people having issues posting

[lshep]

not global -- not spam users.

Not sure related to rendering as I tried to also post a comment of simple "Thank you!" and received Language "so" is not one of your supported languages ['en']! but doing "Thank you Gordon!" worked.

These could be completely unrelated issues

[lshep]

@Natay per your slack message looked at https://github.com/ialbert/biostar-central/blob/a051511350871dcd82bdf0b88ce5cda9fd9ef141/biostar/forum/forms.py#L44

Very interesting that it thought that "Thank you!" was Somalli if I read the language.detect documentation correctly. And I can reproduce locally so langdetect doesnt seem to do a good job with shorter text

(engine) lorikern@jbcj433:~/Projects/Websites/support.bioconductor.org(master)$ python3
Python 3.7.16 (default, Jan 17 2023, 22:20:44) 
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import langdetect
>>> langdetect.detect("Thank you!")
'so'
>>> langdetect.detect("Thank you")
'en'
>>> 

[lshep]

This was the posted text that was tried by a user that also would not post but with no error displaying just text went pink/red and wouldn't post for them or for me --

subject: Error message in bsseq read.bismark command while reading genome wide cytosine report generated by bismark

tags: bsseq read.bismark

Dear List,

Please excuse if this is a duplicate. I posted it 20 minutes ago but don't see it. It did not seem to go through

I am using bsseq to analyze bismark-genrated files. I can use the read.bismark command to read coverage files, but I get an error message when I try reading a genome wide cytosine report. To quote the bsseq reference: "If setting loci = NULL, then we strongly recommend using the’genome wide cytosine report’ output format because this includes strand information for each locus." So it is desirable to be able to read genome wide cytosine reports. Here is an abridged version of my *Rout file.

> library(bsseq)
.
.
,

> library(BiocParallel)

> infile="/Users/raf4/Documents/learning_statistics/learning_methylation/bsseq/4_readbismark/data/test_data_cytorep.txt.CX_report.sort.txt"
> length(infile)
[1] 1
> infile
[1] "/Users/raf4/Documents/learning_statistics/learning_methylation/bsseq/4_readbismark/data/test_data_cytorep.txt.CX_report.sort.txt"

>
> bsseq <- read.bismark(files = infile,
+                             colData=NULL,
+                             rmZeroCov = FALSE,
+                             strandCollapse = TRUE,
+                             BACKEND = "HDF5Array",
+                     BPPARAM = MulticoreParam(workers = 6,progressbar=TRUE),
+                     dir="/Users/raf4/Documents/learning_statistics/learning_methylation/bsseq/4_readbismark/workingdir2/",
+                             replace=TRUE,
+                             verbose = TRUE)
.
.
.
[read.bismark] Parsing files and constructing valid loci ...
Done in 716.9 secs
[read.bismark] Parsing files and constructing 'M' and 'Cov' matrices ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

Error in !bpok : invalid argument type
Calls: read.bismark -> .constructCounts
Execution halted

My session info from the successful run with coverage input is here:

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] HDF5Array_1.28.1            rhdf5_2.44.0              
 [3] DelayedArray_0.26.7         S4Arrays_1.0.5            
 [5] abind_1.4-5                 Matrix_1.6-0              
 [7] BiocParallel_1.34.2         bsseq_1.36.0              
 [9] SummarizedExperiment_1.30.2 Biobase_2.60.0            
[11] MatrixGenerics_1.12.3       matrixStats_1.0.0          
[13] GenomicRanges_1.52.0        GenomeInfoDb_1.36.1        
[15] IRanges_2.34.1              S4Vectors_0.38.1          
[17] BiocGenerics_0.46.0        

loaded via a namespace (and not attached):
 [1] bitops_1.0-7              gtools_3.9.4            
 [3] lattice_0.21-8            sparseMatrixStats_1.12.2
 [5] grid_4.3.1                R.oo_1.25.0              
 [7] R.utils_2.12.2            restfulr_0.0.15          
 [9] limma_3.56.2              BSgenome_1.68.0          
[11] scales_1.2.1              permute_0.9-7            
[13] XML_3.99-0.14             Biostrings_2.68.1        
[15] codetools_0.2-19          cli_3.6.1                
[17] rlang_1.1.1               crayon_1.5.2            
[19] XVector_0.40.0            R.methodsS3_1.8.2        
[21] munsell_0.5.0             yaml_2.3.7              
[23] tools_4.3.1               parallel_4.3.1          
[25] colorspace_2.1-0          Rhdf5lib_1.22.0          
[27] locfit_1.5-9.8            GenomeInfoDbData_1.2.10  
[29] Rsamtools_2.16.0          R6_2.5.1                
[31] BiocIO_1.10.0             lifecycle_1.0.3          
[33] rtracklayer_1.60.0        zlibbioc_1.46.0          
[35] data.table_1.14.8         Rcpp_1.0.11              
[37] GenomicAlignments_1.36.0  rhdf5filters_1.12.1      
[39] rjson_0.2.21              DelayedMatrixStats_1.22.1
[41] compiler_4.3.1            RCurl_1.98-1.12          
>

[lshep]

@Natay should I just comment this out https://github.com/Bioconductor/support.bioconductor.org/blob/master/biostar/forum/forms.py#L182 would this potential stop this issue (and repost #96) as well as potentially #94 . This would probably be temporary until we can sync versions of biostars/bioconductor since biostars does not appear to have these issues? But not sure if we should wait for the captcha final stages (we were thinking of adding captcha when posting too) so that might help if spam increases from turning off the language validation

[lshep]

temporarily disable language check until we can update ff0424f