R Development Page

supraHex log file (check_x86_64_linux)

Mon May 24 05:08:58 2021: Checking package supraHex (SVN revision 127) ...
* using log directory ‘/srv/rf/building/build_2021-05-24-05-07/RF_PKG_CHECK/PKGS/supraHex.Rcheck’
* using R version 4.1.0 Patched (2021-05-22 r80357)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘supraHex/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘supraHex’ version ‘1.31.1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Hai Fang ’

Package duplicated from https://bioconductor.org/packages/3.13/bioc

Found the following (possibly) invalid URLs:
  URL: http://html-color-codes.info/color-names (moved to https://html-color-codes.info/color-names/)
    From: man/visColorbar.Rd
          man/visColormap.Rd
          man/visCompReorder.Rd
          man/visDmatCluster.Rd
          man/visDmatHeatmap.Rd
          man/visHeatmap.Rd
          man/visHeatmapAdv.Rd
          man/visHexAnimate.Rd
          man/visHexBarplot.Rd
          man/visHexComp.Rd
          man/visHexMulComp.Rd
          man/visHexPattern.Rd
          man/visTreeBSclust.Rd
          man/visTreeBootstrap.Rd
    Status: 200
    Message: OK
  URL: http://rdrr.io/cran/ape/man/nodelabels.html (moved to https://rdrr.io/cran/ape/man/nodelabels.html)
    From: man/visTreeBSclust.Rd
          man/visTreeBootstrap.Rd
    Status: 200
    Message: OK
  URL: http://rdrr.io/cran/ape/man/plot.phylo.html (moved to https://rdrr.io/cran/ape/man/plot.phylo.html)
    From: man/visTreeBSclust.Rd
          man/visTreeBootstrap.Rd
    Status: 200
    Message: OK
  URL: http://www.imagemagick.org/script/advanced-unix-installation.php
    From: man/visHexAnimate.Rd
    Status: 404
    Message: Not Found
  URL: http://www.sciencedirect.com/science/article/pii/S0006291X13020056 (moved to https://www.sciencedirect.com/science/article/pii/S0006291X13020056)
    From: inst/CITATION
    Status: 200
    Message: OK

The Title field starts with the package name.
The Title field should be in title case. Current version is:
‘supraHex: a supra-hexagonal map for analysing tabular omics data’
In title case that is:
‘supraHex: a Supra-Hexagonal Map for Analysing Tabular Omics Data’

Size of tarball: 6131570 bytes
* 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 ‘supraHex’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘nohup.out’
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [10s/10s] OK
* checking Rd files ... [1s/1s] OK
* 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 ... NOTE
File 'data/datalist' is out-of-date:
  Data objects in 'datalist' not in 'data' directory:
    Fang.geneinfo Fang.sampleinfo
Please re-create using tools::add_datalist(force = TRUE).
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘supraHex_vignettes.pdf’ from 2.2Mb to 1.6Mb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [9s/9s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘sData_base_output.txt’ ‘sData_output.txt’
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/srv/rf/building/build_2021-05-24-05-07/RF_PKG_CHECK/PKGS/supraHex.Rcheck/00check.log’
for details.


Run time: 98.57 seconds.