* using log directory ‘/srv/hornik/tmp/CRAN/GSNA.Rcheck’
* using R Under development (unstable) (2024-01-10 r85799)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (3)
    Debian flang-new version 17.0.6 (3)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘GSNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSNA’ version ‘0.1.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/7s] NOTE
Maintainer: ‘Jonathan M Urbach <jurbach@mgh.harvard.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  CERNO (9:52)
  GSEA (9:59)
  GSNA (8:91, 11:15, 13:57)
  epigenetic (13:3)
  transcriptomic (12:113)

Authors@R field gives persons with deprecated elements:
  Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
    It is recommended to use ‘given’ instead of ‘middle’.
  Calls: <Anonymous> ... FUN -> with -> with.default -> eval -> eval -> person1

Found the following (possibly) invalid file URIs:
  URI: makeOneColorEncodeFunction
    From: man/makeLinearNColorGradientFunction.Rd
  URI: makeTwoColorEncodeFunction
    From: man/makeLinearNColorGradientFunction.Rd

The Description field should not start with the package name,
  'This package' or similar.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GSNA’ can be installed ... [15s/15s] OK
* used C++ compiler: ‘Debian clang version 17.0.6 (3)’
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [12s/12s] NOTE
gsnHierarchicalDendrogram: warning in make1ColorLegend(numbers =
  numbers, oneColorEncode.fun = oneColorEncode.fun, n = colors.n, lab =
  legend.ylab, .plt = c(legend_left_x.fig, legend_left_x.fig +
  legend_x_size.fig, 0, legend_top_y.fig), cex.lab = legend.lab.cex,
  cex.axis = legend.axis.cex, draw.legend.box.bool =
  draw.legend.box.bool, h.adjust = "left", render.bool = FALSE,
  optimize.legend.size = TRUE): partial argument match of '.plt' to
  '.plt.leg'
gsnHierarchicalDendrogram: warning in makeLeafSizeLegend(numbers =
  gs_numbers, sizeEncode.fun = sizeEncode.fun, .plt.leg =
  c(legend_left_x.fig, legend_left_x.fig + legend_x_size.fig, 0,
  legend_top_y.fig), legend.lab = n_col, pch = leaves_pch, cex = cex,
  leaf_border_color = leaf_border_color, leaf.col = legend.leaf.col,
  legend.fg = legend.fg, legend.bg = legend.bg, h.adjust = "left",
  v.adjust = "top", render.bool = FALSE, optimize.legend.size = TRUE):
  partial argument match of 'cex' to 'cex.ticks'
gsnHierarchicalDendrogram: warning in make1ColorLegend(numbers =
  numbers, oneColorEncode.fun = oneColorEncode.fun, cex.lab =
  legend.lab.cex, cex.axis = legend.axis.cex, legend.fg = legend.fg,
  legend.bg = legend.bg, n = colors.n, lab = legend.ylab, .plt =
  plt.l[[plt.idx]], draw.legend.box.bool = draw.legend.box.bool,
  v.adjust = "center"): partial argument match of '.plt' to '.plt.leg'
gsnPlotNetwork: warning in make1ColorLegend(numbers = numbers,
  oneColorEncode.fun = oneColorEncode.fun, n = colors.n, lab =
  legend.ylab, .plt = c(legend_left_x.fig, legend_left_x.fig +
  max_legend_x_size.fig, 0, legend_top_y.fig), cex.lab =
  legend.lab.cex, draw.legend.box.bool = draw.legend.box.bool, h.adjust
  = "left", render.bool = FALSE, legend.fg = legend.fg, legend.bg =
  legend.bg, optimize.legend.size = TRUE): partial argument match of
  '.plt' to '.plt.leg'
gsnPlotNetwork: warning in make1ColorLegend(numbers = numbers,
  oneColorEncode.fun = oneColorEncode.fun, cex.lab = legend.lab.cex,
  cex.axis = legend.axis.cex, n = colors.n, lab = legend.ylab, .plt =
  plt.l[[plt.idx]], draw.legend.box.bool = draw.legend.box.bool,
  v.adjust = "center", legend.fg = legend.fg, legend.bg = legend.bg):
  partial argument match of '.plt' to '.plt.leg'
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) Bai_data.Rd:16-27: Lost braces
    16 | {Bai_CiHep_DN.cerno}{: An object of class \code{data.frame} with 2895 rows and 8 columns.
       |                     ^
checkRd: (-1) Bai_data.Rd:29: Lost braces; missing escapes or markup?
    29 | {Bai_CiKrt_DN.cerno}{: An object of class \code{data.frame} with 2895 rows and 8 columns.
       | ^
checkRd: (-1) Bai_data.Rd:29-30: Lost braces
    29 | {Bai_CiKrt_DN.cerno}{: An object of class \code{data.frame} with 2895 rows and 8 columns.
       |                     ^
checkRd: (-1) Bai_data.Rd:32: Lost braces; missing escapes or markup?
    32 | {Bai_CiHep_dorothea_UP.Gsea}{: An object of class \code{data.frame} with 84 rows and 12 columns.
       | ^
checkRd: (-1) Bai_data.Rd:32-47: Lost braces
    32 | {Bai_CiHep_dorothea_UP.Gsea}{: An object of class \code{data.frame} with 84 rows and 12 columns.
       |                             ^
checkRd: (-1) Bai_data.Rd:49: Lost braces; missing escapes or markup?
    49 | {Bai_CiHep_dorothea_DN.Gsea}{: An object of class \code{data.frame} with 180 rows and 12 columns.
       | ^
checkRd: (-1) Bai_data.Rd:49-50: Lost braces
    49 | {Bai_CiHep_dorothea_DN.Gsea}{: An object of class \code{data.frame} with 180 rows and 12 columns.
       |                             ^
checkRd: (-1) Bai_data.Rd:52: Lost braces; missing escapes or markup?
    52 | {Bai_CiHep_v_Fib2.de}{ An object of class \code{data.frame} with 8769 rows and 5 columns.
       | ^
checkRd: (-1) Bai_data.Rd:52-60: Lost braces
    52 | {Bai_CiHep_v_Fib2.de}{ An object of class \code{data.frame} with 8769 rows and 5 columns.
       |                      ^
checkRd: (-1) Bai_data.Rd:62: Lost braces; missing escapes or markup?
    62 | {Bai_CiKrt_v_Fib2.de}{ An object of class \code{data.frame} with 8166 rows and 5 columns.
       | ^
checkRd: (-1) Bai_data.Rd:62-63: Lost braces
    62 | {Bai_CiKrt_v_Fib2.de}{ An object of class \code{data.frame} with 8166 rows and 5 columns.
       |                      ^
checkRd: (-1) Bai_data.Rd:65: Lost braces; missing escapes or markup?
    65 | {Bai_empty_expr_mat}{: An object of class \code{matrix} (inherits from \code{array}) with 20035 rows and 0 columns.
       | ^
checkRd: (-1) Bai_data.Rd:65-68: Lost braces
    65 | {Bai_empty_expr_mat}{: An object of class \code{matrix} (inherits from \code{array}) with 20035 rows and 0 columns.
       |                     ^
checkRd: (-1) Bai_data.Rd:70: Lost braces; missing escapes or markup?
    70 | {Bai_gsc.tmod}{: A tmod class object containing 94 gene sets. }
       | ^
checkRd: (-1) Bai_data.Rd:70: Lost braces
    70 | {Bai_gsc.tmod}{: A tmod class object containing 94 gene sets. }
       |               ^
checkRd: (-1) gsnORAtest.Rd:39: Lost braces
    39 | \item{\code{E = (d / (c+d)) / ((b+d)/(a+b+c+d))}}
       |      ^
checkRd: (-1) gsnORAtest_cpp.Rd:33: Lost braces
    33 | \item{\code{E = (d / (c+d)) / ((b+d)/(a+b+c+d))}}
       |      ^
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [10s/10s] OK
  Running ‘testthat.R’ [10s/10s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [12s/12s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 NOTEs