thierrygosselin
commented
2 years ago Hi Amandine, Sorry for the bug, I know exactly what is the bug and thought it was fix. I'll have a new release ready in about 1 hour. Best Thierry
Closed CornilleAmandine closed 1 year ago
thierrygosselin
commented
2 years ago Hi Amandine, Sorry for the bug, I know exactly what is the bug and thought it was fix. I'll have a new release ready in about 1 hour. Best Thierry
CornilleAmandine
commented
2 years ago Super thanks a lot ! best, Amandine
On Fri, 17 Dec 2021 at 15:21, Thierry Gosselin @.***> wrote:
Hi Amandine, Sorry for the bug, I know exactly what is the bug and thought it was fix. I'll have a new release ready in about 1 hour. Best Thierry
— Reply to this email directly, view it on GitHub https://github.com/thierrygosselin/radiator/issues/145#issuecomment-996759122, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYVPNQRM4XG57HLR4SDURNBOVANCNFSM5KIMATJQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
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Twitter: @CornilleAmand or @PommierVerger Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/eclectic/ On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297 or @PommierVerger
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CornilleAmandine
commented
2 years ago Hi Thierry, Just to be sure: I just have to re-install the new release right? Because I tried to run it and I still have the same problem. Thanks!! best, Amandine
On Fri, 17 Dec 2021 at 15:23, Amandine Cornille @.***> wrote:
Super thanks a lot ! best, Amandine
On Fri, 17 Dec 2021 at 15:21, Thierry Gosselin @.***> wrote:
Hi Amandine, Sorry for the bug, I know exactly what is the bug and thought it was fix. I'll have a new release ready in about 1 hour. Best Thierry
— Reply to this email directly, view it on GitHub https://github.com/thierrygosselin/radiator/issues/145#issuecomment-996759122, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYVPNQRM4XG57HLR4SDURNBOVANCNFSM5KIMATJQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
You are receiving this because you authored the thread.Message ID: @.***>
-- Leader of the ECLECTIC "Ecological genomics of multi-species interactions" group CNRS Researcher Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52
Twitter: @CornilleAmand or @PommierVerger Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/eclectic/ On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297 or @PommierVerger
Tout message que j’envoie en dehors des heures de travail réglementaires ne nécessite aucune réponse immédiate
-- Leader of the ECLECTIC "Ecological genomics of multi-species interactions" group CNRS Researcher Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52
Twitter: @CornilleAmand or @PommierVerger Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/eclectic/ On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297 or @PommierVerger
Tout message que j’envoie en dehors des heures de travail réglementaires ne nécessite aucune réponse immédiate
thierrygosselin
commented
2 years ago remove the package and re-install the new release (v. 1.2.2)
Should work, but the arlequin file was not tested in arlequin.
Please re-open the issue if you're still experiencing a problem.
CornilleAmandine
commented
2 years ago Hi,
Super Thanks!
There is no error message, but a warning message (see below), the . arp (see below) is generated, BUT the arlequin output generated is a weird mixing of number and letter, and when I run it with arlsumstat it does not work then, here an example:
###OUTPUT RADIATOR:
################################################################################ ######################### radiator::genomic_converter ########################## ################################################################################ Execution @.: @. Folder created: @. Function call and arguments stored in: @. Filters parameters file generated: @.***
Importing data: vcf.file
Reading VCF...
Data summary: number of samples: 160 number of markers: 374506
Filter monomorphic markers Number of individuals / strata / chrom / locus / SNP: Blacklisted: 0 / 0 / 0 / 164690 / 164690
Filter common markers: Number of individuals / strata / chrom / locus / SNP: Blacklisted: 0 / 0 / 0 / 881 / 881
Generating individual stats... Generating markers stats... [==================================================] 100%, completed, 1s [==================================================] 100%, completed, 1s
Number of chromosome/contig/scaffold: 1 Number of locus: 208935 Number of markers: 208935 Number of strata: 8 Number of individuals: 160
Number of ind/strata: X = 24 Y = 7 Z = 29 A = 37 B = 17 C = 10 D = 9 E = 27
Number of duplicate id: 0 radiator Genomic Data Structure (GDS) file: @.***
Genotypes formats generated with 208935 SNPs: GT_BIN (the dosage of ALT allele: 0, 1, 2 NA): TRUE GT_VCF (the genotype coding VCFs: 0/0, 0/1, 1/1, ./.): TRUE GT_VCF_NUC (the genotype coding in VCFs, but with nucleotides: A/C, ./.): TRUE GT (the genotype coding 'a la genepop': 001002, 001001, 000000): TRUE LOCUS field empty... adding unique id instead
Tidy data file written: @.***
Computation time, overall: 116 sec
Writing tidy data set: @.***
Preparing data for output
Data is bi-allelic Calibrating REF/ALT alleles... Generating arlequin file File written: @.***_arlequin.csv ################################### RESULTS #################################### Data format of input: vcf.file Biallelic data Number of markers: 208935 Number of chromosome/contig/scaffold: 1 Number of strata: 8 Number of individuals: 160
Computation time, overall: 1300 sec ######################### completed genomic_converter ##########################
Warning messages:1: Unknown or uninitialised column: LOCUS.
2: Unknown or uninitialised column: VARIANT_ID
###################EXAMPLE ARLEQUIN CONVERTED [Profile] Title = "radiator_arlequin_export @.** " NbSamples = 8 GenotypicData = 1 LocusSeparator = WHITESPACE GameticPhase = 0 MissingData = '?' DataType = STANDARD [Data] [[Samples]] SampleName = "X" SampleSize = 27 SampleData = { 0-XX-01 001 002 AAA CTC 001 CTA 003 003 004 GTG 003 003 ACT 004 GAG* AGT 004 002 001 003 002 003 ATG ATT ATG 003 002 004 002 002 003 002 001 002 001 001 001 002 GTC 003 004 004 004 001 001 004 001 004 004 CAC TCA AAA TCT 003 004 001 002 001 001 004 003 001 AAT TTC 002 001 003 003 003 002 001 003 001 002 002 001 002 003 003 003 004 004 004 004 GCT 001 003 TAA TAA 003 001 003 002 001 001 GAA 002 004 004 002 AAT 003 001 GTG 003 002 001 002 003 003 002 003 002 004 003 001 001 002 001 002 GTG 003 004 003 001 002 004 002 002 004 002 003 003 002 003 001 001 003 004 CAA 003 ACA 002 001 TCC TCA 003 GAA 001 ATT 004 004 004 002 004 002 002 002 003 003 GCT 004 004 GAA 004 002 AGC 003 003 002 002 004 004 002 004 004 004 CAG 004 -9 004 CGT 003 GTC 001 002 002 004 004 001 003 001 004 001 ACG 004 TTT AAC 002 AAA TCT GTG 003 ACT 002 CGT GGT GCT AAA AGG 004 003 002 GAG 003 003 003 004 001 004 003 004 002 004 AAT 003 AAA TTG AGA AGA AAA ACA 003 TTA ATT 002 002 002 001 002 002 003 001 002 002 002 004 002 001 001 003 001 001 002 003 004 003 003 GAG 003 003 002 004 001 001 002 004 002 004 001 002 004 001 003 003 004 001 001 002 003 004 004 002 004 003 TCC TAA 004 001 004 CGA 001 003 003 004 003 CAT 004 002 001 GGA GGG 002 002 TCT GAG 004 002 003 004 001 001 003 AGA 001 002 004 001 CAT GGT CGC ATG ACA CAA 004 002 CAA CAC TTA CTA 004 AGC TTT 002 004 003 004 TCT 001 TAA GCA GAA 003 TAA TGC 001 CAA TGA ATA 002 004 ATG CTT 002 003 GTC TCC ATC 001 002 GAA 003 004 003 ACA ATA 004 003 003 CAC TCT 002 001 002 ACC 003 002 003 CAA 001 002 TCT 001 TTG TTT GCA 002 002 004 003 TTG 004 TAT ACT 003 CAA TAG 002 002 004 004 003 002 CAC 003 001 001 002 002 002 001 004 001 GGG 002 AGT 001 002 002 003 004 003 ATA 003 002 AAA 002 002 AGG 004 001 001 001 002 001 003 TGC 004 001 AGA 002 GTC 003 002 004 003 003 003 001 002 ATG 004 002 TCC CAC 003 TAT 003
Indels have been removed FYI.
Any ideas? Thanks! best, Amandine
On Mon, 20 Dec 2021 at 20:23, Thierry Gosselin @.***> wrote:
remove the package and re-install the new release (v. 1.2.2)
Should work, but the arlequin file was not tested in arlequin.
Please re-open the issue if you're still experiencing a problem.
— Reply to this email directly, view it on GitHub https://github.com/thierrygosselin/radiator/issues/145#issuecomment-998206747, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYQ3BKE3QV53OOA3TLTUR57EJANCNFSM5KIMATJQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
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Twitter: @CornilleAmand or @PommierVerger Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/eclectic/ On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297 or @PommierVerger
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thierrygosselin
commented
2 years ago Hum, I did the test with a Genepop and genind file. Will try with some of my VCFs
CornilleAmandine
commented
2 years ago ok thanks!! Any results from these tests? Thanks best, Amandine
On Wed, 22 Dec 2021 at 15:54, Thierry Gosselin @.***> wrote:
Hum, I did the test with a Genepop and genind file. Will try with some of my VCFs
— Reply to this email directly, view it on GitHub https://github.com/thierrygosselin/radiator/issues/145#issuecomment-999634585, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYU6L4ROCRDNPXVTK3TUSHRBXANCNFSM5KIMATJQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
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Twitter: @CornilleAmand or @PommierVerger Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/eclectic/ On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297 or @PommierVerger
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dferran1
commented
2 years ago Hello,
I am having the same error when trying to read in a vcf file and save the output in the "hierfstat" format. I am on version 1.2.2. When I run rlang::last_trace() it seems to show the issue as coming from dplyr::arrange(., MARKERS, POP_ID, INDIVIDUALS).
Do I need to reformat my vcf file somehow?
Best,
David
thierrygosselin
commented
2 years ago no I'll check more
thierrygosselin
commented
1 year ago works on my end Update radiator and if you still have a problem, re-open issue following guidelines so that I can reproduce the bug
Hi,
I am trying ton convert a vcf in .arp, and I got this error message.
_Generating arlequin file Error: Can't subset columns that don't exist. x Column
POP_IDdoesn't exist_**Here the complete script I cannot send the vcf file (too big), but I put the strata file"**
vcf <- read.vcfR( "dianthus_select_02_Dcar.vcf.gz", verbose = FALSE ) strata<-read.table("strata.txt", header=T)
test1 <- radiator::genomic_converter( data = "dianthus_select_02_Dcar.vcf.gz", strata = strata, output = "arlequin", parallel.core = 1L )
* the complete error message
################################################################################ ######################### radiator::genomic_converter ########################## ################################################################################ Execution date@time: 20211217@1020 Folder created: 09_radiator_genomic_converter_20211217@1020 Function call and arguments stored in: radiator_genomic_converter_args_20211217@1020.tsv Filters parameters file generated: filters_parameters_20211217@1020.tsv
Importing data: vcf.file
Reading VCF...
Data summary: number of samples: 160 number of markers: 374506
Filter monomorphic markers Number of individuals / strata / chrom / locus / SNP: Blacklisted: 0 / 0 / 0 / 164690 / 164690
Filter common markers: Number of individuals / strata / chrom / locus / SNP: Blacklisted: 0 / 0 / 0 / 881 / 881
Generating individual stats... Generating markers stats... [==================================================] 100%, completed, 1s [==================================================] 100%, completed, 0s
Number of chromosome/contig/scaffold: 1 Number of locus: 208935 Number of markers: 208935 Number of strata: 8 Number of individuals: 160
Number of ind/strata: Dcar_FR_PY = 24 Dcar_FR_JUR_ORG = 7 Dcar_RO = 29 Dcar_FR_AL = 37 HYB = 17 Dcar_FR_JUR_VAL = 10 Dcar_SWI = 9 Dcar_CZ = 27
Number of duplicate id: 0 radiator Genomic Data Structure (GDS) file: radiator_20211217@1020.gds
Genotypes formats generated with 208935 SNPs: GT_BIN (the dosage of ALT allele: 0, 1, 2 NA): TRUE GT_VCF (the genotype coding VCFs: 0/0, 0/1, 1/1, ./.): TRUE GT_VCF_NUC (the genotype coding in VCFs, but with nucleotides: A/C, ./.): TRUE GT (the genotype coding 'a la genepop': 001002, 001001, 000000): TRUE LOCUS field empty... adding unique id instead
Tidy data file written: radiator_20211217@1021.rad
Computation time, overall: 109 sec
Writing tidy data set: radiator_data_20211217@1020.rad
Preparing data for output
Data is bi-allelic Calibrating REF/ALT alleles... Generating arlequin file Error: Can't subset columns that don't exist. x Column
POP_IDdoesn't exist. Runrlang::last_error()to see where the error occurred.Computation time, overall: 207 sec
* the output of
devtools::session_info()─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── package version date lib source
ade4 1.7-17 2021-06-17 [1] CRAN (R 4.1.0)
adegenet 2.1.3 2020-05-10 [1] CRAN (R 4.1.0)
ape 5.5 2021-04-25 [1] CRAN (R 4.1.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
BiocGenerics 0.38.0 2021-05-19 [1] Bioconductor
Biostrings 2.60.2 2021-08-05 [1] Bioconductor
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.0)
boot 1.3-28 2021-05-03 [1] CRAN (R 4.1.0)
cachem 1.0.5 2021-05-15 [1] CRAN (R 4.1.0)
calibrate 1.7.7 2020-06-19 [1] CRAN (R 4.1.0)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0)
class 7.3-19 2021-05-03 [1] CRAN (R 4.1.0)
classInt 0.4-3 2020-04-07 [1] CRAN (R 4.1.0)
cli 3.0.1 2021-07-17 [1] CRAN (R 4.1.0)
cluster 2.1.2 2021-04-17 [1] CRAN (R 4.1.0)
coda 0.19-4 2020-09-30 [1] CRAN (R 4.1.0)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.1.0)
colorspace 2.0-1 2021-05-04 [1] CRAN (R 4.1.0)
combinat 0.0-8 2012-10-29 [1] CRAN (R 4.1.0)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.1.0)
data.table 1.14.0 2021-02-21 [1] CRAN (R 4.1.0)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.0)
deldir 0.2-10 2021-02-16 [1] CRAN (R 4.1.0)
desc 1.3.0 2021-03-05 [1] CRAN (R 4.1.0)
devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.0)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.1.0)
dismo 1.3-5 2021-10-11 [1] CRAN (R 4.1.0)
dplyr 1.0.6 2021-05-05 [1] CRAN (R 4.1.0)
e1071 1.7-7 2021-05-23 [1] CRAN (R 4.1.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
expm 0.999-6 2021-01-13 [1] CRAN (R 4.1.0)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0)
farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0)
fst 0.9.4 2020-08-27 [1] CRAN (R 4.1.0)
gap 1.2.3-1 2021-04-21 [1] CRAN (R 4.1.0)
gdata 2.18.0 2017-06-06 [1] CRAN (R 4.1.0)
gdistance 1.3-6 2020-06-29 [1] CRAN (R 4.1.0)
gdsfmt 1.28.1 2021-09-16 [1] Bioconductor
generics 0.1.0 2020-10-31 [1] CRAN (R 4.1.0)
genetics 1.3.8.1.3 2021-03-01 [1] CRAN (R 4.1.0)
GenomeInfoDb 1.28.4 2021-09-09 [1] Bioconductor
GenomeInfoDbData 1.2.6 2021-11-29 [1] Bioconductor
GenomicRanges 1.44.0 2021-05-19 [1] Bioconductor
GGally 2.1.2 2021-06-21 [1] CRAN (R 4.1.0)
ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.1.0)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.0)
gmodels 2.18.1 2018-06-25 [1] CRAN (R 4.1.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
gtools 3.9.2 2021-06-06 [1] CRAN (R 4.1.0)
hms 1.1.0 2021-05-17 [1] CRAN (R 4.1.0)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0)
httpuv 1.6.1 2021-05-07 [1] CRAN (R 4.1.0)
igraph 1.2.6 2020-10-06 [1] CRAN (R 4.1.0)
IRanges 2.26.0 2021-05-19 [1] Bioconductor
KernSmooth 2.23-20 2021-05-03 [1] CRAN (R 4.1.0)
knitr 1.33 2021-04-24 [1] CRAN (R 4.1.0)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.0)
later 1.2.0 2021-04-23 [1] CRAN (R 4.1.0)
lattice 0.20-44 2021-05-02 [1] CRAN (R 4.1.0)
LearnBayes 2.15.1 2018-03-18 [1] CRAN (R 4.1.0)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.1.0)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0)
MASS 7.3-54 2021-05-03 [1] CRAN (R 4.1.0)
Matrix 1.3-3 2021-05-04 [1] CRAN (R 4.1.0)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.0)
memuse 4.2-1 2021-10-20 [1] CRAN (R 4.1.0)
mgcv 1.8-35 2021-04-18 [1] CRAN (R 4.1.0)
mime 0.10 2021-02-13 [1] CRAN (R 4.1.0)
mmod 1.3.3 2017-04-06 [1] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
mvtnorm 1.1-2 2021-06-07 [1] CRAN (R 4.1.0)
nlme 3.1-152 2021-02-04 [1] CRAN (R 4.1.0)
pegas 1.0-1 2021-05-17 [1] CRAN (R 4.1.0)
permute 0.9-5 2019-03-12 [1] CRAN (R 4.1.0)
pillar 1.6.1 2021-05-16 [1] CRAN (R 4.1.0)
pinfsc50 1.2.0 2020-06-03 [1] CRAN (R 4.1.0)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.1.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0)
polysat 1.7-6 2021-12-08 [1] CRAN (R 4.1.0)
PopGenReport 3.0.4 2019-02-04 [1] CRAN (R 4.1.0)
poppr 2.9.3 2021-09-07 [1] CRAN (R 4.1.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.1.0)
proxy 0.4-26 2021-06-07 [1] CRAN (R 4.1.0)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.1.0)
R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.1.0)
R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.1.0)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.1.0)
radiator 1.2.1 2021-11-29 [1] Github (thierrygosselin/radiator@9c92544) raster 3.5-2 2021-10-11 [1] CRAN (R 4.1.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0)
Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.0)
RCurl 1.98-1.5 2021-09-17 [1] CRAN (R 4.1.0)
readr 1.4.0 2020-10-05 [1] CRAN (R 4.1.0)
remotes 2.4.0 2021-06-02 [1] CRAN (R 4.1.0)
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.0)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.0)
rgdal 1.5-27 2021-09-16 [1] CRAN (R 4.1.0)
RgoogleMaps 1.4.5.3 2020-02-12 [1] CRAN (R 4.1.0)
rlang 0.4.11 2021-04-30 [1] CRAN (R 4.1.0)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0)
S4Vectors 0.30.2 2021-10-03 [1] Bioconductor
scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0)
SeqArray 1.32.0 2021-05-19 [1] Bioconductor
seqinr 4.2-8 2021-06-09 [1] CRAN (R 4.1.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0)
sf 1.0-0 2021-06-09 [1] CRAN (R 4.1.0)
shiny 1.6.0 2021-01-25 [1] CRAN (R 4.1.0)
sp 1.4-5 2021-01-10 [1] CRAN (R 4.1.0)
spData 0.3.10 2021-06-18 [1] CRAN (R 4.1.0)
spdep 1.1-8 2021-05-23 [1] CRAN (R 4.1.0)
stringi 1.6.2 2021-05-17 [1] CRAN (R 4.1.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
terra 1.4-22 2021-11-24 [1] CRAN (R 4.1.0)
testthat 3.0.4 2021-07-01 [1] CRAN (R 4.1.0)
tibble 3.1.2 2021-05-16 [1] CRAN (R 4.1.0)
tidyr 1.1.3 2021-03-03 [1] CRAN (R 4.1.0)
tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0)
units 0.7-2 2021-06-08 [1] CRAN (R 4.1.0)
UpSetR 1.4.0 2019-05-22 [1] CRAN (R 4.1.0)
usethis 2.0.1 2021-02-10 [1] CRAN (R 4.1.0)
utf8 1.2.1 2021-03-12 [1] CRAN (R 4.1.0)
vcfR * 1.12.0 2020-09-01 [1] CRAN (R 4.1.0)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0)
vegan 2.5-7 2020-11-28 [1] CRAN (R 4.1.0)
viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.0)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0)
xfun 0.23 2021-05-15 [1] CRAN (R 4.1.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.0)
XVector 0.32.0 2021-05-19 [1] Bioconductor
zlibbioc 1.38.0 2021-05-19 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
Could you please help me ? Thanks!! best, Amandine