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thierrygosselin / radiator

RADseq Data Exploration, Manipulation and Visualization using R
https://thierrygosselin.github.io/radiator/
GNU General Public License v3.0
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"Error in SeqArray::seqOpen(gds.fn = data.safe$result, readonly = FALSE) :" despite the use of the last release? #143

Closed CornilleAmandine closed 2 years ago

CornilleAmandine commented 2 years ago

Hi Thierry,

Thanks a lot for this nice package!

I have having an issue when I want to convert my vcf.

Here my command line :

data<-genomic_converter(

  • "d.vcf",
  • strata = "strata.txt",
  • output = "genepop",
  • filename = NULL,
  • parallel.core = parallel::detectCores() - 1,
  • verbose = TRUE,
  • )

I got this error:

"################################################################################ ######################### radiator::genomic_converter ########################## ################################################################################ Execution date@time: 20211129@2135 Folder created: 04_radiator_genomic_converter_20211129@2135 Function call and arguments stored in: radiator_genomic_converter_args_20211129@2135.tsv Filters parameters file generated: filters_parameters_20211129@2135.tsv

Importing data: vcf.file

Reading VCF... Error in SeqArray::seqOpen(gds.fn = data.safe$result, readonly = FALSE) : is.character(gds.fn) is not TRUE In addition: Warning message: In socketAccept(socket = socket, blocking = TRUE, open = "a+b", : problem in accepting connections on this socket

Computation time, overall: 20 sec

Computation time, overall: 20 sec ######################### completed genomic_converter ##########################"

I have already seen discussions/bug report about this topic and you proposed to use the latest release of radiator, which is the one I use. So I am not sure what do to next?

Could you please help me ?

Thanks a lot!! Cheers Amandine

thierrygosselin commented 2 years ago

Hi Amandine,

could you please give me the output of this command: devtools::session_info()

Best thierry

CornilleAmandine commented 2 years ago

Hi Thierry,

Thanks a lot!

I finally found the solution just now, I have added radiator::g before genomic_converter, but I have another problem now which is

################################################################################ Execution @.: @. Folder created: @. Function call and arguments stored in: @. Filters parameters file generated: @.***

Importing data: vcf.file

Reading VCF...

Error in SeqArray::seqOpen(gds.fn = data.safe$result, readonly = FALSE) : is.character(gds.fn) is not TRUEIn addition: Warning message:In socketAccept(socket = socket, blocking = TRUE, open = "a+b", : problem in accepting connections on this socket

Computation time, overall: 20 sec

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

Here my devtool library

evtools::session_info() ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.1.0 (2021-05-18) os macOS 12.0.1 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/Paris date 2021-11-30

─ 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)

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)

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)

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)

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)

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)

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)

PopGenReport * 3.0.4 2019-02-04 [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 @.***) 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)

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)

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)

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)

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

Thanks a lot! Best, Amandine

On Tue, 30 Nov 2021 at 17:40, Thierry Gosselin @.***> wrote:

Hi Amandine,

could you please give me the output of this command: devtools::session_info()

Best thierry

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/thierrygosselin/radiator/issues/143#issuecomment-982813044, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYUILHXAWH4VP5EYSOTUOT5ARANCNFSM5JAB3DMA . 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.

-- 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

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thierrygosselin commented 2 years ago

Hi Amandine, could you send me your vcd and strata file via email please?

Thanks Thierry

thierrygosselin commented 2 years ago

Also try the command below after restarting R and RStudio (if using that one), but the idea is to have a fresh session

test1 <- radiator::genomic_converter(
  data = "d.vcf",
  strata = "strata.txt",
  output = "genepop",
  parallel.core = 1L
)
CornilleAmandine commented 2 years ago

Hi Thierry,

Thanks a lot! It works now!

Thanks a lot for your help!!

best, Amandine

On Fri, 3 Dec 2021 at 19:02, Thierry Gosselin @.***> wrote:

Also try the command below after restarting R and RStudio (if using that one), but the idea is to have a fresh session

test1 <- radiator::genomic_converter( data = "d.vcf", strata = "strata.txt", output = "genepop", parallel.core = 1L )

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/thierrygosselin/radiator/issues/143#issuecomment-985721158, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYXEY2G4P4RKGV4IDODUPEA4FANCNFSM5JAB3DMA . 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.

-- 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