processors arguments of kmFit() not working

[FerranLlobetC]

Describe the bug
Regardless of N of threads given to the processors arguments of kmFit() the function uses the total number of logical threads.

Expected behavior
Setting processors to N should cause the function to use N processors.

Code to Reproduce

library(devtools)
install_github("BIGslu/kimma")
example.voom <- kimma::example.voom
lm_virus <- kmFit(dat = example.voom, 
               model = "~ virus",
               run.lm = TRUE,
               processors = 4) -> **8 processors being used** (given that my computer has 8 processors). 

Software:

• OS: Ubuntu 20.04.6 LTS
• R session (from sessionInfo( )):

R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS/LAPACK: /opt/miniconda3/envs/R_env/lib/libopenblasp-r0.3.21.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] stringr_1.5.0  kimma_1.4.4    edgeR_3.40.0   limma_3.54.0   optparse_1.7.1
[6] tidyr_1.3.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3     magrittr_2.0.3   tidyselect_1.2.0 getopt_1.20.3
 [5] lattice_0.20-45  R6_2.5.1         rlang_1.1.1      foreach_1.5.2
 [9] fansi_1.0.4      dplyr_1.1.2      tools_4.2.3      grid_4.2.3
[13] utf8_1.2.3       cli_3.6.1        iterators_1.0.14 tibble_3.2.1
[17] lifecycle_1.0.3  purrr_1.0.1      codetools_0.2-19 vctrs_0.6.2
[21] glue_1.6.2       stringi_1.7.12   compiler_4.2.3   pillar_1.9.0
[25] generics_0.1.3   locfit_1.5-9.5   pkgconfig_2.0.3

Additional context
Apparently the issue resides in the lines of code 104 to 115 of kmFit.R. While in the file here at GitHub the code looks perfect in the source of the kmFit function that I got there is an extra line break which does not allow the number of processors to be set:

if (nzchar(chk) && chk == "TRUE") {
    processors.to.use <- 2
  }
  else if (is.null(processors)) {
    processors.to.use <- parallel::detectCores() - 2
    if (processors.to.use == 0) {
      stop("Error processors: Default resulted in 0. Please correct.")
    }
  }
  else {
    processors.to.use <- processors
  }

[kdillmcfarland]

Thank you so much for reporting this error! I believe the bug is fixed in the latest release (v1.6.1). Can you check on your system as I do not have a Ubuntu machine to test with?

[FerranLlobetC]

Hi Kimberley,
I appreciate your assistance, but I regret to inform you that the issue persists.

Furthermore, I continue to observe an excessive amount of line breaks when examining the source code of the kmFit() function.

R session (from sessionInfo( )):

` R version 4.2.3 (2023-03-15)
Plaform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS/LAPACK: /opt/miniconda3/envs/R_env/lib/libopenblasp-r0.3.21.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] stats graphics grDevices utils datasets methods base

other attached packages:
[1] kimma_1.6.1

loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 compiler_4.2.3 magrittr_2.0.3 cli_3.6.1
[5] glue_1.6.2 codetools_0.2-19 iterators_1.0.14 foreach_1.5.2
[9] rlang_1.1.1 `