update vignette

[mhallal1]

Part of https://github.com/insightsengineering/coredev-tasks/issues/155

Updated the name of vignette Introduction.Rmd to hermes.Rmd so that we get the content of this vignette in Get started in the header.

Reproduce the pkgdown locally:

usethis::use_pkgdown()
pkgdown::build_site()

[github-actions]

Code Coverage Summary

Filename                   Stmts    Miss  Cover    Missing
-----------------------  -------  ------  -------  ------------------------
R/assertthat.R                19       1  94.74%   149
R/calc_cor.R                  25       0  100.00%
R/checkmate.R                  4       0  100.00%
R/connections.R              143     125  12.59%   27-161, 215-287, 356-381
R/differential.R             101       3  97.03%   190, 193, 196
R/dplyr_compatibility.R        3       1  66.67%   23
R/draw_barplot.R              34       0  100.00%
R/draw_boxplot.R              71       5  92.96%   81, 88-89, 106, 109
R/draw_scatterplot.R          32       4  87.50%   73-74, 87, 93
R/GeneSpec-class.R            68       0  100.00%
R/graphs.R                   107       3  97.20%   107-109
R/HermesData-class.R          35       4  88.57%   131-134
R/HermesData-methods.R       194       0  100.00%
R/HermesData-validate.R       44       0  100.00%
R/join_cdisc.R                37       0  100.00%
R/normalization.R            100       2  98.00%   194, 223
R/pca_cor_samplevar.R         59       0  100.00%
R/pca.R                       28       0  100.00%
R/quality.R                   75       3  96.00%   109-112
R/top_genes.R                 51       0  100.00%
R/utils.R                     93       0  100.00%
TOTAL                       1323     151  88.59%

Results for commit: aaf25d6

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

    1 files    22 suites   2m 9s ⏱️
271 tests 253 ✔️ 18 💤 0 ❌
843 runs  821 ✔️ 22 💤 0 ❌

Results for commit 4d7e6e5.

[github-actions]

BiocCheck PASSED.

This is BiocCheck version 1.30.0. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...

Click here to show log

* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* Checking R Version dependency...
    * NOTE: Update R version dependency from 3.5 to 4.1.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      Sequencing, Coverage
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
    * NOTE: License 'Apache License 2.0 | file LICENSE' unknown;
      licenses cannot restrict use
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking package installation calls in R code...
Warning in parse_Rd(infile) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_deseq2.Rd:42: unknown macro '\insertRef'
Warning in parse_Rd(infile) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_voom.Rd:43: unknown macro '\insertRef'
Warning in parse_Rd(infile) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_voom.Rd:45: unknown macro '\insertRef'
* Checking for library/require of hermes...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.............................................................................................
    * NOTE: Recommended function length <= 50 lines.
      There are 1 functions > 50 lines.
      The longest 5 functions are:
        draw_boxplot() (R/draw_boxplot.R, line 62): 51 lines
        draw_scatterplot() (R/draw_scatterplot.R, line 49): 48 lines
        top_genes() (R/top_genes.R, line 41): 48 lines
        draw_barplot() (R/draw_barplot.R, line 51): 47 lines
        h_get_size_biomart() (R/connections.R, line 212): 45 lines
* Checking man page documentation...
Warning in parse_Rd(manpage) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_deseq2.Rd:42: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_voom.Rd:43: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_voom.Rd:45: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_deseq2.Rd:42: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_voom.Rd:43: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_voom.Rd:45: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_deseq2.Rd:42: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_voom.Rd:43: unknown macro '\insertRef'
Warning in parse_Rd(manpage) :
  /tmp/Rtmp0DEXNg/file8f167ba3dd7/hermes/man/h_diff_expr_voom.Rd:45: unknown macro '\insertRef'
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
    * NOTE: skip_on_bioc() found in testthat files: test-connections.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 776 lines (9%) are > 80 characters
      long.
    First 6 lines:
      R/assertthat.R:17 #' @param class2 (`character` or class definition)\cr...
      R/assertthat.R:72 #' @param elements (`character`)\cr names of elements...
      R/assertthat.R:98 #' @describeIn assertions checks that exactly one of ...
      R/assertthat.R:126 #' @describeIn assertions checks whether the vector ...
      R/calc_cor.R:10 #' The `correlate()` method can calculate the correlati...
      R/calc_cor.R:11 #' counts from a specified assay. This produces a [`Her...
    * NOTE: Consider multiples of 4 spaces for line indents, 1315
      lines(15%) are not.
    First 6 lines:
      R/assertthat.R:24   is(x, class2)
      R/assertthat.R:28   obj_name <- deparse(call$x)
      R/assertthat.R:29   class <- eval(call$class2, env)
      R/assertthat.R:30   paste(obj_name, "is not of class", class)
      R/assertthat.R:43   is_class(x, "AnyHermesData")
      R/assertthat.R:47   obj_name <- deparse(call$x)
    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://packagemanager.rstudio.com/cran/__linux__/focal/2022-03-09

* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      bioc-devel mailing list (requires admin credentials).  Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

Summary:

ERROR count: 0
WARNING count: 0
NOTE count: 9

For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output