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adegenet: a R package for the multivariate analysis of genetic markers

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adegenet's Issues

repool issue

Hi Thibaut,
I tried to use the function repool, and the following issue came up:

library(adegenet)
data(nancycats)
sep <- seppop(nancycats)
repool(sep[[1]], sep[[2]])

Error in repool(sep[[1]], sep[[2]]) :
objects have different levels of ploidy

Any suggestions?

All the best,
Christine

pairwise.fst() not working in 2.0.0

"mygenind" is a list containing multiple genind objects, each imported from an individual structure file.

myseploc <- seploc(mygenind, truenames=TRUE)

myfst <- lapply(myseploc, function(x) pairwise.fst(x))
This function has been moved to the package hierfstat. You can still use it in adegenet, but this version is deprecated.
Error in pairwise.fst(x) : x is not a valid genind object

Also tried:
library(parallel)
cl <- makeCluster(2)
clusterExport(cl, "pairwise.fst")
myfst <- parLapply(cl, myseploc, function(x) pairwise.fst(x))
Same deprecated version error as above.

myfst <-parLapply(cl, myseploc, function(x) pp.fst(x))
Error: incorrect number of dimensions

Observed heterozygosity of summary(nancycats) is zero

When trying the new version of adegenet, locus-wide observed heterozygosities of the test dataset were all zeros.

library(devtools)
install_github("thibautjombart/adegenet")
data(nancycats)
x <- summary(nancycats)
x$Hobs

Output:
fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37
0 0 0 0 0 0 0 0 0

Installation problems on Yosemite 10.10.3

devtools::install_github('thibautjombart/adegenet')

ERROR: dependencies ‘ade4’, ‘spdep’ are not available for package ‘adegenet’

removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/adegenet’
Error: Command failed (1)
In addition: Warning messages:
1: In utils::install.packages(deps, dependencies = NA, Ncpus = threads) :
installation of package ‘ade4’ had non-zero exit status
2: In utils::install.packages(deps, dependencies = NA, Ncpus = threads) :
installation of package ‘spdep’ had non-zero exit status

DAPC-Server: change cross-validation to submit button input

Currently the cross-validation in DAPC is controlled by a checkbox input. From how I've seen users interact with this feature, a submit button would be more appropriate. The cross-validation is re-run every time any slider is moved and the checkbox is active. It might not be inherent to the user to deactivate the checkbox before moving the sliders, and this results in time spent waiting for mistaken cross-validations to run.

hierarchy namespace clash with igraph

> library("adegenet")
Loading required package: ade4
   ==========================
    adegenet 2.0.0 is loaded
   ==========================

 - to start: type '?adegenet'
 - to browse the adegenet website: type 'adegenetWeb()'
 - to post questions/comments: adegenet-forum@lists.r-forge.r-project.org
 - to report bugs, request features, contribute: http://goo.gl/dZuu5X


> data(microbov)
> hierarchy(microbov)
NULL
Warning message:
Strata must be specified before defining a hierarchy. See ?strata for details. 
> library(igraph)

Attaching package: ‘igraph’

The following object is masked from ‘package:adegenet’:

    hierarchy

> hierarchy(microbov)
Error in slot(x, name) : 
  no slot of name "blockTree" for this object of class "genind"

perhaps we could change it to hier? It becomes much easier to type that way :)

Remove dependency on genetics / re-implement HWE test

I think current dependency is merely for HWE test, which is easy enough to re-implement / remove. Need to check if pegas or hierfstat implements it with @emmanuelparadis and @jgx65 . If so, just move the feature from adegenet -> pegas / hierfstat

seppop changes levels order in @loc.fac

porting documentation to roxygen2

I was thinking of porting the documentation to roxygen2. Would something like this be within the project goals?

add @hierarchy slot and methods

These will come from poppr

Quick issue (or maybe not an issue?)

I thought that "read.fstat" would import the file as a genind object. This doesn't happen (at least when I run "HWE.test" it says that the file isn't a genind object. For running summary stats using functions (basic.stats, and allelic.richness), the analysis will run. But not with HWE.test. This issue can be avoided by using the import2genind function instead of read.fstat.

make print optional for 'summary' of objects

Roman Lustrik [[email protected]]
[Reply] [Reply All] [Forward]
Actions
To:
Jombart, Thibaut

02 February 2015 12:58
You replied on 02/02/2015 13:04.
Dear mr. Jombart,

we have been using adegenet for our analyses for some time and it has become an invaluable tool in our daily routine.
The summary method prints various statements through cat and print which produces a verbose output in e.g. a simulation environment. So far we have been catching the messages through sink(), but we would be grateful if you would consider making output printing optional. I can think of integrating a "verbose" argument that turns off printing or using message() which can be caught through suppressMessages().

Cheers,
Roman

flags for genlight constructor not passed in rbind.genlight or cbind.genlight

Using the example in the documentation:

a <- new("genlight", list(toto=rep(1,10), tata=rep(c(0,1), each=5), titi=c(NA, rep(1,9)) ))
ara <- rbind(a,a) # Works
rbind(a, a, parallel = FALSE) 
## Error in rbind(deparse.level, ...) : 
##  some objects are not genlight objects

allele names in feat sel (dapc server)

In the dapc server, feature selection tab, the names of selected alleles are generic names (e.g. L01,12); actual names would be more useful.

Negative expected heterozygosity values for nancycats.

This is from the master branch. Caught by one of my tests.

> summary(nancycats)

 # Total number of genotypes:  237

 # Population sample sizes:
 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17
10 22 12 23 15 11 14 10  9 11 20 14 13 17 11 12 13

 # Number of alleles per locus:
L1 L2 L3 L4 L5 L6 L7 L8 L9
16 11 10  9 12  8 12 12 18

 # Number of alleles per population:
 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17
36 53 50 67 48 56 42 54 43 46 70 52 44 61 42 40 35

 # Percentage of missing data:
[1] 2.344116

 # Observed heterozygosity:
     fca8     fca23     fca43     fca45     fca77     fca78     fca90     fca96
0.6682028 0.6666667 0.6793249 0.7083333 0.6329114 0.5654008 0.6497890 0.6184211
    fca37
0.4514768

 # Expected heterozygosity:
     fca8     fca23     fca43     fca45     fca77     fca78     fca90     fca96
-2.822527 -3.101081 -3.014881 -2.716926 -8.790725 -5.689321 -6.191750 -4.804451
    fca37
-2.937880

df2genind does not handle missing data correctly.

data("microbov")
micdf <- genind2df(microbov, sep = "/", usepop = FALSE)
mic2 <- df2genind(micdf, sep = "/")
all(colnames(mic2@tab) == colnames(microbov@tab))
## [1] FALSE
all(colnames(mic2@tab) %in% colnames(microbov@tab))
## [1] TRUE
mic2tab <- mic2@tab[, colnames(microbov@tab)]
all.equal(mic2tab, microbov@tab)
## [1] "Attributes: < Component “dimnames”: Component 1: names for current but not for target >"
## [2] "'is.NA' value mismatch: 6325 in current 6385 in target"      
mismatches <- is.na(mic2tab) & !is.na(microbov@tab) | !is.na(mic2tab) & is.na(microbov@tab)
(bad_inds <- which(apply(mismatches, 1, sum) > 0))
## AFBTND223 FRBTBDA35864 FRBTCHA25015 FRBTCHA30886  FRBTMA26321  FRBTMA29948 
##       167          381          426          473          611          622 
(bad_alls <- which(apply(mismatches, 2, sum) > 0))
## HEL13.178 HEL13.182 HEL13.184 HEL13.186 HEL13.188 HEL13.190 HEL13.192 HEL13.194 HEL13.196 
##      176       177       178       179       180       181       182       183       184 
## HEL13.200 
##      185

I attempted to try to fix it, but nothing's working. I believe the problem lies within df2genind since those samples are typed at those loci in the original data set and in micdf

Bug reported by CRAN

Dear maintainers,

This concerns the packages

SASxport adegenet apex gstudio mmod qdapDictionaries

maintained by one of you, which now fail in r-devel due to

\subsection{SIGNIFICANT USER-VISIBLE CHANGES}{
\itemize{
\item \code{nchar(x, *)} gains a new argument \code{keepNA} which
governs how the result for \code{NA}s in \code{x} is determined.
The new default \code{keepNA = NA} returns \code{NA} where
\code{x} is \code{NA}, unless for \code{type = "width"} which still
returns \code{2}, the formatting / printing width of \code{NA}.

  \code{nzchar(x)} gets the same new argument, with default
  \code{keepNA = FALSE} however.  Consequently \code{nzchar(x)} keeps
  returning a non-\code{NA} logical vector, back compatibly.
}

}

Can you please provide updates of your packages which work again under
current r-devel within the next 2 weeks?

When doing so, pls make sure you address all issues shown on your
package check pages.

Best
-k

Check encoding

No package encoding and non-ASCII characters in the following R files:
R/adegenet.package.R
173: #' Moazami-Goudarzi, Denis Lalo, Dominique Pontier, Daniel Maillard, Francois
R/dapc.R
1102: ## There's a bunch of problems down there, commenting it for now
R/datasets.R
503: #' @references Cassar S (2008) Organisation spatiale de la variabilit
504: #' gntique et phnotypique a l'chelle du paysage: le cas du chamois et du
R/glPlot.R
35: ## "plot,genlight: no visible binding for global variable <80><98>y<80><99>"
R/pairDist.R
2: ## airDistPlot.dist: no visible binding for global variable <80><98>groups<80><99>
3: ## pairDistPlot.dist: no visible binding for global variable <80><98>distance<80><99>

Remove .o and .so files from src

The *.o and *.so files prevent installation from source using install_github("thibautjombart/adegenet/pkg").

Here's the error msg:

Error in dyn.load(dllfile) :
  unable to load shared object '/Users/zhian/Documents/adegenet/pkg/src/adegenet.so':
  dlopen(/Users/zhian/Documents/adegenet/pkg/src/adegenet.so, 6): no suitable image found.  Did find:
    /Users/zhian/Documents/adegenet/pkg/src/adegenet.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00

removing these files will allow installation for users who have a C compiler.

compile, clean, debug: genomics tutorial

is this behavior in subsetting loci from genind object by design?

Hello,

I was wondering if subsetting based on loci names is not possible by design? It works for subsetting based on "position" (L1, L2...).

library(adegenet)
data(nancycats)
nancycats[, loc = "L1"] # works
nancycats[, loc = "fca8"] # doesn't work

DAPC: add variable loadings as option

So far we have (unsigned) variable contributions as an option. The signed contributions would be useful too.

Recompile tutorials with new version

This will probably need a few tweaks as some previously available functions have disappeared.

Change genind using integers for @tab

I'm on it.

import2genind() taking very long

R version 3.1.1
Adegenet version 2.0.0

The import2genind('input.stru') is taking too long on big data sets. For example, one of my data set has 94K markers and 242 individuals. This file is being converted to genind since yesterday morning and it still not has finished. I tried this on two computers with same result. The data file itself seems ok because STRUCTURE runs fine on it.

I am happy to provide further information. Thanks.

Retaining original locus names

Version: 2.0

When importing a structure data set as a genind object, original locus names are discarded and replaced with generic names. Adegenet does assign unique generic names and when markers removed due to being 'entirely nontype' etc, the generic names aren't reshuffled (which is good and very important).

But the fix we really need is retention of original names i.e. truenames. This is particularly necessary for data sets with very large number of loci. Linking generic names back to actual names is cumbersome.

mygenind <- import2genind('input.str', onerowperind=F, n.ind=5, n.loc=10, col.lab=1, col.pop=2, ask=F)
mygenind

#####################

Genind object

#####################

genotypes of individuals -

S4 class: genind
@call: read.structure(file = file, n.ind = 5, n.loc = 10, onerowperind = ..1,
col.lab = 1, col.pop = 2, ask = ..6, quiet = quiet)

@tab: 5 x 20 matrix of genotypes

@ind.names: vector of 5 individual names
@loc.names: vector of 20 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the 20 columns of @tab
@all.names: list of 20 components yielding allele names for each locus
@ploidy: 2 2 2 2 2 2
@type: codom

Optional contents:
@strata: - empty -
@hierarchy: - empty -
@pop: factor giving the population of each individual
@pop.names: character giving the name of each population
@other: - empty -

[email protected]
"L0001" "L0002" "L0003" "L0004" "L0005" "L0006" "L0007" "L0008" "L0009" "L0010"

FDIST2: adaptive divergence based on Fst

The ability to run "outlier test" (1: for critical review) with large SNP dataset would serve a large community.
Outlier test define adaptive SNPs with Fst value that exceed the permutated value of similar (similare He) SNP. It is commonly used and woudl be of value to many evolutionary biologisd

Additionally, permutation of the perumtations would be great.

1: Lotterhos, K. E. and M. C. Whitlock, Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests. Molecular Ecology, 2014. 23: p. 2178-2192.

compile, clean, debug: dapc tutorial

We need to make sure the tutorials work with the new version. DAPC should be fairly straightforward.

genind2df

genind2df conversion fails for microbov and rupica:

genind2df(microbov)

issue seems to be in function recod within genind2df

inbreeding example doesnt work

>   ## cattle breed microsatellite data
>      data(microbov)
>      
>      ## isolate Lagunaire breed
>      lagun <- seppop(microbov)$Lagunaire
>      
>      ## estimate inbreeding - return sample of F values
>      Fsamp <- inbreeding(lagun, N=30)
Error in apply(tabfreq2, 1, tapply, x$loc.fac, sum) : 
  dim(X) must have a positive length

try compiler to speedup stuff

List of things to try:

df2genind
genind2df
??? (feel free to complete)

DAPC server: add data.frame input

In the DAPC server: we need to be able to input non-genetic data. Basic form could be a data.frame with a column indicating groups.

is.genind() prints duplicate sample names

I noticed is.genind() prints duplicate sample names. Issuing a warning would perhaps be enough? Another option would be to use message() to "print" duplicated sample names, in which case user is able to suppress the message through suppressMessages().

data(nancycats)
xy <- nancycats[c(1, 1, 2, 3)]
is.genind(xy)
N215
2
[1] TRUE
Warning message:
In validityMethod(object) :
duplicate names in ind.names:

suppressWarnings(is.genind(xy))
N215
2
[1] TRUE

importFrom for spdep

Currently importing all spdep causes a conflict coz of mstree in both ade4 and spdep.

yeahhh

jndkfjbdkjfbdkj

change methods to camelCase

Stylistically synched with the rest of adegenet.

setpop -> setPop
addstrata -> addStrata
splitstrata -> splitStrata
namestrata -> nameStrata

compile, clean, debug: spatial tutorial

possible bug in hybridize

From: [email protected] [[email protected]] on behalf of Benjamin Alric [[email protected]]
Sent: 21 February 2015 16:59
To: [email protected]
Subject: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and

Dear all,

I would like simulated hybridization between two population to assess
the power of admixture analysis (STRUCTURE).
I built two subsamples consisting of 30 indivudals showing the highest q
values for the cluster1 or cluster2 of previously STRUCTURE analysis.
From these two subsamples I would like simulated hybridization (using
hybridize function of the adegenet R package) to assess the power of
admixture analysis.
For each population, genotype were determined through 8 microsatellite
loci for wichi one allele is code by a character string of 3 numbers.
Here you are the command:

Dg<-import2genind("B_Dg.gtx",package="adegenet")
Dl<-import2genind("B_Dl.gtx",package="adegenet")
Dg<- #####################
### Genind object ###
#####################

genotypes of individuals -

S4 class: genind
@call: read.genetix(file = file, missing = missing, quiet = quiet)

@tab: 30 x 33 matrix of genotypes

@ind.names: vector of 30 individual names
@loc.names: vector of 8 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the 33 columns of @tab
@all.names: list of 8 components yielding allele names for each locus
@ploidy: 2
@type: codom

Optional contents:
@pop: factor giving the population of each individual
@pop.names: factor giving the population of each individual

@other: - empty -

Dl<-#####################
### Genind object ###
#####################

genotypes of individuals -

S4 class: genind
@call: read.genetix(file = file, missing = missing, quiet = quiet)

@tab: 30 x 33 matrix of genotypes

Optional contents:
@pop: factor giving the population of each individual
@pop.names: factor giving the population of each individual

@other: - empty -

hybrdis<-hybridize(Dg,Dl,n=100,pop="Hybrids")
g1<-genind2df(hybrids)
g1<-
pop 10_14 Dp512 SwiD1 SwiD10
SwiD12 SwiD14 SwiD15 SwiD5
h001 Hybrids 226226 129 131143 194201 112119
181185 093098 161161165
h002 Hybrids 220226 129 126138 200201 112 175
181181 089098 151153165
h003 Hybrids 220226 129 126134143 200 123123 185185
093098 153163165
h004 Hybrids 220226 129 126131 200201 119123
185185 093098 153153165
h005 Hybrids 220226 129 126136136 199 123123 181185
089098 153161165
h006 Hybrids 226226 129129 136136 194 112112 181181
089098 153161165
h007 Hybrids 220226 129133 134143 194 119 175
181185 093 151153163165
....

We would expect to see two allele for each locus but it is not the case
for all microsatellite loci.
Somebody know why and where does the problem?

I checked the example dataset "microbov" for hybridize function, and I
see that temp$Salers and temp$Zebu (used to perform simulated
hybridization with hybridize function) presented the same count of
alleles at each locus.
When I check now my two datasets, I see that there are not the same
number of allele between the two populations. such a difference in the
number of allele between the two population could be the origne of the
problem...

[email protected]
$L1
1 2 3
"220" "226" "231"

$L2
1 2 3
"125" "129" "133"

$L3
1 2 3 4 5 6
"126" "131" "134" "136" "138" "143"

[email protected]
$L1
1 2 3
"223" "226" "229"

$L2
1 2 3 4 5 6
"129" "133" "136" "137" "138" "139"

$L3
1 2 3 4 5 6 7
"118" "134" "136" "138" "145" "150" "152"

Thank in advence for your help.

Sincerely yours,

Benjamin ALRIC

compile, clean, debug: basics tutorial

Create short vignette for strata

This could largely be lifted from Section 2.1 of poppr's Data import and manipulation vignette with some tweaking.

formatting DESCRIPTION

The Title field should be in title case, current version then in title case:
‘adegenet: an R Package for the Exploratory Analysis of Genetic and Genomic Data’
‘Adegenet: An R Package for the Exploratory Analysis of Genetic and Genomic Data’

The Description field should not start with the package name,
'This package' or similar.

The Date field is not in ISO 8601 yyyy-mm-dd format.

checking package namespace information ... OK

bug in xval DAPC server - max nb PCs

In the dapc server X val, setting the max number of PCs to less than the default triggers an error.

register S3 methods

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
as.POSIXct.haploGen as.data.frame.genind as.data.frame.genlight
as.data.frame.genpop as.integer.SNPbin as.lda.dapc as.list.genlight
as.matrix.genind as.matrix.genlight as.matrix.genpop c.SNPbin
colorplot.default colorplot.spca dapc.data.frame dapc.dudi
dapc.genind dapc.genlight dapc.matrix find.clusters.data.frame
find.clusters.genind find.clusters.genlight find.clusters.matrix
findMutations.DNAbin gengraph.DNAbin gengraph.default gengraph.dist
gengraph.genind gengraph.genpop gengraph.matrix
get.likelihood.seqTrack graphMutations.DNAbin labels.haploGen
loadingplot.default loadingplot.glPca pairDistPlot.DNAbin
pairDistPlot.default pairDistPlot.dist pairDistPlot.genind
pairDistPlot.matrix plot.haploGen plot.monmonier plot.seqTrack
plot.spca predict.dapc print.dapc print.glPca print.haploGen
print.monmonier print.spca scatter.dapc scatter.glPca screeplot.spca
seqTrack.default seqTrack.haploGen seqTrack.matrix
snpposi.plot.DNAbin snpposi.plot.integer snpposi.plot.numeric
snpposi.test.DNAbin snpposi.test.integer snpposi.test.numeric
summary.dapc summary.spca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

importing objects from readVCF (pegas) into genlight objects

repool and hybridize assume ploidy vector of length 1. Problem with df2genind

Coming from the repool examples:

zebler <- hybridize(temp$Salers, temp$Zebu, n=40)
Error in `colnames<-`(`*tmp*`, value = c("167", "171", "173", "175", "177",  : 
  length of 'dimnames' [2] not equal to array extent
In addition: Warning messages:
1: In if (x1@ploidy%%2 != 0) stop("not implemented for odd levels of ploidy") :
  the condition has length > 1 and only the first element will be used
2: In if (x2@ploidy != x1@ploidy) stop("not implemented for genotypes with different ploidy levels") :
  the condition has length > 1 and only the first element will be used

Repooling populations.

repool(temp$Somba, temp$Zebu)
 Error in df2genind(tab, pop = pop, ploidy = x[[1]]@ploidy, type = x[[1]]@type) : 
  Not enough information to convert data: please indicate the separator (sep=...) or the number of characters coding an allele (ncode=...)

Add method to check if hierarchy is hierarchical.

The hierarchy slot currently will store a formula defining what levels of the strata slot are hierarchical. One thing that we do not have implemented is a method to actually confirm that the the assigned levels are indeed hierarchical. If I recall, both @jgx65 and @EricArcher have devised methods to address this. Once written, the method could be placed in this line of code.

The function should ideally take in a data frame representing the hierarchy and return TRUE or FALSE.

Output of allele freq, changes in allele freq

Output of some standard population genetics data that is already calculated:
For each locus:
SNP minor/major allele freq/pop,
changes in allele frequency,
Fst/loci,
N

propShared calculation incorrect

The function propShared returns incorrect results.
From the example in version 2.0:

> data(microbov)
> obj <- microbov[1:5, loc = locNames(microbov)[1:2]]
> propShared(obj)
            AFBIBOR9503 AFBIBOR9504 AFBIBOR9505 AFBIBOR9506 AFBIBOR9507
AFBIBOR9503         1.0         1.0         1.0         1.5         1.0
AFBIBOR9504         1.0         1.0         1.5         1.5         1.5
AFBIBOR9505         1.0         1.5         1.0         1.5         2.0
AFBIBOR9506         1.5         1.5         1.5         1.0         1.5
AFBIBOR9507         1.0         1.5         2.0         1.5         1.0

From version 1.3:

> data(microbov)
> obj <- microbov[1:5,microbov@loc.fac %in% c("L01","L02")]
> propShared(obj)
            AFBIBOR9503 AFBIBOR9504 AFBIBOR9505 AFBIBOR9506 AFBIBOR9507
AFBIBOR9503        1.00        0.50        0.50        0.75        0.50
AFBIBOR9504        0.50        1.00        0.75        0.75        0.75
AFBIBOR9505        0.50        0.75        1.00        0.75        1.00
AFBIBOR9506        0.75        0.75        0.75        1.00        0.75
AFBIBOR9507        0.50        0.75        1.00        0.75        1.00

Function to convert old data to version 2.0

I don't know if this should be a function or simply just a gist, but to help people convert from adegenet 1.4 to 2.0, should we include a couple of converter functions that will add slots and reparse data to be in the right format?

I have a function called data_replacer in this gist that will convert genind (and genclone) objects, but one would need to be created for genlight objects (not too hard, just adding hierarchy and strata slots).

Again, should this be a formal set of functions or should we just point the users to a gist that they can download and run?

unable to install package through devtools, works through console

I'm trying to install adegenet package using install_github(), but I get a few errors. I'm able to install the package if I build and install the package from console. For the latter output see below. I'm using 64-bit Windows 7. I wonder to what can we attribute the discrepancy between these two ways of installing a package?

Installation through devtools (fail)

> install_github("thibautjombart/adegenet/pkg")
Downloading github repo thibautjombart/adegenet@master
Installing adegenet
"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" --vanilla CMD INSTALL  \
  "C:/Users/romunov/AppData/Local/Temp/RtmpSo6w8C/devtools15882f7c4022/thibautjombart-adegenet-8cca9e1/pkg"  \
  --library="C:/Users/romunov/Documents/R/win-library/3.1" --install-tests 

* installing *source* package 'adegenet' ...
** libs

*** arch - i386
gcc -m32 -shared -s -static-libgcc -o adegenet.dll tmp.def GLfunctions.o adesub.o monmonier-utils.o sharedAll.o snpbin.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lR
Cannot export AreaSign: symbol not found
Cannot export Assignpx: symbol not found
Cannot export Between: symbol not found
Cannot export CheckAllSeg: symbol not found
Cannot export Collinear: symbol not found
Cannot export DiagobgComp: symbol not found
Cannot export GLdotProd: symbol not found
Cannot export GLsumFreq: symbol not found
Cannot export GLsumInt: symbol not found
Cannot export NEARZERO: symbol not found
Cannot export Parallel: symbol not found
Cannot export SegSeg: symbol not found
Cannot export alea: symbol not found
Cannot export aleapermutmat: symbol not found
Cannot export aleapermutvec: symbol not found
Cannot export binIntToBytes: symbol not found
Cannot export byteToBinDouble: symbol not found
Cannot export byteToBinInt: symbol not found
Cannot export bytesToBinInt: symbol not found
Cannot export bytesToDouble: symbol not found
Cannot export bytesToInt: symbol not found
Cannot export dAbs: symbol not found
Cannot export dEqual: symbol not found
Cannot export dtodelta: symbol not found
Cannot export freeinttab: symbol not found
Cannot export freeintvec: symbol not found
Cannot export freetab: symbol not found
Cannot export freevec: symbol not found
Cannot export genlightTogenlightC: symbol not found
Cannot export getpermutation: symbol not found
Cannot export initvec: symbol not found
Cannot export makesnpbin: symbol not found
Cannot export matcentrage: symbol not found
Cannot export matmodifcm: symbol not found
Cannot export matmodifcn: symbol not found
Cannot export matmodifcp: symbol not found
Cannot export matmodifcs: symbol not found
Cannot export matmodiffc: symbol not found
Cannot export matpermut: symbol not found
Cannot export maxvec: symbol not found
Cannot export min_int: symbol not found
Cannot export nLoc: symbol not found
Cannot export nb_shared_all: symbol not found
Cannot export ploidy: symbol not found
Cannot export printsnpbin: symbol not found
Cannot export prodmatAAtB: symbol not found
Cannot export prodmatABC: symbol not found
Cannot export prodmatAtAB: symbol not found
Cannot export prodmatAtBC: symbol not found
Cannot export prodmatAtBrandomC: symbol not found
Cannot export sharedAll: symbol not found
Cannot export snpbin2freq: symbol not found
Cannot export snpbin2intvec: symbol not found
Cannot export snpbin_dotprod_freq: symbol not found
Cannot export snpbin_dotprod_int: symbol not found
Cannot export snpbin_isna: symbol not found
Cannot export sqrvec: symbol not found
Cannot export taballoc: symbol not found
Cannot export tabintalloc: symbol not found
Cannot export testRaw: symbol not found
Cannot export testSizePointer: symbol not found
Cannot export traceXtdLXq: symbol not found
Cannot export trild: symbol not found
Cannot export trildintswap: symbol not found
Cannot export trildswap: symbol not found
Cannot export trirap: symbol not found
Cannot export trirapideint: symbol not found
Cannot export trirapideintswap: symbol not found
Cannot export vecalloc: symbol not found
Cannot export vecintalloc: symbol not found
Cannot export vecpermut: symbol not found
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `GLfunctions.o' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `adesub.o' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `monmonier-utils.o' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `sharedAll.o' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `snpbin.o' is incompatible with i386 output
GLfunctions.o: In function `GLsumInt':
/home/thibaut/dev/adegenet/pkg/src/GLfunctions.c:85: undefined reference to `calloc'
GLfunctions.o: In function `GLsumFreq':
/home/thibaut/dev/adegenet/pkg/src/GLfunctions.c:116: undefined reference to `calloc'
adesub.o: In function `tabintalloc':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:58: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:63: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:66: undefined reference to `free'
adesub.o: In function `freeinttab':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:92: undefined reference to `free'
adesub.o: In function `alea':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:148: undefined reference to `rand'
adesub.o: In function `freetab':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:450: undefined reference to `free'
adesub.o: In function `sqrvec':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:950: undefined reference to `sqrt'
adesub.o: In function `taballoc':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:962: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:964: undefined reference to `calloc'
adesub.o: In function `vecalloc':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:1098: undefined reference to `calloc'
adesub.o: In function `matmodifcs':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:663: undefined reference to `sqrt'
adesub.o: In function `matmodifcn':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:611: undefined reference to `sqrt'
adesub.o: In function `DiagobgComp':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:369: undefined reference to `sqrt'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:245: undefined reference to `sqrt'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:357: undefined reference to `sqrt'
adesub.o:/home/thibaut/dev/adegenet/pkg/src/adesub.c:339: more undefined references to `sqrt' follow
adesub.o: In function `vecintalloc':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:1111: undefined reference to `calloc'
adesub.o: In function `getpermutation':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:491: undefined reference to `clock'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:493: undefined reference to `srand'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:495: undefined reference to `rand'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:491: undefined reference to `clock'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:493: undefined reference to `srand'
adesub.o: In function `freeinttab':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:95: undefined reference to `free'
adesub.o: In function `freeintvec':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:437: undefined reference to `free'
adesub.o: In function `freetab':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:452: undefined reference to `free'
adesub.o: In function `freevec':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:460: undefined reference to `free'
snpbin.o: In function `byteToBinInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:105: undefined reference to `pow'
snpbin.o: In function `byteToBinDouble':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:128: undefined reference to `pow'
snpbin.o: In function `bytesToBinInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:146: undefined reference to `calloc'
snpbin.o: In function `bytesToInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:185: undefined reference to `calloc'
snpbin.o: In function `bytesToDouble':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:213: undefined reference to `calloc'
snpbin.o: In function `binIntToBytes':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:253: undefined reference to `pow'
snpbin.o: In function `snpbin2intvec':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:315: undefined reference to `calloc'
snpbin.o: In function `snpbin2freq':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:330: undefined reference to `calloc'
snpbin.o: In function `printsnpbin':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:349: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:354: undefined reference to `Rprintf'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:357: undefined reference to `Rprintf'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:359: undefined reference to `Rprintf'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:363: undefined reference to `Rprintf'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:365: undefined reference to `Rprintf'
snpbin.o: In function `snpbin_dotprod_int':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:399: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:400: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:429: undefined reference to `free'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:430: undefined reference to `free'
snpbin.o: In function `snpbin_dotprod_freq':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:446: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:447: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:476: undefined reference to `free'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:477: undefined reference to `free'
snpbin.o: In function `genlightTogenlightC':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:494: undefined reference to `calloc'
snpbin.o: In function `testSizePointer':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:540: undefined reference to `calloc'
snpbin.o: In function `bytesToBinInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:156: undefined reference to `free'
snpbin.o: In function `bytesToInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:203: undefined reference to `free'
snpbin.o: In function `bytesToDouble':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:230: undefined reference to `free'
snpbin.o: In function `snpbin2intvec':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:318: undefined reference to `free'
snpbin.o: In function `snpbin2freq':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:338: undefined reference to `free'
snpbin.o:/home/thibaut/dev/adegenet/pkg/src/snpbin.c:369: more undefined references to `free' follow
collect2: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'adegenet'
* removing 'C:/Users/romunov/Documents/R/win-library/3.1/adegenet'
* restoring previous 'C:/Users/romunov/Documents/R/win-library/3.1/adegenet'
 Show Traceback

 Rerun with Debug
 Error: Command failed (1)

Installation from the console.

This is the check log:

* using log directory 'D:/R/adegenet.Rcheck'
* using R version 3.1.2 (2014-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: CP1250
* checking for file 'adegenet/DESCRIPTION' ... OK
* this is package 'adegenet' version '1.4-3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'adegenet' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data    2.6Mb
    files   1.6Mb
* checking package 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... NOTE
HWE.test.genind : ftest: no visible global function definition for
  'HWE.chisq'
HWE.test.genind : ftest: no visible global function definition for
  'genotype'
alignment2genind: no visible binding for global variable 's2c'
chooseCN: no visible global function definition for 'tri2nb'
chooseCN: no visible global function definition for 'gabrielneigh'
chooseCN: no visible global function definition for 'graph2nb'
chooseCN: no visible global function definition for 'relativeneigh'
chooseCN: no visible global function definition for 'dnearneigh'
chooseCN: no visible global function definition for 'knearneigh'
chooseCN: no visible global function definition for 'knn2nb'
chooseCN: no visible global function definition for 'nb2listw'
chooseCN: no visible global function definition for 'mat2listw'
fasta2DNAbin: no visible global function definition for 'seg.sites'
fasta2genlight: no visible global function definition for 'mclapply'
fstat: no visible global function definition for 'varcomp.glob'
genind2genotype : f2: no visible global function definition for
  'as.genotype'
genind2genotype: no visible global function definition for
  'makeGenotypes'
glPca: no visible global function definition for 'mclapply'
gstat.randtest: no visible global function definition for
  'g.stats.glob'
gstat.randtest : <anonymous>: no visible global function definition for
  'g.stats.glob'
gstat.randtest : <anonymous>: no visible global function definition for
  'samp.within'
gstat.randtest : <anonymous>: no visible global function definition for
  'samp.between'
plot.spca: no visible global function definition for 'card'
read.PLINK: no visible global function definition for 'mclapply'
read.snp: no visible global function definition for 'mclapply'
snpposi.plot.DNAbin: no visible global function definition for
  'seg.sites'
snpposi.test.DNAbin: no visible global function definition for
  'seg.sites'
spca: no visible global function definition for 'mat2listw'
spca: no visible global function definition for 'nb2listw'
summary.spca: no visible global function definition for 'listw2mat'
summary.spca: no visible binding for global variable 'lag.listw'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING

  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                  old_size new_size compress
  H3N2.RData         108Kb     49Kb       xz
  dapcIllus.RData     84Kb     38Kb    bzip2
  eHGDP.RData        2.2Mb    1.1Mb    bzip2
  microbov.RData      57Kb     29Kb    bzip2
  rupica.RData        43Kb     31Kb       xz
  sim2pop.RData       10Kb      7Kb    bzip2
  spcaIllus.RData     29Kb     16Kb    bzip2
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File 'adegenet/libs/i386/adegenet.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'adesub.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'adesub.o'
File 'adegenet/libs/x64/adegenet.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'adesub.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'adesub.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the C RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE
WARNING: There was 1 warning.
NOTE: There were 3 notes.

and the installation process

D:\R>R CMD INSTALL --build adegenet_1.4-3.tar.gz                                
* installing to library 'C:/Users/romunov/Documents/R/win-library/3.1'          
* installing *source* package 'adegenet' ...                                    
** libs                                                                         

*** arch - i386                                                                 
cygwin warning:                                                                 
  MS-DOS style path detected: C:/PROGRA~1/R/R-31~1.2/etc/i386/Makeconf          
  Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-31~1.2/etc/i386/Makeco
nf                                                                              
  CYGWIN environment variable option "nodosfilewarning" turns off this warning. 
  Consult the user's guide for more details about POSIX paths:                  
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames                  
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c G
Lfunctions.c -o GLfunctions.o                                                   
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c a
desub.c -o adesub.o                                                             
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c m
onmonier-utils.c -o monmonier-utils.o                                           
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c s
haredAll.c -o sharedAll.o                                                       
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c s
npbin.c -o snpbin.o                                                             
gcc -m32 -shared -s -static-libgcc -o adegenet.dll tmp.def GLfunctions.o adesub.
o monmonier-utils.o sharedAll.o snpbin.o -Ld:/RCompile/CRANpkg/extralibs64/local
/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/b
in/i386 -lR                                                                     
installing to C:/Users/romunov/Documents/R/win-library/3.1/adegenet/libs/i386   

*** arch - x64                                                                  
cygwin warning:                                                                 
  MS-DOS style path detected: C:/PROGRA~1/R/R-31~1.2/etc/x64/Makeconf           
  Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-31~1.2/etc/x64/Makecon
f                                                                               
  CYGWIN environment variable option "nodosfilewarning" turns off this warning. 
    Consult the user's guide for more details about POSIX paths:                  
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames                  
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c G
Lfunctions.c -o GLfunctions.o                                                   
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c a
desub.c -o adesub.o                                                             
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c m
onmonier-utils.c -o monmonier-utils.o                                           
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c s
haredAll.c -o sharedAll.o                                                       
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP    -I"d:/R
Compile/CRANpkg/extralibs64/local/include"     -O2  -std=gnu99 -mtune=core2 -c s
npbin.c -o snpbin.o                                                             
gcc -m64 -shared -s -static-libgcc -o adegenet.dll tmp.def GLfunctions.o adesub.
o monmonier-utils.o sharedAll.o snpbin.o -Ld:/RCompile/CRANpkg/extralibs64/local
/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bi
n/x64 -lR                                                                       
installing to C:/Users/romunov/Documents/R/win-library/3.1/adegenet/libs/x64    
** R                                                                            
** data                                                                         
** inst                                                                         
** preparing package for lazy loading                                           
Creating a generic function for 'plot' from package 'graphics' in package 'adege
net'                                                                            
** help                                                                         
*** installing help indices                                                     
** building package indices                                                     
** testing if installed package can be loaded                                   
*** arch - i386                                                                 
*** arch - x64                                                                  
* MD5 sums                                                                      
packaged installation of 'adegenet' as adegenet_1.4-3.zip                       
* DONE (adegenet)

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