Hi Xiao-fan,
Thanks for your package, however, I still have some errors in installation.

ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [CIMLR.so] Error 1
ERROR: compilation failed for package ‘CIMLR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/CIMLR’
Error: Failed to install 'MOVICS' from GitHub:
  Failed to install 'CIMLR' from GitHub:
  (converted from warning) installation of package ‘/var/folders/h1/wph5l7kn6sq020007z1bq2d00000gn/T//RtmpQHMklX/filef791774317eb/CIMLR_1.0.0.tar.gz’ had non-zero exit status
> 

Dr. XF:
I found that I cannot install MOVICS in my RStudio workstation. I tried many times, but I faced the same error is :

object 'geom_table' is not exported by 'namespace:ggpmisc'

How to solve this problems? please , thank you !

> cmoic.brca <- getConsensusMOIC(moic.res.list = moic.res.list,
+                                fig.name      = "CONSENSUS HEATMAP",
+                                distance      = "euclidean",
+                                linkage       = "average")

Error: C stack usage  7969424 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969280 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969328 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969360 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969232 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969376 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969248 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969232 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969312 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969408 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969408 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969184 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969184 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969200 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969200 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969280 is too close to the limit
Graphics error: Plot rendering error
Error: C stack usage  7969296 is too close to the limit
Graphics error: Plot rendering error

my PC information

 sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/R/lib/libRlapack.so

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

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

other attached packages:
[1] dplyr_1.0.2         MOVICS_0.99.5       Biobase_2.50.0     
[4] BiocGenerics_0.36.0 kableExtra_1.3.1    knitr_1.30         

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1              CIMLR_1.0.0                
  [3] tableone_0.12.0             oompaData_3.1.1            
  [5] InterSIM_2.2.0              ggpmisc_0.3.6              
  [7] pkgmaker_0.32.2             tidyr_1.1.2                
  [9] ggplot2_3.3.2               bit64_4.0.5                
 [11] irlba_2.3.3                 DelayedArray_0.16.0        
 [13] data.table_1.13.2           RCurl_1.98-1.2             
 [15] doParallel_1.0.16           generics_0.1.0             
 [17] preprocessCore_1.52.0       cowplot_1.1.0              
 [19] RSQLite_2.2.1               shadowtext_0.0.7           
 [21] bit_4.0.4                   enrichplot_1.10.0          
 [23] webshot_0.5.2               xml2_1.3.2                 
 [25] SummarizedExperiment_1.20.0 assertthat_0.2.1           
 [27] viridis_0.5.1               xfun_0.19                  
 [29] hms_0.5.3                   evaluate_0.14              
 [31] caTools_1.18.0              readxl_1.3.1               
 [33] km.ci_0.5-2                 igraph_1.2.6               
 [35] DBI_1.1.0                   geneplotter_1.68.0         
 [37] stats4_4.0.2                purrr_0.3.4                
 [39] ellipsis_0.3.1              iClusterPlus_1.26.0        
 [41] ggpubr_0.4.0                backports_1.2.0            
 [43] permute_0.9-5               survey_4.0                 
 [45] geepack_1.3-1               annotate_1.68.0            
 [47] gridBase_0.4-7              RcppParallel_5.0.2         
 [49] MatrixGenerics_1.2.0        vctrs_0.3.4                
 [51] ggalluvial_0.12.2           Cairo_1.5-12.2             
 [53] maftools_2.6.0              jstable_1.0.0              
 [55] entropy_1.2.1               abind_1.4-5                
 [57] withr_2.3.0                 ggforce_0.3.2              
 [59] bdsmatrix_1.3-4             checkmate_2.0.0            
 [61] vegan_2.5-6                 mclust_5.4.6               
 [63] cluster_2.1.0               DOSE_3.16.0                
 [65] alluvial_0.1-2              CMScaller_0.99.2           
 [67] crayon_1.3.4                genefilter_1.72.0          
 [69] edgeR_3.32.0                pkgconfig_2.0.3            
 [71] tweenr_1.0.1                GenomeInfoDb_1.26.0        
 [73] nlme_3.1-148                rlang_0.4.8                
 [75] lifecycle_0.2.0             downloader_0.4             
 [77] registry_0.5-1              cellranger_1.1.0           
 [79] polyclip_1.10-0             GSVA_1.38.0                
 [81] matrixStats_0.57.0          PINSPlus_2.0.5             
 [83] pamr_1.56.1                 graph_1.68.0               
 [85] rngtools_1.5                Matrix_1.2-18              
 [87] KMsurv_0.1-5                carData_3.0-4              
 [89] heatmap.plus_1.3            boot_1.3-25                
 [91] zoo_1.8-8                   GlobalOptions_0.1.2        
 [93] png_0.1-7                   viridisLite_0.3.0          
 [95] rjson_0.2.20                oompaBase_3.2.9            
 [97] bitops_1.0-6                ConsensusClusterPlus_1.54.0
 [99] KernSmooth_2.23-17          blob_1.2.1                 
[101] shape_1.4.5                 stringr_1.4.0              
[103] qvalue_2.22.0               rstatix_0.6.0              
[105] S4Vectors_0.28.0            ggsignif_0.6.0             
[107] scales_1.1.1                memoise_1.1.0              
[109] graphite_1.36.0             GSEABase_1.52.0            
[111] magrittr_1.5                plyr_1.8.6                 
[113] gplots_3.1.0                zlibbioc_1.36.0            
[115] compiler_4.0.2              scatterpie_0.1.5           
[117] mogsa_1.24.0                RColorBrewer_1.1-2         
[119] lme4_1.1-25                 clue_0.3-57                
[121] DESeq2_1.30.0               XVector_0.30.0             
[123] patchwork_1.0.1             MASS_7.3-51.6              
[125] mgcv_1.8-31                 tidyselect_1.1.0           
[127] stringi_1.5.3               forcats_0.5.0              
[129] prettyGraphs_2.1.6          mitools_2.4                
[131] GOSemSim_2.16.1             locfit_1.5-9.4             
[133] ggrepel_0.8.2               survMisc_0.5.5             
[135] grid_4.0.2                  fastmatch_1.1-0            
[137] tools_4.0.2                 rio_0.5.16                 
[139] uuid_0.1-4                  circlize_0.4.11            
[141] rstudioapi_0.11             foreach_1.5.1              
[143] foreign_0.8-80              clusterRepro_0.9           
[145] coxme_2.2-16                gridExtra_2.3              
[147] farver_2.0.3                ggraph_2.0.3               
[149] digest_0.6.27               rvcheck_0.1.8              
[151] BiocManager_1.30.10         flexclust_1.4-0            
[153] FNN_1.1.3                   Rcpp_1.0.5                 
[155] GenomicRanges_1.42.0        car_3.0-10                 
[157] ClassDiscovery_3.3.12       broom_0.7.2                
[159] httr_1.4.2                  survminer_0.4.8            
[161] AnnotationDbi_1.52.0        ComplexHeatmap_2.7.1       
[163] colorspace_1.4-1            rvest_0.3.6                
[165] XML_3.99-0.5                IRanges_2.24.0             
[167] splines_4.0.2               statmod_1.4.35             
[169] graphlayouts_0.7.1          xtable_1.8-4               
[171] nloptr_1.2.2.2              SNFtool_2.3.0              
[173] tidygraph_1.2.0             corpcor_1.6.9              
[175] modeltools_0.2-23           ExPosition_2.8.23          
[177] R6_2.5.0                    ridge_2.7                  
[179] pillar_1.4.6                htmltools_0.5.0            
[181] NMF_0.23.0                  minqa_1.2.4                
[183] glue_1.4.2                  clusterProfiler_3.18.0     
[185] BiocParallel_1.24.1         class_7.3-17               
[187] codetools_0.2-16            aricode_1.0.0              
[189] fgsea_1.16.0                lattice_0.20-41            
[191] tibble_3.0.4                sva_3.38.0                 
[193] curl_4.3                    svd_0.5                    
[195] officer_0.3.15              gtools_3.8.2               
[197] IntNMF_1.2.0                zip_2.1.1                  
[199] GO.db_3.12.1                openxlsx_4.2.3             
[201] coca_1.1.0                  survival_3.1-12            
[203] limma_3.46.0                rmarkdown_2.5              
[205] munsell_0.5.0               DO.db_2.9                  
[207] GetoptLong_1.0.4            GenomeInfoDbData_1.2.4     
[209] iterators_1.0.13            labelled_2.7.0             
[211] impute_1.64.0               haven_2.3.1                
[213] reshape2_1.4.4              gtable_0.3.0               

However,

according to those links:
https://sr-c.github.io/2019/02/16/Error-C-stack-usage-is-too-close-to-the-limit/
LifeWorks/biojazz#9

(base) [zhou@localhost strelka2]$ ulimit -s 16384
(base) [zhou@localhost strelka2]$ R --slave -e 'Cstack_info()["size"]'
    size 
15938355 
(base) [zhou@localhost strelka2]$ ulimit -s 102400
bash: ulimit: stack size: cannot modify limit: Operation not permitted
(base) [zhou@localhost strelka2]$ ulimit -s 102400
bash: ulimit: stack size: cannot modify limit: Operation not permitted
(base) [zhou@localhost strelka2]$ ulimit -m unlimited
(base) [zhou@localhost strelka2]$ ulimit -s unlimited
bash: ulimit: stack size: cannot modify limit: Operation not permitted
(base) [zhou@localhost strelka2]$ conda activate strelka2

R function "getConsensusMOIC" gets consensus from different algorithms, so I have a question about how to select the best combination. I know the silhouette is the evaluation indicator. But in my test, the combination having 0.9 silhouette does not have a survival difference. So if I wanna compare the difference and select the best, which functions I can perform, or whether you have a try.

Hi Dr. Xiaofan,

MOVICS is fantastic. When installing this package, I am curious about how to install on R 3.6.0. Would you please offer some help?

Best,
Yingcheng

yau.pam.pred <- runPAM(train.expr = fpkm,
moic.res = cmoic.brca,
test.expr = brca.yau$mRNA.expr)
--all samples matched.
--a total of 8545 genes shared and used.
--log2 transformation done for training expression data.
--testing expression profile seems to have been standardised (z-score or log transformation), no more action will be performed.
Error in quantile.default(sd, offset.percent/100) :
'na.rm'如果设为FALSE的话不允许有遺漏值和NaN

I'm sure there's no NA.

Hi, I'm getting new errors when trying to install the package:

* installing *source* package ‘MOVICS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘get_fun_from_pkg’ is not exported by 'namespace:rvcheck'
Execution halted
ERROR: lazy loading failed for package ‘MOVICS’
* removing ‘/home/prvst/R/x86_64-pc-linux-gnu-library/4.0/MOVICS’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpKdm5a1/file284e6df30d7/MOVICS_0.99.17.tar.gz’ had non-zero exit status

I'm on a Linux system, using R 4.0.4

Hi, I tried to install MOVICS but could not do it because one of the dependencies is now deprecated and not available for R's latest version.

Error: Failed to install 'MOVICS' from GitHub: (converted from warning) package ‘SNFtool’ is not available for this version of R

The package SNFtool was removed from CRAN.

Hi,

I ran a problem with my copy number data in a position by sample matrix. Binary data of mutations are ok.

#Part of my copy number
[TAB] BRA08.T BRA10.T BRA13.T BRA15.T KAL0004.T
1_108276812_108276812 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108276813_108286811 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108286812_108286812 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108286813_108296810 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108296811_108296811 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
1_108296812_108306810 -0.000720281 -0.454077 0.0047503 0.00339646 0.255127
[TAB] KAL0013.T KAL0022.T KAL0043.T KAL0054.T KAL0072.T
1_108276812_108276812 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108276813_108286811 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108286812_108286812 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108286813_108296810 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108296811_108296811 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276
1_108296812_108306810 -0.425851 0.0213336 -0.200039 0.00249974 -0.103276

#Command
Hrpcaall <- list(omics1 = Hrpcassm_mat,
omics2 = Hrpcacna_data )

optk.hrpca <- getClustNum(data = Hrpcaall,
is.binary = c(T,F),
try.N.clust = 2:6,
fig.name = "CLUSTER NUMBER")

Error

90% complete
95% complete
100% complete
calculating Gap-statistics...
Error in svd(B, nv = 0) : infinite or missing values in 'x'
Calls: getClustNum ... -> msvd -> svd.sol -> nsmall.svd -> svd
Execution halted

I tried to transform data by adding +20 or round numbers to 3 digits. It still didn't work. I am not sure what causes the error. It seems not to be negative numbers. Or is it about column names? Your suggestion would be appreciated. I tried to debug myself for many days.

Thanks,
James

Thanks for such a wonderful package.
is there a conda version
and can it be installed in R3.6.3. I see your manual docs saying it needs R4.0.1

The windows exhibited:
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
错误: 'namespace:ggpmisc'没有出口'geom_table'这个对象
停止执行
The same error occurred after a successful installation.

Hi,
Thanks for your perfect package. I have problem in in compTMB() command. I have prepared my input data according to your sample file and instructions. But, it shows error:
#######################
--89 samples mismatched from current subtypes.
-Validating
--Removed 4190 duplicated variants
-Silent variants: 70969
-Summarizing
--Possible FLAGS among top ten genes:
TTN
SYNE1
MUC16
OBSCN
-Processing clinical data
--Missing clinical data
-Finished in 2.840s elapsed (2.660s cpu)
Error in .rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names':
##############################

Then I deleted entire rows with "-" values in nucleotide columns (the last three columns). Then it shows this error:
#############################
--89 samples mismatched from current subtypes.
-Validating
--Removed 3712 duplicated variants
-Silent variants: 65787
-Summarizing
--Possible FLAGS among top ten genes:
TTN
MUC16
SYNE1
OBSCN
-Processing clinical data
--Missing clinical data
-Finished in 2.840s elapsed (2.610s cpu)
Error in .rowNamesDF<-(x, value = value) :
missing values in 'row.names' are not allowed
##############################

Then I deleted all nucleotide which were non SNP and finally it works. But, unfortunately the results was not reasonable (not significant that I know it should be significant among 4 clusters).

I will be thankful if you help me in this regard.

HI
When I install MOVICS (devtools::install_github("xlucpu/MOVICS")), I get this problem Error: objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:BiocGenerics'
Execution halted

My biocgenerics version is 0.47.0
sessionInfo()

`R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so; LAPACK version 3.9.0

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

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

other attached packages:
[1] BiocGenerics_0.47.0

loaded via a namespace (and not attached):
[1] miniUI_0.1.1.1 compiler_4.3.0 BiocManager_1.30.22
[4] crayon_1.5.2 promises_1.2.0.1 Rcpp_1.0.10
[7] stringr_1.5.0 callr_3.7.3 later_1.3.1
[10] fastmap_1.1.1 mime_0.12 R6_2.5.1
[13] curl_5.0.0 htmlwidgets_1.6.2 desc_1.4.2
[16] profvis_0.3.8 rprojroot_2.0.3 shiny_1.7.4
[19] rlang_1.1.1 cachem_1.0.8 stringi_1.7.12
[22] httpuv_1.6.11 fs_1.6.2 pkgload_1.3.2
[25] memoise_2.0.1 cli_3.6.1 withr_2.5.0
[28] magrittr_2.0.3 ps_1.7.5 digest_0.6.31
[31] processx_3.8.1 rstudioapi_0.14 xtable_1.8-4
[34] remotes_2.4.2 devtools_2.4.5 lifecycle_1.0.3
[37] prettyunits_1.1.1 vctrs_0.6.2 glue_1.6.2
[40] urlchecker_1.0.1 sessioninfo_1.2.2 pkgbuild_1.4.0
[43] purrr_1.0.1 usethis_2.1.6 tools_4.3.0
[46] ellipsis_0.3.2 htmltools_0.5.5 `

Hope you could help me fix it.

install.packages("~/R/x86_64-pc-linux-gnu-library/MOVICS-master.tar.gz", repos = NULL, type = "source")
将程序包安装入‘/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3’
(因为‘lib’没有被指定)
ERROR: dependency ‘CIMLR’ is not available for package ‘MOVICS’

install.packages("/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/CIMLR-1.0.0_R.tar.gz", repos = NULL, type = "source")
将程序包安装入‘/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3’
(因为‘lib’没有被指定)

• installing source package ‘CIMLR’ ...
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu122.04) 11.4.0’
  using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu122.04) 11.4.0’
  g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-DdVjkr/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o
  g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-DdVjkr/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rtsne.cpp -o Rtsne.o
  gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-DdVjkr/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c projsplx_R.c -o projsplx_R.o
  g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-DdVjkr/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sptree.cpp -o sptree.o
  g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-DdVjkr/r-base-4.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tsne.cpp -o tsne.o
  tsne.cpp: In member function ‘void TSNE::computeSquaredEuclideanDistance(double*, int, int, double*)’:
  tsne.cpp:883:11: error: too few arguments to function ‘void dgemm_(const char*, const char*, const int*, const int*, const int*, const double*, const double*, const int*, const double*, const int*, const double*, double*, const int*, size_t, size_t)’
  883 | dgemm_("T", "N", &N, &N, &D, &a1, X, &D, X, &D, &a2, DD, &N);
  | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from /usr/share/R/include/R.h:78,
  from /home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp/r/headers.h:66,
  from /home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/RcppCommon.h:30,
  from /home/guozhuangjie/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:27,
  from tsne.cpp:39:
  /usr/share/R/include/R_ext/BLAS.h:207:10: note: declared here
  207 | F77_NAME(dgemm)(const char transa, const char transb, const int m,
  | ^~~~~
  /usr/share/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
  77 | # define F77_CALL(x) x ## _
  | ^
  /usr/share/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro ‘F77_NAME’
  207 | F77_NAME(dgemm)(const char transa, const char transb, const int m,
  | ^~~~~~~~
  tsne.cpp: In member function ‘bool TSNE::load_data(double, int, int, int, double, double*, int*)’:
  tsne.cpp:938:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  938 | fread(n, sizeof(int), 1, h); // number of datapoints
  | ~~~~~^~~~~~~~~~~~~~~~~~~~~~
  tsne.cpp:939:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  939 | fread(d, sizeof(int), 1, h); // original dimensionality
  | ~~~~~^~~~~~~~~~~~~~~~~~~~~~
  tsne.cpp:940:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  940 | fread(theta, sizeof(double), 1, h); // gradient accuracy
  | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  tsne.cpp:941:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  941 | fread(perplexity, sizeof(double), 1, h); // perplexity
  | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  tsne.cpp:942:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  942 | fread(no_dims, sizeof(int), 1, h); // output dimensionality
  | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
  tsne.cpp:945:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  945 | fread(*data, sizeof(double), n * d, h); // the data
  | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  tsne.cpp:946:27: warning: ignoring return value of ‘size_t fread(void, size_t, size_t, FILE)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  946 | if(!feof(h)) fread(rand_seed, sizeof(int), 1, h); // random seed
  | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  make: *** [/usr/lib/R/etc/Makeconf:200：tsne.o] 错误 1
  ERROR: compilation failed for package ‘CIMLR’

that is all .who can help me plz. thank you