.2    
[21] Biobase_2.52.0       BiocGenerics_0.38.0  biomaRt_2.48.3       fs_1.5.2             tibble_3.1.6        
[26] magrittr_2.0.2       htmlwidgets_1.5.4    svDialogs_1.0.3      gridExtra_2.3        VennDiagram_1.7.1   
[31] futile.logger_1.4.3  statmod_1.4.36       pdftools_3.0.1       xml2_1.3.3           Peptides_2.4.4      
[36] plotly_4.10.0        openxlsx_4.2.5.9000  coin_1.4-2           survival_3.2-11      snow_0.4-4          
[41] minpack.lm_1.2-1     modeest_2.4.0        rstudioapi_0.13      ggrepel_0.9.1        rgl_0.108.3         
[46] reshape2_1.4.4       reshape_0.8.8        gtools_3.9.2         ggpubr_0.4.0         ggplot2_3.3.5       
[51] gplots_3.1.1         stringr_1.4.0       

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3              tidyr_1.2.0                 bit64_4.0.5                 knitr_1.37                 
  [5] multcomp_1.4-18             DelayedArray_0.18.0         data.table_1.14.2           rpart_4.1-15               
  [9] KEGGREST_1.32.0             doParallel_1.0.17           generics_0.1.2              preprocessCore_1.54.0      
 [13] callr_3.7.0                 lambda.r_1.2.4              TH.data_1.1-0               usethis_2.1.5              
 [17] timeSeries_3062.100         bit_4.0.4                   tzdb_0.2.0                  httpuv_1.6.5               
 [21] SummarizedExperiment_1.22.0 assertthat_0.2.1            xfun_0.29                   fBasics_3042.89.1          
 [25] hms_1.1.1                   promises_1.2.0.1            fansi_1.0.2                 progress_1.2.2             
 [29] caTools_1.18.2              dbplyr_2.1.1                DBI_1.1.2                   purrr_0.3.4                
 [33] ellipsis_0.3.2              dplyr_1.0.8                 backports_1.4.1             annotate_1.70.0            
 [37] libcoin_1.0-9               MatrixGenerics_1.4.3        vctrs_0.3.8                 remotes_2.4.2              
 [41] imputeLCMD_2.0              Cairo_1.5-14                abind_1.4-5                 cachem_1.0.6               
 [45] withr_2.4.3                 prettyunits_1.1.1           cluster_2.1.2               lazyeval_0.2.2             
 [49] crayon_1.5.0                labeling_0.4.2              edgeR_3.34.1                pkgconfig_2.0.3            
 [53] GenomeInfoDb_1.28.4         pkgload_1.2.4               devtools_2.4.3              rlang_1.0.1                
 [57] spatial_7.3-14              lifecycle_1.0.1             sandwich_3.0-1              filelock_1.0.2             
 [61] affyio_1.62.0               BiocFileCache_2.0.0         rprojroot_2.0.2             matrixStats_0.61.0         
 [65] Matrix_1.3-3                carData_3.0-5               zoo_1.8-9                   processx_3.5.2             
 [69] GlobalOptions_0.1.2         png_0.1-7                   viridisLite_0.4.0           rjson_0.2.21               
 [73] stabledist_0.7-1            bitops_1.0-7                shinydashboard_0.7.2        KernSmooth_2.23-20         
 [77] Biostrings_2.60.2           blob_1.2.2                  shape_1.4.6                 qpdf_1.1                   
 [81] readr_2.1.2                 NbClust_3.0                 rstatix_0.7.0               tmvtnorm_1.4-10            
 [85] ggsignif_0.6.3              scales_1.1.1                memoise_2.0.1               plyr_1.8.6                 
 [89] zlibbioc_1.38.0             RColorBrewer_1.1-2          pcaMethods_1.84.0           clue_0.3-60                
 [93] cli_3.2.0                   affy_1.70.0                 XVector_0.32.0              ps_1.6.0                   
 [97] formatR_1.11                MASS_7.3-54                 tidyselect_1.1.1            vsn_3.60.0                 
[101] rawrr_1.0.3                 stringi_1.7.6               askpass_1.1                 locfit_1.5-9.4             
[105] norm_1.0-9.5                MALDIquant_1.21             tools_4.1.0                 circlize_0.4.14            
[109] MsCoreUtils_1.4.0           foreach_1.5.2               statip_0.2.3                farver_2.1.0               
[113] mzID_1.30.0                 stable_1.1.4                digest_0.6.29               BiocManager_1.30.16        
[117] shiny_1.7.1                 GenomicRanges_1.44.0        car_3.0-12                  broom_0.7.12               
[121] later_1.3.0                 ncdf4_1.19                  httr_1.4.2                  ComplexHeatmap_2.8.0       
[125] colorspace_2.0-2            brio_1.1.3                  XML_3.99-0.8                splines_4.1.0              
[129] rmutil_1.1.8                gmm_1.6-6                   sessioninfo_1.2.2           xtable_1.8-4               
[133] jsonlite_1.7.3              futile.options_1.0.1        timeDate_3043.102           testthat_3.1.2             
[137] modeltools_0.2-23           R6_2.5.1                    mime_0.12                   pillar_1.7.0               
[141] htmltools_0.5.2             svGUI_1.0.1                 glue_1.6.1                  fastmap_1.1.0              
[145] DT_0.20                     codetools_0.2-18            pkgbuild_1.3.1              mvtnorm_1.1-3              
[149] utf8_1.2.2                  lattice_0.20-44             curl_4.3.2                  zip_2.2.0                  
[153] desc_1.4.0                  munsell_0.5.0               GetoptLong_1.0.5            GenomeInfoDbData_1.2.6     
[157] iterators_1.0.14            impute_1.66.0               gtable_0.3.0
Arthfael commented 2 years ago

Here is a discussion which may be related: https://github.com/kaskr/adcomp/issues/230 Installing RcppEigen did not solve my issue, but I wasn't able to make sense of the alternative solution proposed at the end of the discussion.

tvpham commented 2 years ago

Hi,

No we did not use RccpEigen, but the Eigen header files directly. You can try to install R package from source

https://github.com/tvpham/iq/archive/refs/tags/v1.9.tar.gz

I will also upload the Eigen files for completeness.

Cheers, Thang

tvpham commented 2 years ago

devtools::install_github("tvpham/iq") should work.

Compilation warnings from Eigen can be ignored.

Arthfael commented 2 years ago

Wow, that was a lot of compilation warnings. But it seems to work, thanks!

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devtools::install_github("tvpham/iq") should work.

Compilation warnings from Eigen can be ignored.

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tvpham commented 2 years ago

iq is back on CRAN.