CRAN Package Check Results for Package idiogramFISH

Last updated on 2020-01-27 00:48:05 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.12.1 9.74 95.12 104.86 OK
r-devel-linux-x86_64-debian-gcc 1.12.1 8.25 72.54 80.79 OK
r-devel-linux-x86_64-fedora-clang 1.12.1 127.00 OK
r-devel-linux-x86_64-fedora-gcc 1.12.1 140.39 OK
r-devel-windows-ix86+x86_64 1.12.1 22.00 136.00 158.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.12.1 36.00 106.00 142.00 OK
r-patched-linux-x86_64 1.12.1 9.49 85.03 94.52 OK
r-patched-solaris-x86 1.12.1 145.10 WARN
r-release-linux-x86_64 1.12.1 9.38 85.81 95.19 OK
r-release-windows-ix86+x86_64 1.12.1 17.00 92.00 109.00 OK
r-release-osx-x86_64 1.12.1 WARN
r-oldrel-windows-ix86+x86_64 1.12.1 12.00 75.00 87.00 OK
r-oldrel-osx-x86_64 1.12.1 WARN

Check Details

Version: 1.12.1
Check: installed package size
Result: NOTE
     installed size is 5.4Mb
     sub-directories of 1Mb or more:
     doc 4.2Mb
Flavor: r-patched-solaris-x86

Version: 1.12.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘AplotIdiogramsVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 46-104 (AplotIdiogramsVig.Rmd)
    Error: processing vignette 'AplotIdiogramsVig.Rmd' failed with diagnostics:
    argument is of length zero
    --- failed re-building ‘AplotIdiogramsVig.Rmd’
    
    --- re-building ‘BplotIdiogramsHoloVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species one has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species one checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species one of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Colors provided in to dfMarkColor are not enough, internal colors will be used.
    
    Species one:
    Calculating karyotype index A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species one has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species two has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species three has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU species two checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: species two of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    species three:
    Calculating karyotype index A2
    
    species two:
    Calculating karyotype index A2
    
    species one:
    Calculating karyotype index A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species one has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species two has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species three has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU species two checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: species two of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Parental 1 has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Parental 2 has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Allopolyploid has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Allopolyploid checked
    
    
    OK marks of OTU Parental 1 checked
    
    
    OK marks of OTU Parental 2 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Parental 1 of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Parental 2 of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Allopolyploid of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    Allopolyploid:
    Calculating karyotype index A2
    
    Parental 2:
    Calculating karyotype index A2
    
    Parental 1:
    Calculating karyotype index A2
    
    --- finished re-building ‘BplotIdiogramsHoloVig.Rmd’
    
    --- re-building ‘CgroupsVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Warning: Chromosome names duplicated in data.frame 1, will be renamed
     this correction is available when no marks to be plotted, otherwise, is fatal
    group column present - remove column if not using
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    group column present - remove column if not using
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    group column present - remove column if not using
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species name has all columns with info to have holocen. If not, you have to clean your data
    
    Warning: Chromosome names duplicated in data.frame Species name, will be renamed
     this correction is available when no marks to be plotted, otherwise, is fatal
    group column present - remove column if not using
    --- finished re-building ‘CgroupsVig.Rmd’
    
    --- re-building ‘DphylogenyVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Loading required package: ggplot2
    Loading required package: phytools
    Loading required package: ape
    Loading required package: maps
    Loading required package: ggpubr
    Loading required package: magrittr
    
    Attaching package: 'ggpubr'
    
    The following object is masked from 'package:ape':
    
     rotate
    
    Loading required package: grid
    Loading required package: ggtree
    ggtree v2.0.1 For help: https://yulab-smu.github.io/treedata-book/
    
    If you use ggtree in published research, please cite the most appropriate paper(s):
    
    <1b>[36m-<1b>[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194
    <1b>[36m-<1b>[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
    
    
    
    Attaching package: 'ggtree'
    
    The following object is masked from 'package:ggpubr':
    
     rotate
    
    The following object is masked from 'package:magrittr':
    
     inset
    
    The following object is masked from 'package:ape':
    
     rotate
    
    Read 1 item
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_F has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_H has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_C has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_B has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_A has all columns with info to have monocen. If not, you have to clean your data
    
    Calculating chromosome indexes in Species_F
    
    Calculating chromosome indexes in Species_H
    
    Calculating chromosome indexes in Species_C
    
    Calculating chromosome indexes in Species_B
    
    Calculating chromosome indexes in Species_A
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species_C checked
    
    
    OK marks of OTU Species_A checked
    
    
    OK marks of OTU Species_H checked
    
    
    OK marks of OTU Species_B checked
    
    
    OK marks of OTU Species_F checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU Species_C checked
    
    
    OK cen. marks of OTU Species_A checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_F of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_H of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_B of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Species_A:
    Calculating karyotype indexes A and A2
    
    Species_B:
    Calculating karyotype indexes A and A2
    
    Species_C:
    Calculating karyotype indexes A and A2
    
    Species_H:
    Calculating karyotype indexes A and A2
    
    Species_F:
    Calculating karyotype indexes A and A2
    
    Loading required package: treeio
    treeio v1.10.0 For help: https://yulab-smu.github.io/treedata-book/
    
    If you use treeio in published research, please cite:
    
    LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution 2019, accepted. doi: 10.1093/molbev/msz240
    
    
    Attaching package: 'treeio'
    
    The following object is masked from 'package:phytools':
    
     read.newick
    
    The following object is masked from 'package:ape':
    
     drop.tip
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_B has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_A has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_H has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_C has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_F has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species_C checked
    
    
    OK marks of OTU Species_H checked
    
    
    OK marks of OTU Species_A checked
    
    
    OK marks of OTU Species_B checked
    
    
    OK marks of OTU Species_F checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_B of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_H of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_F of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Species_F:
    Calculating karyotype index A2
    
    Species_C:
    Calculating karyotype index A2
    
    Species_H:
    Calculating karyotype index A2
    
    Species_A:
    Calculating karyotype index A2
    
    Species_B:
    Calculating karyotype index A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_B has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_A has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_H has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_C has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_F has all columns with info to have monocen. If not, you have to clean your data
    
    Calculating chromosome indexes in Species_A
    
    Calculating chromosome indexes in Species_C
    
    Calculating chromosome indexes in Species_F
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species_C checked
    
    
    OK marks of OTU Species_A checked
    
    
    OK marks of OTU Species_F checked
    
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species_H checked
    
    
    OK marks of OTU Species_B checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU Species_C checked
    
    
    OK cen. marks of OTU Species_A checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_F of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_B of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_H of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Species_F:
    Calculating karyotype indexes A and A2
    
    Species_C:
    Calculating karyotype indexes A and A2
    
    Species_H:
    Calculating karyotype index A2
    
    Species_A:
    Calculating karyotype indexes A and A2
    
    Species_B:
    Calculating karyotype index A2
    
    --- finished re-building ‘DphylogenyVig.Rmd’
    
    --- re-building ‘EhumanVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu2 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu3 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu4 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU otu1 checked
    
    
    OK marks of OTU otu2 checked
    
    
    OK marks of OTU otu3 checked
    
    
    OK marks of OTU otu4 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: otu1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: otu2 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: otu3 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: otu4 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    group column present - remove column if not using
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu3 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU otu3 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: otu3 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    --- finished re-building ‘EhumanVig.Rmd’
    
    --- re-building ‘index.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    ## ferroao/idiogramFISH is out of date...
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    1:
    Calculating karyotype indexes A and A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    1:
    Calculating karyotype index A2
    
    Loading required package: plyr
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species mono has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species holo has all columns with info to have holocen. If not, you have to clean your data
    
    Calculating chromosome indexes in Species mono
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species mono checked
    
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species holo checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU Species mono checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species mono of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species holo of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species mono of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Species holo:
    Calculating karyotype index A2
    
    Species mono:
    Calculating karyotype indexes A and A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Parental 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Parental 2 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Allopolyploid has all columns with info to have monocen. If not, you have to clean your data
    
    Calculating chromosome indexes in Parental 1
    
    Calculating chromosome indexes in Parental 2
    
    Calculating chromosome indexes in Allopolyploid
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Allopolyploid checked
    
    
    OK marks of OTU Parental 1 checked
    
    
    OK marks of OTU Parental 2 checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU Allopolyploid checked
    
    
    OK cen. marks of OTU Parental 1 checked
    
    
    OK cen. marks of OTU Parental 2 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Parental 1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Parental 2 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Allopolyploid of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Parental 1 of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    Comparing OTU named: Parental 2 of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    Comparing OTU named: Allopolyploid of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    Allopolyploid:
    Calculating karyotype indexes A and A2
    
    Parental 2:
    Calculating karyotype indexes A and A2
    
    Parental 1:
    Calculating karyotype indexes A and A2
    
    trying URL 'https://liberapay.com/assets/widgets/donate.svg'
    Content type 'image/svg+xml' length 1457 bytes
    ==================================================
    downloaded 1457 bytes
    
    trying URL 'http://img.shields.io/liberapay/receives/ferroao.svg'
    downloaded 977 bytes
    
    --- finished re-building ‘index.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘AplotIdiogramsVig.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.12.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘AplotIdiogramsVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 46-104 (AplotIdiogramsVig.Rmd)
    Error: processing vignette 'AplotIdiogramsVig.Rmd' failed with diagnostics:
    argument is of length zero
    --- failed re-building ‘AplotIdiogramsVig.Rmd’
    
    --- re-building ‘BplotIdiogramsHoloVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species one has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species one checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species one of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Colors provided in to dfMarkColor are not enough, internal colors will be used.
    
    Species one:
    Calculating karyotype index A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species one has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species two has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species three has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU species two checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: species two of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    species three:
    Calculating karyotype index A2
    
    species two:
    Calculating karyotype index A2
    
    species one:
    Calculating karyotype index A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species one has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species two has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU species three has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU species two checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: species two of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Parental 1 has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Parental 2 has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Allopolyploid has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Allopolyploid checked
    
    
    OK marks of OTU Parental 1 checked
    
    
    OK marks of OTU Parental 2 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Parental 1 of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Parental 2 of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Allopolyploid of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    Allopolyploid:
    Calculating karyotype index A2
    
    Parental 2:
    Calculating karyotype index A2
    
    Parental 1:
    Calculating karyotype index A2
    
    --- finished re-building ‘BplotIdiogramsHoloVig.Rmd’
    
    --- re-building ‘CgroupsVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Warning: Chromosome names duplicated in data.frame 1, will be renamed
     this correction is available when no marks to be plotted, otherwise, is fatal
    group column present - remove column if not using
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    group column present - remove column if not using
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    group column present - remove column if not using
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species name has all columns with info to have holocen. If not, you have to clean your data
    
    Warning: Chromosome names duplicated in data.frame Species name, will be renamed
     this correction is available when no marks to be plotted, otherwise, is fatal
    group column present - remove column if not using
    --- finished re-building ‘CgroupsVig.Rmd’
    
    --- re-building ‘DphylogenyVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Loading required package: ggplot2
    Loading required package: phytools
    Loading required package: ape
    Loading required package: maps
    Loading required package: ggpubr
    Loading required package: magrittr
    
    Attaching package: 'ggpubr'
    
    The following object is masked from 'package:ape':
    
     rotate
    
    Loading required package: grid
    Loading required package: ggtree
    ggtree v1.16.6 For help: https://yulab-smu.github.io/treedata-book/
    
    If you use ggtree in published research, please cite the most appropriate paper(s):
    
    <1b>[36m-<1b>[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194
    <1b>[36m-<1b>[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
    
    
    
    Attaching package: 'ggtree'
    
    The following object is masked from 'package:ggpubr':
    
     rotate
    
    The following object is masked from 'package:magrittr':
    
     inset
    
    The following object is masked from 'package:phytools':
    
     read.newick
    
    The following object is masked from 'package:ape':
    
     rotate
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_F has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_H has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_C has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_B has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_A has all columns with info to have monocen. If not, you have to clean your data
    
    Calculating chromosome indexes in Species_F
    
    Calculating chromosome indexes in Species_H
    
    Calculating chromosome indexes in Species_C
    
    Calculating chromosome indexes in Species_B
    
    Calculating chromosome indexes in Species_A
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species_C checked
    
    
    OK marks of OTU Species_A checked
    
    
    OK marks of OTU Species_H checked
    
    
    OK marks of OTU Species_B checked
    
    
    OK marks of OTU Species_F checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU Species_C checked
    
    
    OK cen. marks of OTU Species_A checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_F of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_H of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_B of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Species_A:
    Calculating karyotype indexes A and A2
    
    Species_B:
    Calculating karyotype indexes A and A2
    
    Species_C:
    Calculating karyotype indexes A and A2
    
    Species_H:
    Calculating karyotype indexes A and A2
    
    Species_F:
    Calculating karyotype indexes A and A2
    
    Loading required package: treeio
    
    Attaching package: 'treeio'
    
    The following object is masked from 'package:phytools':
    
     read.newick
    
    The following object is masked from 'package:ape':
    
     drop.tip
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_B has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_A has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_H has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_C has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_F has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species_C checked
    
    
    OK marks of OTU Species_H checked
    
    
    OK marks of OTU Species_A checked
    
    
    OK marks of OTU Species_B checked
    
    
    OK marks of OTU Species_F checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_B of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_H of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_F of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Species_F:
    Calculating karyotype index A2
    
    Species_C:
    Calculating karyotype index A2
    
    Species_H:
    Calculating karyotype index A2
    
    Species_A:
    Calculating karyotype index A2
    
    Species_B:
    Calculating karyotype index A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_B has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_A has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_H has all columns with info to have holocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_C has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species_F has all columns with info to have monocen. If not, you have to clean your data
    
    Calculating chromosome indexes in Species_A
    
    Calculating chromosome indexes in Species_C
    
    Calculating chromosome indexes in Species_F
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species_C checked
    
    
    OK marks of OTU Species_A checked
    
    
    OK marks of OTU Species_F checked
    
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species_H checked
    
    
    OK marks of OTU Species_B checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU Species_C checked
    
    
    OK cen. marks of OTU Species_A checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Species_F of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_B of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing OTU named: Species_H of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species_A of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    Comparing OTU named: Species_C of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Species_F:
    Calculating karyotype indexes A and A2
    
    Species_C:
    Calculating karyotype indexes A and A2
    
    Species_H:
    Calculating karyotype index A2
    
    Species_A:
    Calculating karyotype indexes A and A2
    
    Species_B:
    Calculating karyotype index A2
    
    --- finished re-building ‘DphylogenyVig.Rmd’
    
    --- re-building ‘EhumanVig.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu2 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu3 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu4 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU otu1 checked
    
    
    OK marks of OTU otu2 checked
    
    
    OK marks of OTU otu3 checked
    
    
    OK marks of OTU otu4 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: otu1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: otu2 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: otu3 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: otu4 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    group column present - remove column if not using
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU otu3 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU otu3 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: otu3 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    --- finished re-building ‘EhumanVig.Rmd’
    
    --- re-building ‘index.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    package is up-to-date devel version
    version 1.12.1 See help: ?idiogramFISH - browseVignettes('idiogramFISH') - https://ferroao.gitlab.io/manualidiogramfish
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    1:
    Calculating karyotype indexes A and A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU 1 has all columns with info to have holocen. If not, you have to clean your data
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU 1 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: 1 of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    1:
    Calculating karyotype index A2
    
    Loading required package: plyr
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species mono has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. without cen.:
    chrName, chrSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Species holo has all columns with info to have holocen. If not, you have to clean your data
    
    Calculating chromosome indexes in Species mono
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species mono checked
    
    
    Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Species holo checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU Species mono checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species mono of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species holo of main data.frame with correspondent data.frame listOfdfMarkPosHolocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Species mono of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    ####
    Checking mandatory columns from dfMarkColor: markName, markColor, style
    
    
    Check OK
    
    Species holo:
    Calculating karyotype index A2
    
    Species mono:
    Calculating karyotype indexes A and A2
    
    Making checks
    
    In case of error see messages and the help ?functionName
    
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Parental 1 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Parental 2 has all columns with info to have monocen. If not, you have to clean your data
    
    Checking columns from dfChrSize
    
    
    Checking mandatory columns from dfChrSize for chr. with cen.:
    chrName, shortArmSize,longArmSize,
     (column OTU is necessary if more than one species)
    
    
    OTU Allopolyploid has all columns with info to have monocen. If not, you have to clean your data
    
    Calculating chromosome indexes in Parental 1
    
    Calculating chromosome indexes in Parental 2
    
    Calculating chromosome indexes in Allopolyploid
    
    Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen,markSize
     (column OTU is necessary if more than one species)
    
    
    OK marks of OTU Allopolyploid checked
    
    
    OK marks of OTU Parental 1 checked
    
    
    OK marks of OTU Parental 2 checked
    
    
    Checking mandatory columns from dfCenMarks: chrName, markName
     (column OTU is necessary if more than one species)
    
    
    OK cen. marks of OTU Allopolyploid checked
    
    
    OK cen. marks of OTU Parental 1 checked
    
    
    OK cen. marks of OTU Parental 2 checked
    
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Parental 1 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Parental 2 of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing OTU named: Allopolyploid of main data.frame with correspondent data.frame listOfdfMarkPosMonocen
    
     No divergence
    
    Comparing chromosome names among data.frames:
    
    
    Comparing OTU named: Parental 1 of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    Comparing OTU named: Parental 2 of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    
    Comparing OTU named: Allopolyploid of main data.frame with correspondent data.frame listOfdfDataCen
    
     No divergence
    Allopolyploid:
    Calculating karyotype indexes A and A2
    
    Parental 2:
    Calculating karyotype indexes A and A2
    
    Parental 1:
    Calculating karyotype indexes A and A2
    
    trying URL 'https://liberapay.com/assets/widgets/donate.svg'
    Content type 'image/svg+xml' length 1457 bytes
    ==================================================
    downloaded 1457 bytes
    
    trying URL 'http://img.shields.io/liberapay/receives/ferroao.svg'
    downloaded 977 bytes
    
    --- finished re-building ‘index.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘AplotIdiogramsVig.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 1.12.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 46-104 (AplotIdiogramsVig.Rmd)
    Error: processing vignette 'AplotIdiogramsVig.Rmd' failed with diagnostics:
    argument is of length zero
    Execution halted
Flavor: r-oldrel-osx-x86_64