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xiaolei-lab / rMVP

:postbox: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study
Apache License 2.0
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Installation problem rMVP #48

Closed rupesht closed 4 years ago

rupesht commented 4 years ago

install.packages("rMVP") Installing package into ‘C:/Users/user/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) package ‘rMVP’ is not available (for R version 3.5.3)

Or the the development version from GitHub:

install.packages("devtools")

devtools::install_github("xiaolei-lab/rMVP") Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘glue’

Or the the development version from GitHub:

install.packages("devtools")

devtools::install_github("xiaolei-lab/rMVP") Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘glue’ devtools::install_github("xiaolei-lab/rMVP") Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘glue’

rupesht commented 4 years ago

In also its showing Full description, Bug report, Suggestion and the latest version: https://github.com/XiaoleiLiuBio/rMVP

YinLiLin commented 4 years ago

This problem is due to the lack of required package, just follow the tips from the reported message, try install.packages("glue"), and then install rMVP if all the required packages are installed successfully.

rupesht commented 4 years ago

YinLiLin, Thank you I tried as you suggested but its giving following error

package ‘glue’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\user\AppData\Local\Temp\Rtmp4Si9gA\downloaded_packages

install.packages("rMVP") Installing package into ‘C:/Users/user/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘rMVP’ is not available (for R version 3.5.3)

YinLiLin commented 4 years ago

We have submitted a new version of rMVP to R CRAN, and it is under inspection by the CRAN team now, hopefully it will come to public in the near days, thus it's unavailable during this time, but you can install it from GitHub by package devtools.

rupesht commented 4 years ago

I nstalled again everything and kept only Phenotype and Hapmap file in the folder but still its giving the same error. Can you please help in this regards,

library(rMVP) setwd("C:/Users/user/Documents/R/win-library/3.5/rMVP-master/data") MVP.Data(fileHMP="hapmap.txt", filePhe="Phenotype.txt", sep.hmp="\t", sep.phe="\t", SNP.effect="Add", fileKin=FALSE, filePC=FALSE, out="mvp.hmp",

priority="memory",

     #maxLine=10000

) genotype <- attach.big.matrix("mvp.hmp.geno.desc") phenotype <- read.table("mvp.hmp.phe",head=TRUE) map <- read.table("mvp.hmp.geno.map" , head = TRUE) for(i in 2:ncol(phenotype)){ imMVP <- MVP( phe=phenotype[, c(1, i)], geno=genotype, map=map,

K=Kinship,

#CV.GLM=Covariates,
#CV.MLM=Covariates,
#CV.FarmCPU=Covariates,
nPC.GLM=5,
nPC.MLM=3,
nPC.FarmCPU=3,
priority="speed",
#ncpus=10,
vc.method="BRENT",
maxLoop=10,
method.bin="EMMA",#"FaST-LMM","EMMA", "static"
#permutation.threshold=TRUE,
#permutation.rep=100,
threshold=0.05,
method=c("GLM", "MLM", "FarmCPU")

) gc() } Error Input data has 246 individuals, 131620 markers Phenotype: Y_2016 Relationship matrix mode in speed Scale the genotype matrix Computing Z'Z Deriving relationship matrix successfully Eigen Decomposition Error in eigen(K, symmetric = TRUE) : infinite or missing values in 'x'

rupesht commented 4 years ago

Data Folder.docx

YinLiLin commented 4 years ago

Was it fine when running MVP.Data on your data? if yes, please upload a screenshot of this part, I am just wondering if our rough imputation function was working or not. Also please tell me your used version of rMVP.

rupesht commented 4 years ago

Dear Dr. Lillin,

I am able to install the rMVP and followed the recommendation of Dr. Xiaolei, He was very generous to help me out I am communicating with him. So far I am struggling to execute it completely. Please find the attached screenshot.

Sincerely,

Rupesh Tayade

PhD Research Scholar

School of Applied Biosciences

College of Agriculture and Life Sciences

Kyungpook National University[image: KNU logo에 대한 이미지 검색결과]

80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea

E-mail : rupesh.tayade@gmail.com

On Wed, May 6, 2020 at 10:15 AM Lilin Yin notifications@github.com wrote:

Was it fine when running MVP.Data on your data? if yes, please upload a screenshot of this part, I am just wondering if our rough imputation function was working or not.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/rMVP/issues/48#issuecomment-624394238, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB64KNI4RJDCFOK5KHGQWXDRQC245ANCNFSM4MZPVUGQ .

YinLiLin commented 4 years ago

Sorry, I can not see any screenshot here.

rupesht commented 4 years ago

Please check the attached file.

On Wed, May 6, 2020 at 10:50 AM Lilin Yin notifications@github.com wrote:

Sorry, I can not see any screenshot here.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/rMVP/issues/48#issuecomment-624401992, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB64KNLAOH2YEZI4QEIELJTRQC653ANCNFSM4MZPVUGQ .

--

Rupesh Tayade

PhD Research Scholar

School of Applied Biosciences

College of Agriculture and Life Sciences

Kyungpook National University[image: KNU logo에 대한 이미지 검색결과]

80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea

E-mail : rupesh.tayade@gmail.com

YinLiLin commented 4 years ago

Maybe you should upload it by the website of GitHub, the attached file from an email response may be automatically discarded by GitHub system.

rupesht commented 4 years ago

Screen Shot _R.docx

rupesht commented 4 years ago

Maybe you should upload it by the website of GitHub, the attached file from an email response may be automatically discarded by GitHub system.

Please check I posted now on git hub. Thank You.

YinLiLin commented 4 years ago

Thank you, I can see it now. There are some mistakes from your screenshot, please check the completeness of your code, and insure rMVP has been loaded prior to use. Restart R and try following:

library(rMVP)
setwd("C:/Users/user/Documents/R/win-library/3.5/rMVP-master/data")
MVP.Data(fileHMP="hapmap.txt",
filePhe="Phenotype.txt",
sep.hmp="\t",
sep.phe="\t",
SNP.effect="Add",
fileKin=FALSE,
filePC=FALSE,
out="mvp.hmp",
#priority="memory",
#maxLine=10000
)
genotype <- attach.big.matrix("mvp.hmp.geno.desc")
phenotype <- read.table("mvp.hmp.phe",head=TRUE)
map <- read.table("mvp.hmp.geno.map" , head = TRUE)
for(i in 2:ncol(phenotype)){
imMVP <- MVP(
phe=phenotype[, c(1, i)],
geno=genotype,
map=map,
#K=Kinship,
#CV.GLM=Covariates,
#CV.MLM=Covariates,
#CV.FarmCPU=Covariates,
nPC.GLM=5,
nPC.MLM=3,
nPC.FarmCPU=3,
priority="speed",
#ncpus=10,
vc.method="BRENT",
maxLoop=10,
method.bin="EMMA",#"FaST-LMM","EMMA", "static"
#permutation.threshold=TRUE,
#permutation.rep=100,
threshold=0.05,
method=c("GLM", "MLM", "FarmCPU")
)
gc()
}
rupesht commented 4 years ago

Thank you, I can see it now. There are some mistakes from your screenshot, please check the completeness of your code, and insure rMVP has been loaded prior to use. Restart R and try following:

library(rMVP)
setwd("C:/Users/user/Documents/R/win-library/3.5/rMVP-master/data")
MVP.Data(fileHMP="hapmap.txt",
filePhe="Phenotype.txt",
sep.hmp="\t",
sep.phe="\t",
SNP.effect="Add",
fileKin=FALSE,
filePC=FALSE,
out="mvp.hmp",
#priority="memory",
#maxLine=10000
)
genotype <- attach.big.matrix("mvp.hmp.geno.desc")
phenotype <- read.table("mvp.hmp.phe",head=TRUE)
map <- read.table("mvp.hmp.geno.map" , head = TRUE)
for(i in 2:ncol(phenotype)){
imMVP <- MVP(
phe=phenotype[, c(1, i)],
geno=genotype,
map=map,
#K=Kinship,
#CV.GLM=Covariates,
#CV.MLM=Covariates,
#CV.FarmCPU=Covariates,
nPC.GLM=5,
nPC.MLM=3,
nPC.FarmCPU=3,
priority="speed",
#ncpus=10,
vc.method="BRENT",
maxLoop=10,
method.bin="EMMA",#"FaST-LMM","EMMA", "static"
#permutation.threshold=TRUE,
#permutation.rep=100,
threshold=0.05,
method=c("GLM", "MLM", "FarmCPU")
)
gc()
}

Please check I restart R again and given follwoing code so far. package ‘devtools’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\user\AppData\Local\Temp\Rtmp0urTDM\downloaded_packages

utils:::menuInstallPkgs() Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) : no packages were specified install.packages("glue") Installing package into ‘C:/Users/user/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://mran.microsoft.com/snapshot/2019-04-15/bin/windows/contrib/3.5/glue_1.3.1.zip' Content type 'application/zip' length 172477 bytes (168 KB) downloaded 168 KB

package ‘glue’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\user\AppData\Local\Temp\Rtmp0urTDM\downloaded_packages

install.packages("bigmemory") Installing package into ‘C:/Users/user/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://mran.microsoft.com/snapshot/2019-04-15/bin/windows/contrib/3.5/bigmemory_4.5.33.zip' Content type 'application/zip' length 1395547 bytes (1.3 MB) downloaded 1.3 MB

package ‘bigmemory’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\user\AppData\Local\Temp\Rtmp0urTDM\downloaded_packages

library(rMVP) Loading required package: bigmemory Full description, Bug report, Suggestion and the latest version: https://github.com/XiaoleiLiuBio/rMVP

rupesht commented 4 years ago

After that when I put following code it showing message setwd("C:/Users/user/Documents/R/win-library/3.5/rMVP-master/data")

MVP.Data(fileHMP="hapmap.txt",

  • filePhe="Phenotype.txt",
  • sep.hmp="\t",
  • sep.phe="\t",
  • SNP.effect="Add",
  • fileKin=FALSE,
  • filePC=FALSE,
  • out="mvp.hmp",

  • priority="memory",

  • maxLine=10000

  • ) Error: unexpected end of input
rupesht commented 4 years ago

When I put the entire code it showing as following. Secondly, Why it is not executing ? or still its running ? library(rMVP)

setwd("C:/Users/user/Documents/R/win-library/3.5/rMVP-master/data") MVP.Data(fileHMP="hapmap.txt",

  • filePhe="Phenotype.txt",
  • sep.hmp="\t",
  • sep.phe="\t",
  • SNP.effect="Add",
  • fileKin=FALSE,
  • filePC=FALSE,
  • out="mvp.hmp",

  • priority="memory",

  • maxLine=10000

  • ) Preparing data for MVP... Reading file... inds: 313 markers:131620 Number of threads: 1 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Preparation for GENOTYPE data is done within 42s 313 common individuals between phenotype and genotype. Preparation for PHENOTYPE data is Done within 0s Imputing... out is NULL, impute inplace. Number of threads: 1 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Impute Genotype File is done! MVP data prepration accomplished successfully! Warning messages: 1: In MVP.Data(fileHMP = "hapmap.txt", filePhe = "Phenotype.txt", sep.hmp = "\t", : SNP.effect has been DEPRECATED. 2: In MVP.Data(fileHMP = "hapmap.txt", filePhe = "Phenotype.txt", sep.hmp = "\t", : sep.hmp has been DEPRECATED. genotype <- attach.big.matrix("mvp.hmp.geno.desc") phenotype <- read.table("mvp.hmp.phe",head=TRUE) map <- read.table("mvp.hmp.geno.map" , head = TRUE) for(i in 2:ncol(phenotype)){
  • imMVP <- MVP(
  • phe=phenotype[, c(1, i)],
  • geno=genotype,
  • map=map,

  • K=Kinship,

  • CV.GLM=Covariates,

  • CV.MLM=Covariates,

  • CV.FarmCPU=Covariates,

  • nPC.GLM=5,
  • nPC.MLM=3,
  • nPC.FarmCPU=3,
  • priority="speed",

  • ncpus=10,

  • vc.method="BRENT",
  • maxLoop=10,
  • method.bin="EMMA",#"FaST-LMM","EMMA", "static"

  • permutation.threshold=TRUE,

  • permutation.rep=100,

  • threshold=0.05,
  • method=c("GLM", "MLM", "FarmCPU")
  • )
  • gc()
  • }
YinLiLin commented 4 years ago

Thank you. From the log message, you can see that the genotype had been imputed by our rough procedure (note: we don't recommend to impute by rMVP if there are lots of missing in genotype, unless you had done strict QC before using rMVP, otherwise, some other professional imputation software are preferred), thus it should be fine to process the next step of association. BTW, the version you used is not the latest, please use devtools::install_github("xiaolei-lab/rMVP") to update to v1.0.0.

rupesht commented 4 years ago

Thank you. From the log message, you can see that the genotype had been imputed by our rough procedure (note: we don't recommend to impute by rMVP if there are lots of missing in genotype, unless you had done strict QC before using rMVP, otherwise, some other professional imputation software are preferred), thus it should be fine to process the next step of association.

Actually I shared my genotype data with Dr. Xiaolei he said ''There are not many missing values in the attached genotype data'' So now what is exactly happening? I have executed all the code. But there is +} l sign-on console. and not showing >. I don't know it's still performing or stoped?

YinLiLin commented 4 years ago

You should stop it. The "+}" sign means that your input code is not complete. Please check if you have missed something.

rupesht commented 4 years ago

You should stop it. The "+}" sign means that your input code is not complete. Please check if you have missed something.

I input the exact code you given in your previous comment nothing edited. What should I do now?

YinLiLin commented 4 years ago

I have tried again, it works fine at my PC, please check it carefully.

rupesht commented 4 years ago

I have tried again, it works fine at my PC, please check it carefully.

Can you please share again the code exactly what you tried? Installation, Starting to end.

rupesht commented 4 years ago

When I am trying to install as you suggested update version it not getting it.

devtools::install_github("xiaolei-lab/rMVP") Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘processx’

if I put all it showing as below

devtools::install_github("xiaolei-lab/rMVP") to update to v1.0.0. Error: unexpected symbol in "devtools::install_github("xiaolei-lab/rMVP") to"

YinLiLin commented 4 years ago

Please see below: test

rupesht commented 4 years ago

Thank you but How can I remove that thread ?

On Wed, May 6, 2020 at 1:06 PM Lilin Yin notifications@github.com wrote:

Please see below: [image: test] https://user-images.githubusercontent.com/12557293/81137603-b2797680-8fa2-11ea-80ca-8317e7380317.png

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/rMVP/issues/48#issuecomment-624430863, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB64KNMFU5DUG3XBZIYEKZLRQDO5HANCNFSM4MZPVUGQ .

--

Rupesh Tayade

PhD Research Scholar

School of Applied Biosciences

College of Agriculture and Life Sciences

Kyungpook National University[image: KNU logo에 대한 이미지 검색결과]

80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea

E-mail : rupesh.tayade@gmail.com

rupesht commented 4 years ago

I didn’t get you.

On Wed, May 6, 2020 at 1:14 PM Lilin Yin notifications@github.com wrote:

Closed #48 https://github.com/xiaolei-lab/rMVP/issues/48.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/rMVP/issues/48#event-3306825575, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB64KNKO6L5TSVPE5ODE4TTRQDP4BANCNFSM4MZPVUGQ .

--

Rupesh Tayade

PhD Research Scholar

School of Applied Biosciences

College of Agriculture and Life Sciences

Kyungpook National University[image: KNU logo에 대한 이미지 검색결과]

80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea

E-mail : rupesh.tayade@gmail.com

rupesht commented 4 years ago

Please share the code that you are trying I have also posted some curries there on git hub. Devtool installation issue. Pls chek the updates one from github is not getting installed.

On Wed, May 6, 2020 at 1:17 PM Rupesh Tayade rupesh.tayade@gmail.com wrote:

I didn’t get you.

On Wed, May 6, 2020 at 1:14 PM Lilin Yin notifications@github.com wrote:

Closed #48 https://github.com/xiaolei-lab/rMVP/issues/48.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/rMVP/issues/48#event-3306825575, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB64KNKO6L5TSVPE5ODE4TTRQDP4BANCNFSM4MZPVUGQ .

--

Rupesh Tayade

PhD Research Scholar

School of Applied Biosciences

College of Agriculture and Life Sciences

Kyungpook National University[image: KNU logo에 대한 이미지 검색결과]

80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea

E-mail : rupesh.tayade@gmail.com

--

Rupesh Tayade

PhD Research Scholar

School of Applied Biosciences

College of Agriculture and Life Sciences

Kyungpook National University[image: KNU logo에 대한 이미지 검색결과]

80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea

E-mail : rupesh.tayade@gmail.com

YinLiLin commented 4 years ago

Copy the entire codes I showed above, then press enter to start running rMVP. It seems to be hard to install the latest rMVP on your PC from GitHub by devtools due to the lack of some necessary R packages which should be automatically installed when installing devtools, I suggest you to wait our upcoming rMVP from R CRAN in the near days.

rupesht commented 4 years ago

Copy the entire codes I showed above, then press enter to start running rMVP. It seems to be hard to install the latest rMVP on your PC from GitHub by devtools due to the lack of some necessary R packages which should be automatically installed when installing devtools, I suggest you to wait our upcoming rMVP from R CRAN in the near days.

From the code do I need to remove "{" and "}"?

YinLiLin commented 4 years ago

No, you shouldn't.

rupesht commented 4 years ago

package ‘devtools’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\user\AppData\Local\Temp\RtmpaOH12N\downloaded_packages

library(rMVP) Loading required package: bigmemory Full description, Bug report, Suggestion and the latest version: https://github.com/XiaoleiLiuBio/rMVP library(rMVP) setwd("C:/Users/user/Documents/R/win-library/3.5/rMVP-master/data") MVP.Data(fileHMP="hapmap.txt",

  • filePhe="Phenotype.txt",
  • sep.hmp="\t",
  • sep.phe="\t",
  • SNP.effect="Add",
  • fileKin=FALSE,
  • filePC=FALSE,
  • out="mvp.hmp",

  • priority="memory",

  • maxLine=10000

  • ) Preparing data for MVP... Reading file... inds: 313 markers:131620 Number of threads: 1 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Preparation for GENOTYPE data is done within 43s 313 common individuals between phenotype and genotype. Preparation for PHENOTYPE data is Done within 0s Imputing... out is NULL, impute inplace. Number of threads: 1 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Impute Genotype File is done! MVP data prepration accomplished successfully! Warning messages: 1: In MVP.Data(fileHMP = "hapmap.txt", filePhe = "Phenotype.txt", sep.hmp = "\t", : SNP.effect has been DEPRECATED. 2: In MVP.Data(fileHMP = "hapmap.txt", filePhe = "Phenotype.txt", sep.hmp = "\t", : sep.hmp has been DEPRECATED. genotype <- attach.big.matrix("mvp.hmp.geno.desc") phenotype <- read.table("mvp.hmp.phe",head=TRUE) map <- read.table("mvp.hmp.geno.map" , head = TRUE) for(i in 2:ncol(phenotype))
  • imMVP <- MVP(
  • phe=phenotype[, c(1, i)],
  • geno=genotype,
  • map=map,

  • K=Kinship,

  • CV.GLM=Covariates,

  • CV.MLM=Covariates,

  • CV.FarmCPU=Covariates,

  • nPC.GLM=5,
  • nPC.MLM=3,
  • nPC.FarmCPU=3,
  • priority="speed",

  • ncpus=10,

  • vc.method="BRENT",
  • maxLoop=10,
  • method.bin="EMMA",#"FaST-LMM","EMMA", "static"

  • permutation.threshold=TRUE,

  • permutation.rep=100,

  • threshold=0.05,
  • method=c("GLM", "MLM", "FarmCPU")
  • ) ====================== Welcome to MVP ====================== A Memory-efficient, Visualization-enhanced, and
    Parallel-accelerated Tool For GWAS

    | \/ | \ \ / / | \
    | |\/| | \ V / |     /
    || || _/ |_| Version: 0.99.19
    Designed and Maintained by Lilin Yin, Haohao Zhang, and
    Xiaolei Liu
    Contributors: Zhenshuang Tang, Jingya Xu, Dong Yin,
    Zhiwu Zhang, Xiaohui Yuan, Mengjin Zhu, Shuhong Zhao,
    Xinyun Li
    Contact: xiaoleiliu@mail.hzau.edu.cn

    Start: 2020-05-06 13:41:15 The log has been output to the file: C:/Users/user/Documents/R/win-library/3.5/rMVP-master/data/MVP.20200506_134115.log Input data has 246 individuals, 131620 markers Phenotype: Y_2016 Relationship matrix mode in speed Scale the genotype matrix Computing Z'Z Deriving relationship matrix successfully Eigen Decomposition Error in eigen(K, symmetric = TRUE) : infinite or missing values in 'x' gc()

YinLiLin commented 4 years ago

If you don't mind, please seed your dataset to me at ylilin@163.com, I will help to find out what on earth is going on.

rupesht commented 4 years ago

If you don't mind, please seed your dataset to me at ylilin@163.com, I will help to find out what on earth is going on.

I hope you receive my mail.