R Development Page

Pi log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2021-11-29-13-17/RF_PKG_CHECK/PKGS/Pi.Rcheck'
* using R version 4.1.2 Patched (2021-11-25 r81252)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'Pi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pi' version '2.7.2'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Hai Fang '

Package duplicated from https://bioconductor.org/packages/3.14/bioc

Found the following (possibly) invalid URLs:
  URL: http://galahad.well.ox.ac.uk/bigdata (moved to http://galahad.well.ox.ac.uk/bigdata/)
    From: man/xRDataLoader.Rd
    Status: 200
    Message: OK
  URL: http://html-color-codes.info/color-names (moved to https://html-color-codes.info/color-names/)
    From: man/xCircos.Rd
          man/xColormap.Rd
          man/xContour.Rd
          man/xEnrichForest.Rd
          man/xGGnetwork.Rd
          man/xGSEAdotplot.Rd
          man/xHeatmap.Rd
          man/xMLparameters.Rd
          man/xPieplot.Rd
          man/xPierABFheatmap.Rd
          man/xVisEvidence.Rd
          man/xVisEvidenceAdv.Rd
          man/xVisNet.Rd
    Status: 200
    Message: OK
  URL: http://igraph.org/r/doc/layout_nicely.html (moved to https://igraph.org/r/doc/layout_nicely.html)
    From: man/xVisNet.Rd
    Status: 200
    Message: OK
  URL: http://igraph.org/r/doc/plot.common.html (moved to https://igraph.org/r/doc/plot.common.html)
    From: man/xVisEvidence.Rd
          man/xVisNet.Rd
    Status: 200
    Message: OK
  URL: http://igraph.org/r/doc/vertex.shape.pie.html (moved to https://igraph.org/r/doc/vertex.shape.pie.html)
    From: man/xVisNet.Rd
    Status: 200
    Message: OK
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xContour.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xContour.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xGSEAbarplot.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xGSEAbarplot.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xGSEAconciser.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xGSEAconciser.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xGSEAdotplot.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xGSEAdotplot.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xGSsimulator.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xGSsimulator.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xMLcaret.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xMLcaret.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xMLdensity.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xMLdensity.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xMLdotplot.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xMLdotplot.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xMLfeatureplot.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xMLfeatureplot.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xMLparameters.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xMLparameters.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xMLrandomforest.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xMLrandomforest.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xMLzoom.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xMLzoom.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPCHiCplot.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPCHiCplot.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPier.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPier.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierAnno.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierAnno.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierCross.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierCross.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierEvidence.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierEvidence.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierGSEA.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierGSEA.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierGenes.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierGenes.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierManhattan.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierManhattan.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierMatrix.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierMatrix.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierPathways.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierPathways.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierROCR.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierROCR.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierSNPs.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierSNPs.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierSubnet.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierSubnet.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierTrack.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierTrack.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPierTrackAdv.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPierTrackAdv.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPredictCompare.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPredictCompare.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xPredictROCR.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xPredictROCR.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xRWR.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xRWR.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xSNP2cGenes.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xSNP2cGenes.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xSNP2eGenes.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xSNP2eGenes.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://rawgit.com/hfang-bristol/Pi/master/inst/xVisEvidence.html (moved to https://rawgit.com/hfang-bristol/Pi/master/inst/xVisEvidence.html)
    From: inst/doc/Pi_vignettes.html
    Status: 404
    Message: Not Found
  URL: http://www.1000genomes.org/faq/which-populations-are-part-your-study (moved to https://www.internationalgenome.org/faq/which-populations-are-part-your-study)
    From: man/xPierSNPs.Rd
          man/xPierSNPsAdv.Rd
          man/xPierSNPsAdvABF.Rd
          man/xSNPscores.Rd
    Status: 200
    Message: OK
  URL: http://www.immunobase.org (moved to https://genetics.opentargets.org/immunobase)
    From: inst/doc/Pi_vignettes.html
    Status: 200
    Message: OK
  URL: http://www.nature.com/articles/s41588-019-0456-1 (moved to https://www.nature.com/articles/s41588-019-0456-1)
    From: inst/CITATION
    Status: 200
    Message: OK
  URL: http://www.rdocumentation.org/packages/Gviz/topics/plotTracks (moved to https://www.rdocumentation.org/packages/Gviz/topics/plotTracks)
    From: man/xPierTrack.Rd
    Status: 200
    Message: OK
  URL: http://www.rdocumentation.org/packages/lattice/topics/xyplot (moved to https://www.rdocumentation.org/packages/lattice/topics/xyplot)
    From: man/xPierTrackAdv.Rd
    Status: 404
    Message: Not Found
  URL: https://github.com/hfang-bristol/Pi/issues
    From: DESCRIPTION
    Status: 404
    Message: Not Found

Found the following URLs which should use \doi (with the DOI name only):
  File 'xPierSNPs.Rd':
    http://dx.doi.org/10.1016/j.celrep.2016.10.061
  File 'xPierSNPsAdv.Rd':
    http://dx.doi.org/10.1016/j.celrep.2016.10.061
  File 'xPierSNPsAdvABF.Rd':
    http://dx.doi.org/10.1016/j.celrep.2016.10.061
  File 'xSNP2nGenes.Rd':
    http://dx.doi.org/10.1016/j.celrep.2016.10.061
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'Pi' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ROCR::plot' by 'graphics::plot' when loading 'Pi'
See 'R:/run/building/build_2021-11-29-13-17/RF_PKG_CHECK/PKGS/Pi.Rcheck/00install.out' for details.
* 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 ... 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 ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'xPierSNPsAdv.Rd':
  \examples lines wider than 100 characters:
     #ls_pNode <- xPierSNPsAdv(data=AS, include.TAD='GM12878', include.eQTL="JKng_mono", include.HiC='Monocytes', network="PCommonsUN_medium ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'R:/run/building/build_2021-11-29-13-17/RF_PKG_CHECK/PKGS/Pi.Rcheck/00check.log'
for details.


Run time: 366.93 seconds.