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StarTrek #135

Closed claudiacava closed 7 years ago

claudiacava commented 7 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

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bioc-issue-bot commented 7 years ago

Hi @claudiacava

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: StarTrek
Type: Package
Title: StarTrek
Version: 0.99.0
Date: 09-22-2016
Author: Claudia Cava,
    Isabella Castiglioni
Maintainer: Claudia Cava <claudia.cava@ibfm.cnr.it>
Depends:
    R (>= 3.0.0)
Imports:
    SpidermiR,
    KEGGREST,
    org.Hs.eg.db,
    AnnotationDbi,
    TCGAbiolinks,
    e1071,
    ROCR,
    grDevices
Description: This tool StarTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.
License: GPL (>= 3)
biocViews: GeneRegulation,
    Network
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    testthat,
    devtools,
    roxygen2
VignetteBuilder: knitr
LazyData: true
URL: https://github.com/claudiacava/StarTrek
BugReports: https://github.com/claudiacava/StarTrek/issues
RoxygenNote: 5.0.1
lawremi commented 7 years ago

Someone needs to reopen this issue.

bioc-issue-bot commented 7 years ago

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

mtmorgan commented 7 years ago

StarTrek is likely an intellectual property infingement; this package will need to be renamed, but please refrain from doing so until the package has been accepted.

claudiacava commented 7 years ago

Thank you. I will wait the revisions and after I will change the name.

2016-09-23 15:31 GMT+02:00 Martin Morgan notifications@github.com:

StarTrek is likely an intellectual property infingement; this package will need to be renamed, but please refrain from doing so until the package has been accepted.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/135#issuecomment-249193658, or mute the thread https://github.com/notifications/unsubscribe-auth/ALH3HLYMs7L0o2qIjVcmD16op9q2XLNHks5qs9TNgaJpZM4KE6dB .

Dott.ssa Claudia Cava PhD Bioinformatics

National Research Council (CNR) Institute of Molecular Bioimaging and Physiology (IBFM) Laboratory of Innovation and Integration in Molecular Medicine (INLAB) F.lli Cervi 93 I 20093 Segrate (Mi), Italy

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20160923100306.html

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

5537dfd some fixes

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20160923120302.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

954e56c FIX3

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20160930090316.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

a266b3c FIX4

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20160930110028.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

52c3f10 fix5

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20160930121230.html

mtmorgan commented 7 years ago

@vjcitn will provide a formal review of this package.

vjcitn commented 7 years ago

This package v 0.99.4 is not passing check. It must do so ASAP. More comments below.

Accessing GDC. This might take a while... GDCdownload will download 4 files. A total of 1.743321 MB Downloading as: Sun_Oct__2_06_32_56_2016.tar.gz |======================================================================| 100%> ERROR Running examples in ‘StarTrek-Ex.R’ failed The error most likely occurred in:

Name: path_net

Title: Get human KEGG pathway data and network data in order to define

the common gene.

Aliases: path_net

\ Examples

lista_net<-path_net(pathway=path,net_type=netw) Error in ncol(pathway) : object 'path' not found Calls: path_net -> ncol Execution halted

The vignette and examples should not be acquiring data from remote sites, in my opinion, unless this can be accomplished rapidly and in a fail-safe manner. For example, if the network data acquisition times out, a static object in the package can be used to continue the intended computation.

The content of the vignette also needs work. Compiled, the final section reads:

Selection of pathway cross-talk: Selection of the cross-talk pathway

svm_classification: SVM classification

This function is used to find the interacting pathways that are altered in a particular pathology in terms of Area Under Curve (AUC).

cancer <- "TCGA-BRCA" PlatformCancer <- "Illumina HiSeq" tumo<-c("TCGA-BH-A0DL-01A-11R-A115-07","TCGA-AO-A03P-01A-11R-A00Z-07") norm<-c("TCGA-BH-A209-11A-42R-A157-07","TCGA-E9-A1N4-11A-33R-A14M-07") TCGA_data<-get_TCGAdata(cancer,PlatformCancer,tumour,normal, patha = "exampleData") nf <- 60

res_class<-svm_classification(TCGA_matrix=TCGA_data,nfs=nf,normal=norm,tumour=tumo)

The results of svm_classification() are not presented or explained. The purpose of the vignette is to go beyond the man page and examples, which are function-specific. The vignette should narrate the tasks of interest, giving some motivation, illustrating relevant data in a self-contained way, carrying out significant tasks and explaining the results.

I noticed one programming pattern that should be looked at for improvement.

in getdata.R, the following code series is repeated for each possible value of KEGG_path. This repetitive approach is hard to check and maintain. The repeated code should be isolated and reformulated.

if (KEGG_path=="Lip_met") { pathways.list <- keggList("pathway", "hsa")## returns the list of human pathways mer<-select_path_lip(Lipid) common<-intersect(pathways.list,mer) lo<-list() for (i in 1:length(pathways.list)){ if (length(intersect(pathways.list[[i]],common)!=0)){ lo[[i]]<-pathways.list[[i]] names(lo)[[i]]<-names(pathways.list)[[i]] } } pathways.list<-lo[lapply(lo,length)!=0] pathway.codes <- sub("path:", "", names(pathways.list)) a<-do.call("rbind", pathways.list) }

This bit of code seems susceptible to many simplifications, but by having it repeated for each possible setting of KEGG_path, you make it more complicated to achieve the improvements. I also question whether we should have variable "Lipid" passed to select_path_lip [which seems already to 'know' that it is doing something with lipids].

These comments on getdata.R are suggestions, not obligatory, as long as the code is working as a user would expect. However in the longer term where you want to maintain and improve the package, you will find this advice well worth following.

With improvements that enable R CMD check to pass, and some revision of the vignette, I will take another look at the package and may have some additional comments. I think it would be a good idea to look at the vignette of a related package, like KEGGgraph, to see what kind of narrative is typical. You don't have to be exhaustive in the vignette, but provide at least a single compelling example that illustrates how you conceive an analysis benefits from your package.

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

bf4d072 fix version

claudiacava commented 7 years ago

Thank the reviewer for constructive criticisms and valuable comments.

I have checked the error for the function path_net. Now, it works.

I have created a folder data that contain static object in order to avoid acquiring data from remote sites.

I have explained better in the vignette svm_classification the aims of function.

Now, I am working on the examples that show the benefits of my package and the improvement of the function getdata.

Meanwhile, I start a build to see if there are some errors or warnings.

2016-10-02 13:26 GMT+02:00 Vince Carey notifications@github.com:

This package v 0.99.4 is not passing check. It must do so ASAP. More comments below.

Accessing GDC. This might take a while... GDCdownload will download 4 files. A total of 1.743321 MB Downloading as: Sun_Oct__2_06_32_56_2016.tar.gz |======================================================================| 100%> ERROR Running examples in ‘StarTrek-Ex.R’ failed The error most likely occurred in:

Name: path_net Title: Get human KEGG pathway data and network data in order to define the common gene. Aliases: path_net \ Examples

lista_net<-path_net(pathway=path,net_type=netw) Error in ncol(pathway) : object 'path' not found Calls: path_net -> ncol Execution halted

The vignette and examples should not be acquiring data from remote sites, in my opinion, unless this can be accomplished rapidly and in a fail-safe manner. For example, if the network data acquisition times out, a static object in the package can be used to continue the intended computation.

The content of the vignette also needs work. Compiled, the final section

reads:

Selection of pathway cross-talk: Selection of the cross-talk pathway

svm_classification: SVM classification

This function is used to find the interacting pathways that are altered in a particular pathology in terms of Area Under Curve (AUC).

cancer <- "TCGA-BRCA" PlatformCancer <- "Illumina HiSeq" tumo<-c("TCGA-BH-A0DL-01A-11R-A115-07","TCGA-AO-A03P-01A-11R-A00Z-07") norm<-c("TCGA-BH-A209-11A-42R-A157-07","TCGA-E9-A1N4-11A-33R-A14M-07") TCGA_data<-get_TCGAdata(cancer,PlatformCancer,tumour,normal, patha = "exampleData") nf <- 60 res_class<-svm_classification(TCGA_matrix=TCGA_data,nfs=nf, normal=norm,tumour=tumo)

The results of svm_classification() are not presented or explained. The purpose of the vignette is to go beyond the man page and examples, which are function-specific. The vignette should narrate the tasks of interest, giving some motivation, illustrating relevant data in a self-contained way, carrying out significant tasks and explaining the results.

I noticed one programming pattern that should be looked at for improvement.

in getdata.R, the following code series is repeated for each possible value of KEGG_path. This repetitive approach is hard to check and maintain. The repeated code should be isolated and reformulated.

if (KEGG_path=="Lip_met") { pathways.list <- keggList("pathway", "hsa")## returns the list of human pathways mer<-select_path_lip(Lipid) common<-intersect(pathways.list,mer) lo<-list() for (i in 1:length(pathways.list)){ if (length(intersect(pathways.list[[i]],common)!=0)){ lo[[i]]<-pathways.list[[i]] names(lo)[[i]]<-names(pathways.list)[[i]] } } pathways.list<-lo[lapply(lo,length)!=0] pathway.codes <- sub("path:", "", names(pathways.list)) a<-do.call("rbind", pathways.list) }

This bit of code seems susceptible to many simplifications, but by having it repeated for each possible setting of KEGG_path, you make it more complicated to achieve the improvements. I also question whether we should have variable "Lipid" passed to select_path_lip [which seems already to 'know' that it is doing something with lipids].

These comments on getdata.R are suggestions, not obligatory, as long as the code is working as a user would expect. However in the longer term where you want to maintain and improve the package, you will find this advice well worth following.

With improvements that enable R CMD check to pass, and some revision of the vignette, I will take another look at the package and may have some additional comments. I think it would be a good idea to look at the vignette of a related package, like KEGGgraph, to see what kind of narrative is typical. You don't have to be exhaustive in the vignette, but provide at least a single compelling example that illustrates how you conceive an analysis benefits from your package.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/135#issuecomment-250966599, or mute the thread https://github.com/notifications/unsubscribe-auth/ALH3HMpzpQmkaNNLovA9eLauHQOCM6UFks5qv5TwgaJpZM4KE6dB .

Dott.ssa Claudia Cava PhD Bioinformatics

National Research Council (CNR) Institute of Molecular Bioimaging and Physiology (IBFM) Laboratory of Innovation and Integration in Molecular Medicine (INLAB) F.lli Cervi 93 I 20093 Segrate (Mi), Italy

vjcitn commented 7 years ago

On current pull I am finding

StarTrek_Application_Examples.Rmd

has non-ASCII characters.

The manual build fails

Warning in grep("\n", x) : input string 92 is invalid in this locale Warning in grep("^(---|...)\s*$", lines) : input string 92 is invalid in this locale Warning in grepl(chunk.begin, lines) : input string 92 is invalid in this locale Warning in grepl(chunk.end, lines) : input string 92 is invalid in this locale Quitting from lines 2-95 (StarTrek_Application_Examples.Rmd) Error: processing vignette 'StarTrek_Application_Examples.Rmd' failed with diagnostics: invalid multibyte string, element 1 Execution halted

line 92

Case Study n\xb01

             92
bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20161005113319.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

7f8d7a2 TESTING 1

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20161006042446.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

ed1d7da UPDATE

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20161006054211.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

45fd2b8 FIX TEST

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20161006070919.html

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

951b9fb testing4

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20161006104047.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

a1b92d7 fix examples

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20161006105134.html

vjcitn commented 7 years ago

I think you should avoid this. get the data you need into /data or /inst/extdata

Accessing GDC. This might take a while... GDCdownload will download: 1.743321 MB compressed in a tar.gz file Downloading as: Thu_Oct_06_03_31_22_2016.tar.gz

Downloading: 7.7 kB
Downloading: 7.7 kB
Downloading: 8.2 kB
Downloading: 8.2 kB
Downloading: 8.2 kB
Downloading: 8.2 kB

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

79afea9 deleting tcgadownload

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20161006132746.html

claudiacava commented 7 years ago

Thank you ! I have deleted that function. I have just seen a warning in the building system . I Think i can fix easily. Tomorrow I will fix it and I will continue to improve the code and vignette .

Inviato da iPhone

Il giorno 06 ott 2016, alle ore 17:51, Vince Carey notifications@github.com ha scritto:

I think you should avoid this. get the data you need into /data or /inst/extdata

Accessing GDC. This might take a while... GDCdownload will download: 1.743321 MB compressed in a tar.gz file Downloading as: Thu_Oct_06_03_31_22_2016.tar.gz

Downloading: 7.7 kB

Downloading: 7.7 kB

Downloading: 8.2 kB

Downloading: 8.2 kB

Downloading: 8.2 kB

Downloading: 8.2 kB

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or mute the thread.

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

a51e969 fixing warning

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20161007042635.html

vjcitn commented 7 years ago

Good progress. I think you should do something about the list_path_net example. It takes too long. Also a 22 minute build time seems excessive for this package.

Examples with CPU or elapsed time > 5s user system elapsed list_path_net 99.280 1.288 100.564 getNETdata 24.724 8.372 36.912 svm_classification 12.096 2.068 14.161 path_net 12.632 0.000 12.631 SelectedSample 2.700 7.124 9.826 getKEGGdata 4.740 0.288 6.928

claudiacava commented 7 years ago

You are right. I am working on.

2016-10-07 11:51 GMT+02:00 Vince Carey notifications@github.com:

Good progress. I think you should do something about the list_path_net example. It takes too long. Also a 22 minute build time seems excessive for this package.

Examples with CPU or elapsed time > 5s user system elapsed list_path_net 99.280 1.288 100.564 getNETdata 24.724 8.372 36.912 svm_classification 12.096 2.068 14.161 path_net 12.632 0.000 12.631 SelectedSample 2.700 7.124 9.826 getKEGGdata 4.740 0.288 6.928

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/135#issuecomment-252200539, or mute the thread https://github.com/notifications/unsubscribe-auth/ALH3HKeeiWRzp7SYz0S_DyB3-cRvWI8hks5qxhYugaJpZM4KE6dB .

Dott.ssa Claudia Cava PhD Bioinformatics

National Research Council (CNR) Institute of Molecular Bioimaging and Physiology (IBFM) Laboratory of Innovation and Integration in Molecular Medicine (INLAB) F.lli Cervi 93 I 20093 Segrate (Mi), Italy

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

9a2f0d6 fixing list_path_net

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/StarTrek_buildreport_20161007103847.html

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

claudiacava commented 7 years ago

I fixed the function list_path_net. I think now the package is faster. What do yuou think?

vjcitn commented 7 years ago

Be sure to bump the version and have the automated process run, and if you are under 10 mins we should be ready to go.

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

bioc-issue-bot commented 7 years ago

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.