Error(s) in re-building vignettes:
--- re-building 'AVignette.Rmd' using rmarkdown
--- finished re-building 'AVignette.Rmd'

--- re-building 'index.Rmd' using rmarkdown

Pinging www.google.com [172.217.23.196] with 32 bytes of data:
Reply from 172.217.23.196: bytes=32 time=8ms TTL=58
Reply from 172.217.23.196: bytes=32 time=8ms TTL=58
Reply from 172.217.23.196: bytes=32 time=8ms TTL=58
Reply from 172.217.23.196: bytes=32 time=8ms TTL=58

Ping statistics for 172.217.23.196:
    Packets: Sent = 4, Received = 4, Lost = 0 (0% loss),
Approximate round trip times in milli-seconds:
    Minimum = 8ms, Maximum = 8ms, Average = 8ms
package is up-to-date release version
## ferroao/idiogramFISH is out of date...
## ferroao/idiogramFISH is out of date...
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
 (column OTU  is necessary if more than one species)
markSize can be absent when cM style

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  parlistOfdfMarkPosMonocen  

 No divergence

Comparing chromosome names among data.frames:


Comparing OTU named:  1 of main data.frame with correspondent data.frame  parlistOfdfMarkPosDataCen  

 No divergence

####
Checking mandatory columns from dfMarkColor: markName, markColor


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
 (column OTU  is necessary if more than one species)
markSize column is not necessary for style of mark cM

OK marks of OTU 1 checked 


Comparing chromosome names among data.frames:


Comparing OTU named:  1 of main data.frame with correspondent data.frame  parlistOfdfMarkPosHolocen  

 No divergence

####
Checking mandatory columns from dfMarkColor: markName, markColor


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
 (column OTU  is necessary if more than one species)
markSize can be absent when cM style

OK marks of OTU Species mono checked 


Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos
 (column OTU  is necessary if more than one species)
markSize column is not necessary for style of mark cM

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  parlistOfdfMarkPosMonocen  

 No divergence

Comparing chromosome names among data.frames:


Comparing OTU named:  Species holo of main data.frame with correspondent data.frame  parlistOfdfMarkPosHolocen  

 No divergence

Comparing chromosome names among data.frames:


Comparing OTU named:  Species mono of main data.frame with correspondent data.frame  parlistOfdfMarkPosDataCen  

 No divergence

####
Checking mandatory columns from dfMarkColor: markName, markColor


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  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
 (column OTU  is necessary if more than one species)
markSize can be absent when cM style

OK marks of OTU Species mono checked 


Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos
 (column OTU  is necessary if more than one species)
markSize column is not necessary for style of mark cM

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  parlistOfdfMarkPosMonocen  

 No divergence

Comparing chromosome names among data.frames:


Comparing OTU named:  Species holo of main data.frame with correspondent data.frame  parlistOfdfMarkPosHolocen  

 No divergence

Comparing chromosome names among data.frames:


Comparing OTU named:  Species mono of main data.frame with correspondent data.frame  parlistOfdfMarkPosDataCen  

 No divergence

####
Checking mandatory columns from dfMarkColor: markName, markColor


Check OK

Warning: MathJax doesn't work with self_contained when not using the rmarkdown "default" template.
pandoc.exe: pandoc-citeproc: createProcess: does not exist (No such file or directory)
Error: processing vignette 'index.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building 'index.Rmd'

SUMMARY: processing the following file failed:
  'index.Rmd'

Error: Vignette re-building failed.
Execution halted