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nuno-agostinho / psichomics

Interactive R package to quantify, analyse and visualise alternative splicing
http://nuno-agostinho.github.io/psichomics/
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psichomics() Error in xj[i] : invalid subscript type 'list' #435

Closed Ni-Ar closed 2 years ago

Ni-Ar commented 2 years ago

Hi Nuno,

I'm finding myself in a pickle here:

BiocManager::install("psichomics")
library("psichomics")
Loading required package: shiny
Loading required package: shinyBS
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

psichomics 1.16.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics

psichomics()

Returns the error

Error in xj[i] : invalid subscript type 'list'

My version details.

> utils::sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

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     

other attached packages:
[1] psichomics_1.16.0 shinyBS_0.61      shiny_1.7.1      

loaded via a namespace (and not attached):
  [1] backports_1.3.0               Hmisc_4.6-0                   AnnotationHub_2.22.1         
  [4] fastmatch_1.1-3               BiocFileCache_1.14.0          plyr_1.8.6                   
  [7] igraph_1.2.7                  splines_4.0.4                 BiocParallel_1.24.1          
 [10] GenomeInfoDb_1.26.7           fastICA_1.2-3                 ggplot2_3.3.5                
 [13] digest_0.6.28                 foreach_1.5.1                 highcharter_0.8.2            
 [16] htmltools_0.5.2               fansi_0.5.0                   checkmate_2.0.0              
 [19] magrittr_2.0.1                memoise_2.0.0                 BSgenome_1.58.0              
 [22] cluster_2.1.2                 tzdb_0.2.0                    limma_3.46.0                 
 [25] Biostrings_2.58.0             readr_2.0.2                   matrixStats_0.61.0           
 [28] R.utils_2.11.0                xts_0.12.1                    askpass_1.1                  
 [31] pairsD3_0.1.0                 prettyunits_1.1.1             jpeg_0.1-9                   
 [34] colorspace_2.0-2              blob_1.2.2                    rappdirs_0.3.3               
 [37] ggrepel_0.9.1                 xfun_0.28                     dplyr_1.0.7                  
 [40] crayon_1.4.2                  RCurl_1.98-1.5                jsonlite_1.7.2               
 [43] GEOquery_2.58.0               iterators_1.0.13              survival_3.2-13              
 [46] VariantAnnotation_1.36.0      zoo_1.8-9                     glue_1.4.2                   
 [49] gtable_0.3.0                  zlibbioc_1.36.0               XVector_0.30.0               
 [52] DelayedArray_0.16.3           RcppZiggurat_0.1.6            rentrez_1.2.3                
 [55] BiocGenerics_0.36.1           quantmod_0.4.18               scales_1.1.1                 
 [58] rngtools_1.5.2                DBI_1.1.1                     edgeR_3.32.1                 
 [61] derfinderHelper_1.24.1        derfinder_1.24.2              miniUI_0.1.1.1               
 [64] Rcpp_1.0.7                    htmlTable_2.3.0               xtable_1.8-4                 
 [67] progress_1.2.2                bumphunter_1.32.0             foreign_0.8-81               
 [70] bit_4.0.4                     Formula_1.2-4                 stats4_4.0.4                 
 [73] DT_0.19                       htmlwidgets_1.5.4             httr_1.4.2                   
 [76] RColorBrewer_1.1-2            ellipsis_0.3.2                pkgconfig_2.0.3              
 [79] XML_3.99-0.8                  R.methodsS3_1.8.1             sass_0.4.0                   
 [82] nnet_7.3-16                   dbplyr_2.1.1                  locfit_1.5-9.4               
 [85] utf8_1.2.2                    reshape2_1.4.4                tidyselect_1.1.1             
 [88] rlang_0.4.12                  later_1.3.0                   AnnotationDbi_1.52.0         
 [91] munsell_0.5.0                 BiocVersion_3.12.0            tools_4.0.4                  
 [94] cachem_1.0.6                  downloader_0.4                generics_0.1.1               
 [97] RSQLite_2.2.8                 broom_0.7.10                  stringr_1.4.0                
[100] fastmap_1.1.0                 yaml_2.2.1                    knitr_1.36                   
[103] org.Hs.eg.db_3.12.0           bit64_4.0.5                   purrr_0.3.4                  
[106] doRNG_1.8.2                   mime_0.12                     R.oo_1.24.0                  
[109] xml2_1.3.2                    biomaRt_2.46.3                compiler_4.0.4               
[112] rstudioapi_0.13               curl_4.3.2                    png_0.1-7                    
[115] interactiveDisplayBase_1.28.0 tibble_3.1.5                  bslib_0.3.1                  
[118] stringi_1.7.5                 GenomicFeatures_1.42.3        GenomicFiles_1.26.0          
[121] lattice_0.20-45               Matrix_1.3-4                  shinyjs_2.0.0                
[124] vctrs_0.3.8                   pillar_1.6.4                  lifecycle_1.0.1              
[127] BiocManager_1.30.16           jquerylib_0.1.4               data.table_1.14.2            
[130] bitops_1.0-7                  qvalue_2.22.0                 httpuv_1.6.3                 
[133] rtracklayer_1.50.0            GenomicRanges_1.42.0          R6_2.5.1                     
[136] latticeExtra_0.6-29           promises_1.2.0.1              gridExtra_2.3                
[139] IRanges_2.24.1                codetools_0.2-18              colourpicker_1.1.1           
[142] assertthat_0.2.1              fontawesome_0.2.2             SummarizedExperiment_1.20.0  
[145] openssl_1.4.5                 GenomicAlignments_1.26.0      Rsamtools_2.6.0              
[148] S4Vectors_0.28.1              GenomeInfoDbData_1.2.4        rlist_0.4.6.2                
[151] parallel_4.0.4                hms_1.1.1                     grid_4.0.4                   
[154] rpart_4.1-15                  tidyr_1.1.4                   Rfast_2.0.3                  
[157] MatrixGenerics_1.2.1          TTR_0.24.2                    Biobase_2.50.0               
[160] lubridate_1.8.0               base64enc_0.1-3               recount_1.16.1

I hope I can avoid having to upgrade my R to latest version and install psichomics v 1.20 from the new Bioconductor release.

Anyway congratulation for building the most amazing shinyApp I've ever seen!

Nicco

nuno-agostinho commented 2 years ago

Hey Nicco! :)

That bug has been fixed in newer versions of psichomics. Since you aren't interested in upgrading your R version, you can try to install the latest version of psichomics via GitHub:

install.packages("remotes")
remotes::install_github("nuno-agostinho/psichomics")

I am not sure how this will run in your R version, please tell me if any error is raised when you run that.

And thanks for your kind words!! 😄

Cheers, Nuno

Ni-Ar commented 2 years ago

Okay, the latest version solved the bug!

remotes::install_github("nuno-agostinho/psichomics")
Downloading GitHub repo nuno-agostinho/psichomics@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: RcppArmad... (0.10.7.0.0 -> 0.10.7.3.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates: a
Enter one or more numbers, or an empty line to skip updates: 1
RcppArmad... (0.10.7.0.0 -> 0.10.7.3.0) [CRAN]
Installing 1 packages: RcppArmadillo

  There is a binary version available but the source version is later:
                  binary     source needs_compilation
RcppArmadillo 0.10.7.0.0 0.10.7.3.0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y
installing the source package ‘RcppArmadillo’

trying URL 'https://cran.rstudio.com/src/contrib/RcppArmadillo_0.10.7.3.0.tar.gz'
Content type 'application/x-gzip' length 1360186 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... (cached) yes
checking whether we have a suitable tempdir... /var/folders/2_/s4f95b5s2bg0bv464z8gr56h0000gn/T
checking whether R CMD SHLIB can already compile programs using OpenMP... yes
checking LAPACK_LIBS... R-supplied partial LAPACK found
configure: WARNING: Some complex-valued LAPACK functions may not be available
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** 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/usr/local/include  -I../inst/include  -fPIC  -Wall -g -O2  -c RcppArmadillo.cpp -o RcppArmadillo.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/usr/local/include  -I../inst/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/usr/local/include  -I../inst/include  -fPIC  -Wall -g -O2  -c fastLm.cpp -o fastLm.o
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 RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
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: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo’

The downloaded source packages are in
    ‘/private/var/folders/2_/s4f95b5s2bg0bv464z8gr56h0000gn/T/RtmpFdIV0Q/downloaded_packages’
✓  checking for file ‘/private/var/folders/2_/s4f95b5s2bg0bv464z8gr56h0000gn/T/RtmpFdIV0Q/remotesa9571931e28/nuno-agostinho-psichomics-ff7d8f2/DESCRIPTION’ ...
─  preparing ‘psichomics’: (389ms)
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts (398ms)
─  checking for empty or unneeded directories
─  building ‘psichomics_1.20.0.tar.gz’

* installing *source* package ‘psichomics’ ...
** 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/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/usr/local/include   -fPIC  -Wall -g -O2  -c progressBar.cpp -o progressBar.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/usr/local/include   -fPIC  -Wall -g -O2  -c psiFastCalc.cpp -o psiFastCalc.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/usr/local/include   -fPIC  -Wall -g -O2  -c vastToolsParser.cpp -o vastToolsParser.o
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 psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-psichomics/00new/psichomics/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘psichomics’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (psichomics)
Warning message:
In i.p(...) :
  installation of package ‘RcppArmadillo’ had non-zero exit status

(Just to mention that RcppArmadillo had non-zero exit status )

library("psichomics")
Loading required package: shiny
Loading required package: shinyBS
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

psichomics 1.20.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics

And now

psichomics()

Listening on http://127.0.0.1:3364

Info:

R.version.string
[1] "R version 4.0.4 (2021-02-15)"

packageVersion("psichomics")
[1] ‘1.20.0’

Thanks a lot!

nuno-agostinho commented 2 years ago

Glad to know it is working now! If you have any other issue, feel free to talk. :)

All the best!