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RiboDiPA: Differential Pattern Analysis for Ribo-seq data #1741

Closed jipingw closed 3 years ago

jipingw commented 4 years ago

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bioc-issue-bot commented 4 years ago

Hi @jipingw

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: RiboDiPA
Type: Package
Title: Ribosome differential pattern analysis
Date: 2020-10-31
Version: 0.99.0
Authors@R:
    c(person(given = "Keren",
   family = "Li",
   role = c("aut"),
   email = "keren.li@northwestern.edu"),
      person(given = "Matt",
   family = "Hope",
   role = "aut"),
      person(given = "Xiaozhong",
   family = "Wang",
   role = "aut"),
      person(given = "Ji-Ping",
   family = "Wang",
   role = c("aut","cre"),
   email = "jzwang@northwestern.edu"))
Description: This package performs differntial pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization. 
License: LGPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 1.0.2), graphics, stats, data.table, elitism,
        methods, S4Vectors, IRanges, GenomicRanges, matrixStats,
        reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2
LinkingTo: Rcpp
Depends: R (>= 4.0), Rsamtools, GenomicFeatures, GenomicAlignments
NeedsCompilation: yes
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
biocViews: RiboSeq, GeneExpression, GeneRegulation,
        DifferentialExpression, Sequencing, Coverage, Alignment,
        RNASeq, ImmunoOncology, QualityControl, DataImport, Software,
        Normalization
Packaged: 2020-09-12 20:40:56 UTC; keren
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bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jipingw commented 3 years ago

Hi, I pushed a new version to github yesterday, but I haven't see the report yet? Is it on the way or something went wrong? thanks.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 53498d8947c33b71b287c74ca9f9bac88fc7f3b9

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4d779d6085906f77e06f722ae36238ed080e422e

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jipingw commented 3 years ago

@hpages HI, I am just wondering whether there is any update on the review of this package. Or is there anything i should do to make it move? thanks for help.

hpages commented 3 years ago

Hi @jipingw,

We'll review soon. Thanks for your patience.

H.

hpages commented 3 years ago

Hi @jipingw ,

Thanks for submitting RiboDiPA. The package looks good and is almost ready for inclusion in Bioconductor. Only a few cosmetic issues:

  1. You have a typo in "differntial". Should be "differential" ("e" is missing). This is in the Description field of the DESCRIPTION file.

  2. Please remove the build/ folder and the src/symbols.rds file. These don't belong to the package source tree.

  3. Also remove the last line in the DESCRIPTION file:

    Packaged: 2020-09-12 20:40:56 UTC; keren

  4. Bioconductor naming style is to use camelCaps for functions e.g. dataBinning instead of DataBinning, diffPatternTest instead of DPtest, etc... Please consider adopting this style. In any case, only one style should be used so having one function named psitecal and another one named PsiteMapping should be avoided.

  5. Serialized datasets should preferably go in the data/ folder. Using inst/extdata/ is typically for data that is not in a serialized form e.g. for things like GTF, FASTA, or BAM files. The advantage of having the serialized datasets in data/ instead of inst/extdata/ is that they can be discovered and loaded with standard mechanisms like data(package="RiboDiPA") and data(sample). Also please use a more descriptive name for the dataset, or at least a name that is more unique (sample is too generic).

  6. The "Vignette of the RiboDiPA pipeline" section of the vignette should just be called "The RiboDiPA pipeline".

  7. Please use proper indentation of your code. Also put a space after the commas (,). This will make your code a lot easier to read. For example, do:

    plot_track(data=data.psite, genes.list=c("YDR050C","YDR064W"), 
           replicates=NULL, exons=FALSE)

    instead of:

    plot_track(data=data.psite,genes.list=c("YDR050C","YDR064W"), 
replicates=NULL,exons=FALSE)

  8. Also make sure that your lines of code are properly wrapped. For example the code in the Examples section of DPtest.exon's man page looks like this when I open the man page with ?DPtest.exon:

    classlabel <- data.frame(condition = c("mutant","mutant","wildtype",
"wildtype"),
    comparison=c(2,2,1,1))

    This is hard to read. With proper wrapping and indenting, it will look like this:

    classlabel <- data.frame(
    condition = c("mutant","mutant","wildtype","wildtype"),
    comparison = c(2,2,1,1)
)

    This looks a little bit nicer and is a little bit easier to read. Sometimes assigning additional variables helps make the code even easier to format thus easier to read:

    condition  <- c("mutant", "mutant", "wildtype", "wildtype")
comparison <- c(2, 2, 1, 1)
classlabel <- data.frame(condition, comparison)

  9. You seem to be using TeX/LaTeX markup in your man pages (e.g. in the \details section of DataBinning's man page). Note that this is not supported and doesn't render properly. For example, open DataBinning's man page with ?DataBinning and take a look at the formula in the Details section to see what I mean.

Thanks, H.

hpages commented 3 years ago

Hi @jipingw -- do you intend to followup on this submission? Thanks. H.

jipingw commented 3 years ago

Yes. Sorry for the delay. We are still on the revision of the codes. Thanks so much for the reminder.

From: Hervé Pagès notifications@github.com Reply-To: Bioconductor/Contributions reply@reply.github.com Date: Friday, December 11, 2020 at 11:30 AM To: Bioconductor/Contributions Contributions@noreply.github.com Cc: jiping/wang User jzwang@northwestern.edu, Mention mention@noreply.github.com Subject: Re: [Bioconductor/Contributions] RiboDiPA: Differential Pattern Analysis for Ribo-seq data (#1741)

Hi @jipingwhttps://urldefense.com/v3/__https:/github.com/jipingw__;!!Dq0X2DkFhyF93HkjWTBQKhk!A0T0Nzxp9V_I4QHpU1_iAKnrwH8tl-FmEgVXvb5xnW8R5sr_sRiPwHg-IrnEuPzTg6t1Jg$ -- do you intend to followup on this submission? Thanks. H.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/Bioconductor/Contributions/issues/1741*issuecomment-743325703__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!A0T0Nzxp9V_I4QHpU1_iAKnrwH8tl-FmEgVXvb5xnW8R5sr_sRiPwHg-IrnEuPwqj3syTA$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AKYHUXA52HUOE7L5O32TBFDSUJJKTANCNFSM4TGQOGPA__;!!Dq0X2DkFhyF93HkjWTBQKhk!A0T0Nzxp9V_I4QHpU1_iAKnrwH8tl-FmEgVXvb5xnW8R5sr_sRiPwHg-IrnEuPxrkznJnQ$.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 55ce2f9644413431a6ddfce6b238911a4e5d7621

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jipingw commented 3 years ago

@hpages Hi, there is an error from RiboDiPA.Rmd in lines 191-194. But I cannot figure what the error could be as the RiboDiPA.Rmd compile without problem locally. Could you give me some hints on this? I am using mac. Thanks.

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, WARNINGS, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 37749eff88bff6b89ca3504d8edd435045a4246d

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

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Your package has been built on Linux, Mac, and Windows.

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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bioc-issue-bot commented 3 years ago

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jipingw commented 3 years ago

@hpages Hi, could you give me some help on the most recent report? on Windows system, it keeps complaining about an error in index the bam file, which was not encountered in the other two platforms? I don't have any clue about this error. Thanks!

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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jipingw commented 3 years ago

@ttriche @mtmorgan

The RiboDiPA currently has two issues:

  1. warning: R > 4.1 is suggested instead of 4.0. But 4.1 is not available for download yet. Some users requested to set R>4.0. So I still set it as R>4.0.
  2. there was an error in Windows platform, which we don’t understand. Could anyone provide some hints or help on this issue?
mtmorgan commented 3 years ago

The files should be downloaded with mode = "wb" but a better strategy is to use BiocFIleCache as outlined in the vignette http://bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#local-cache-of-an-internet-resource.

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/RiboDiPA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

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jipingw commented 3 years ago

@mtmorgan @hpages @ttriche Could please help? I have no clue why windows platform always generate some error. thanks.

kerenli commented 3 years ago

Here is the section caused error in x64 but works well in i386:

Running examples in 'RiboDiPA-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: psiteCal
> ### Title: P-site position of reads
> ### Aliases: psiteCal
> 
> ### ** Examples
> 
> ex.cigar <- c("21M74731N7M", "2S11M57302N12M3S", "28M", "27M1S")
> ex.start <- c(177640, 249163, 249286, 249290)
> ex.psitemap <- c(9, 18, 9, 9)
> psiteCal(ex.cigar, ex.start, ex.psitemap)

where function psiteCal() is defined by

#include <Rcpp.h>
#include <iostream>
#include <vector>
#include <cstring>
#include <stdio.h>

using namespace Rcpp;

// [[Rcpp::export]]
NumericVector psiteCal(CharacterVector cigar, IntegerVector start, IntegerVector psitemap){

  int n=start.size();
  NumericVector center(n);

  /* prase cigar durations */

  for (int i=0; i < n; i++){

    char temp[strlen(cigar[i])];
    strcpy(temp,cigar[i]);
    /*Rcout << temp<<std::endl;*/
    char * pch;
    pch= strtok(temp,"MIDNSHP=X");
    int j=0;
    NumericVector duration(10);
    while (pch != NULL)
    {
      duration[j]=std::atoi(pch);
      /*Rcout << pch<<std::endl;*/
      pch = strtok (NULL, "MIDNSHP=X");
      j=j+1;
    }
    duration=duration[Rcpp::Range(0,j-1)];
    /*Rcout <<duration<<std::endl;  */
    center[i]= duration[0];
    /*Rcout<<"center:" <<center[i]<<std::endl;*/

    /* prase letters*/
    strcpy(temp,cigar[i]);
    /*Rcout << temp<<std::endl;*/
    pch = strtok(temp, "0123456789");

    j=0;
    CharacterVector letter(10);

    while (pch != NULL)
    {
      letter[j]=pch;
      /*Rcout << pch<<std::endl;*/
      pch = strtok(NULL, "0123456789");
      j=j+1;
    }
    letter=letter[Rcpp::Range(0,j-1)];

    /*Rcout <<letter<<std::endl;  */

    /*calculate read center*/
    int readlength=0;
    for (j=0;j<letter.size();j++){
      if(letter[j]=="M"||letter[j]=="I"||letter[j]=="S"||letter[j]=="="||letter[j]=="X"){
        readlength=readlength+duration[j];
      }
    }

    /*Rcout<<"read length "<<readlength<<std::endl;*/
    int fragmentlength=0;
    int position=start[i];

    if(duration.size()==1)
      center(i)=start[i]+psitemap[i];
    else{
      j=0;
      while(j<duration.size()){
        if(letter[j]=="M"||letter[j]=="X"||letter[j]=="="){
          fragmentlength=fragmentlength+duration[j];
          position=position+duration[j];
          if(fragmentlength>psitemap[i]){
            center[i]=position-(fragmentlength-psitemap[i]);
            j=duration.size();}
        }else if(letter[j]=="I")
          fragmentlength=fragmentlength+duration[j];
        else if(letter[j]=="S"){
          fragmentlength=fragmentlength+duration[j];
          if (j>0)
            position=position+duration[j];
        }else if(letter[j]=="N"||letter[j]=="D"){
          position=position+duration[j];
        }
        j=j+1;
      }
    }
    /*Rcout<<"fragmentlength "<<fragmentlength<<std::endl;*/
  }
  /*Rcout<<"center"<<center<<std::endl;*/
  return center;
}

Is there any library not work in x64?

Thank you.

mtmorgan commented 3 years ago

Isn't this

    char temp[strlen(cigar[i])];
    strcpy(temp,cigar[i]);

memory corruption, because strlen("foo") returns three, but strcpy(temp, "foo") writes four characters (including the \0).

Have you used valgrind or similar to look for these problems?