Install problem

Hi, I have a problem with my Ubuntu system after trying to install GSFA with docker.
Actually, It doesn't work, (devtool install also didn't work)
My computer cannot reboot anymore with a broken GNOME display manager.
How can I fix this problem?
Please let me know if you have any ideas!

Hi, I'm sorry to hear what happened to your computer system. But I don't think installing GSFA will cause that much damage though... My random guess is that installing GSFA in Ubuntu may require additional C++ compiler toolkits. Please post the detailed error message when devtool install failed so we may be able to spot related issues.

Hi, Lifan,

I also had an issue when installing GFSA package. The error is below:

Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
checking for file ‘/tmp/RtmpJqXqOr/remotesc32347216eed/xinhe-lab-GSFA-8e7cf03✔ checking for file ‘/tmp/RtmpJqXqOr/remotesc32347216eed/xinhe-lab-GSFA-8e7cf03/DESCRIPTION’ (1.2s)
─ preparing ‘GSFA’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to build vignettes
E creating vignettes (47m 55.8s)
--- re-building ‘gsfa_intro.Rmd’ using rmarkdown
Using Factor as id variables
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

   filter, lag

The following objects are masked from 'package:base':

   intersect, setdiff, setequal, union

Loading required package: ggplot2
Using gene as id variables
Using gene as id variables
Warning: Using size for a discrete variable is not advised.
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "gsfa_intro", and the latter is "Applying GSFA in a simulated dataset". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
Warning in file(con, "r") :
cannot open file 'gsfa_intro.Rmd': No such file or directory
Error: tangling vignette 'gsfa_intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘gsfa_intro.Rmd’

SUMMARY: processing the following file failed:
‘gsfa_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'GSFA' from GitHub:
! System command 'R' failed

Do you have some suggestions. Thanks!

Best,

Thanks for your feedback. We are still figuring out what happened.

Meanwhile, you may first try installing GSFA with build_vignettes set to false. If installation finish without errors, you can download and run the Rmd file stored here: https://github.com/xinhe-lab/GSFA/blob/master/vignettes/gsfa_intro.Rmd and see what the problem is.

Dear Lifan,

I tried installing GSFA with devtools::install_github("xinhe-lab/GSFA", build_vignettes = TRUE) as suggested on my windows computer. However, I ran into the following error:

> devtools::install_github("xinhe-lab/GSFA", build_vignettes = TRUE)
Registered S3 method overwritten by 'htmlwidgets':
  method           from         
  print.htmlwidget tools:rstudio
Downloading GitHub repo xinhe-lab/GSFA@HEAD
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file 'C:\Users\Do\AppData\Local\Temp\RtmpCmgIJ7\remotes731c75827fa\xinhe-lab-GSFA-8e7cf03/DESCRIPTION'
─  preparing 'GSFA': (414ms)
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to build vignettes
         -----------------------------------
─  installing *source* package 'GSFA' ...
   ** using staged installation
   ** libs
   using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
   g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-44~1.0/include" -DNDEBUG  -I'C:/Users/Do/Documents/R/win-library/4.2/Rcpp/include' -I'C:/Users/Do/Documents/R/win-library/4.2/RcppArmadillo/include'   -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -fdiagnostics-color=always -c GSFA_gibbs_inference.cpp -o GSFA_gibbs_inference.o
   g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-44~1.0/include" -DNDEBUG  -I'C:/Users/Do/Documents/R/win-library/4.2/Rcpp/include' -I'C:/Users/Do/Documents/R/win-library/4.2/RcppArmadillo/include'   -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -fdiagnostics-color=always -c GSFA_gibbs_two_groups.cpp -o GSFA_gibbs_two_groups.o
   g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-44~1.0/include" -DNDEBUG  -I'C:/Users/Do/Documents/R/win-library/4.2/Rcpp/include' -I'C:/Users/Lan Do/Documents/R/win-library/4.2/RcppArmadillo/include'   -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
   g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-44~1.0/include" -DNDEBUG  -I'C:/Users/Do/Documents/R/win-library/4.2/Rcpp/include' -I'C:/Users/Do/Documents/R/win-library/4.2/RcppArmadillo/include'   -I"C:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -fdiagnostics-color=always -c sampling_functions.cpp -o sampling_functions.o
   sampling_functions.cpp:n function ' move_seed_rbinom()
   sampling_functions.cpp:16:10:warning: used variable 'tmp-Wunused-variable]
      16 |   double tmp:rbinom(1, 0.5);
         |          ^~~
   sampling_functions.cpp:n function ' initialize_given_Z(int, arma::mat, arma::mat&, arma::mat&, arma::mat&)
   sampling_functions.cpp:333:8:warning: mparison of integer expressions of different signedness: 'intand 'const arma::uword{aka 'const unsigned int-Wsign-compare
     333 |   if(K != Z.n_cols
         |      ~~^~~~~~~~~~~
   g++ -std=gnu++17 -shared -s -static-libgcc -o GSFA.dll tmp.def GSFA_gibbs_inference.o GSFA_gibbs_two_groups.o RcppExports.o sampling_functions.o -LC:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/RBuildTools/4.4/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-44~1.0/bin/x64 -lR
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0x2a60): undefined reference to `ddot_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0x4395): undefined reference to `ddot_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0x6753): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0x6e9f): undefined reference to `ddot_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0x7018): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0x764b): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0x79ab): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0xdbcc): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0xdd73): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0xe5bb): more undefined references to `dgemv_' follow
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0x1086f): undefined reference to `dtrtri_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0x4d1): undefined reference to `dgemm_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0x5d0): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0x6b5): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0xc27): undefined reference to `dgemm_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0xd2c): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0xf76): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0x1144): undefined reference to `dsyrk_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0x1a19): undefined reference to `dgemm_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0x1b27): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0x1c05): undefined reference to `dgemv_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text.hot+0x2024): undefined reference to `dsyrk_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6op_dot10direct_dotIdEENS_14arma_real_onlyIT_E6resultEjPKS3_S7_[_ZN4arma6op_dot10direct_dotIdEENS_14arma_real_onlyIT_E6resultEjPKS3_S7_]+0xa4): undefined reference to `ddot_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib6svd_dcIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_[_ZN4arma6auxlib6svd_dcIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_]+0x26b): undefined reference to `dgesdd_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib6svd_dcIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_[_ZN4arma6auxlib6svd_dcIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_]+0x4c7): undefined reference to `dgesdd_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib3svdIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_[_ZN4arma6auxlib3svdIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_]+0x23f): undefined reference to `dgesvd_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib3svdIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_[_ZN4arma6auxlib3svdIdEEbRNS_3MatIT_EERNS_3ColIS3_EES5_S5_]+0x4a8): undefined reference to `dgesvd_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib16chol_band_commonIdEEbRNS_3MatIT_EEjj[_ZN4arma6auxlib16chol_band_commonIdEEbRNS_3MatIT_EEjj]+0x18b): undefined reference to `dpbtrf_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib9inv_sympdIdEEbRNS_3MatIT_EERb[_ZN4arma6auxlib9inv_sympdIdEEbRNS_3MatIT_EERb]+0x79): undefined reference to `dpotrf_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib9inv_sympdIdEEbRNS_3MatIT_EERb[_ZN4arma6auxlib9inv_sympdIdEEbRNS_3MatIT_EERb]+0xa4): undefined reference to `dpotri_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib10eig_sym_dcIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7_[_ZN4arma6auxlib10eig_sym_dcIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7_]+0x21e): undefined reference to `dsyevd_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib10eig_sym_dcIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7_[_ZN4arma6auxlib10eig_sym_dcIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7_]+0x355): undefined reference to `dsyevd_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib7eig_symIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7_[_ZN4arma6auxlib7eig_symIdEEbRNS_3ColIT_EERNS_3MatIS3_EERKS7_]+0x1b4): undefined reference to `dsyev_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma7op_chol12apply_directINS_3MatIdEEEEbRNS2_INT_9elem_typeEEERKNS_4BaseIS5_S4_EEj[_ZN4arma7op_chol12apply_directINS_3MatIdEEEEbRNS2_INT_9elem_typeEEERKNS_4BaseIS5_S4_EEj]+0x2c1): undefined reference to `dpotrf_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma11glue_mvnrnd13apply_noaliasIdEEbRNS_3MatIT_EERKS4_S7_j[_ZN4arma11glue_mvnrnd13apply_noaliasIdEEbRNS_3MatIT_EERKS4_S7_j]+0x3d9): undefined reference to `dnrm2_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma11glue_mvnrnd13apply_noaliasIdEEbRNS_3MatIT_EERKS4_S7_j[_ZN4arma11glue_mvnrnd13apply_noaliasIdEEbRNS_3MatIT_EERKS4_S7_j]+0xa50): undefined reference to `dnrm2_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib3invIdEEbRNS_3MatIT_EE[_ZN4arma6auxlib3invIdEEbRNS_3MatIT_EE]+0x96): undefined reference to `dgetrf_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib3invIdEEbRNS_3MatIT_EE[_ZN4arma6auxlib3invIdEEbRNS_3MatIT_EE]+0xf9): undefined reference to `dgetri_'
   C:\RBuildTools\4.4\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text$_ZN4arma6auxlib3invIdEEbRNS_3MatIT_EE[_ZN4arma6auxlib3invIdEEbRNS_3MatIT_EE]+0x1ec): undefined reference to `dgetri_'
   collect2.exe: error: ld returned 1 exit status
   keine DLL erzeugt
   ERROR: compilation failed for package 'GSFA'
─  removing 'C:/Users/DO~1/AppData/Local/Temp/RtmpU3Yka3/Rinst2dd8a3502a/GSFA'
         -----------------------------------
   ERROR: package installation failed
Fehler: Failed to install 'GSFA' from GitHub:
  ! System command 'Rcmd.exe' failed

I have tried various potential solutions suggested by other users with this type of errors, but none have worked. The only hint I have left is, that it could have something to do with the Windows C compiler having troubles to process the C code part.

Do you have any idea?

> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=German_Germany.utf8  LC_CTYPE=German_Germany.utf8    LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C                    LC_TIME=German_Germany.utf8    

time zone: Europe/Berlin
tzcode source: internal

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Install problem #3

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LifanLiang commented on Nov 9, 2023

hanhuajun40 commented on May 2, 2024

LifanLiang commented on May 6, 2024

THLDo commented on Jun 30, 2024

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