CasedUgr commented 5 years ago

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

Repository: https://github.com/CasedUgr/KnowSeq

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 5 years ago

Hi @CasedUgr

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: KnowSeq
Type: Package
Title: A R package to extract knowledge by using RNA-seq raw files. 
Version: 0.9.99
Author: Daniel Castillo, Juan Manuel Galvez, Luis Javier Herrera and Ignacio Rojas.
Maintainer: Daniel Castillo Secilla <cased@ugr.es>
Description: KnowSeq proposes a whole pipeline that comprises the most relevant steps in the RNA-seq gene expression analysis. In this sense, this package allows align raw data from the original fastq files by using the most renowned aligners such as tophat2, hisat2, salmon and kallisto. This is the most important implementation of this package as with only a text file with the information of the samples to align, the tool will perform the download and alignment of all of them automatically with the selected aligner. Furthermore, the package includes functions to calculate the gene expression values, to remove batch effect, to calculate the Differentially Expressed Genes (DEGs), to plot different graphs, and to perform the DEGs enrichment with the GO information, pathways visualization and related diseases information retrieval.
VignetteBuilder: knitr
License: GPL (>=2)
Depends: R (>= 3.5.0), quantreg, mclust, Biobase, multtest, topGO (>= 2.34.0), pathview (>= 1.22.3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
biocViews: GeneExpressionWorkflow
Imports: stringr, factoextra, ggplot2, reshape2, gplots, caret, RCurl, XML, class, praznik, R.utils, e1071, randomForest, httr, jsonlite, sva (>= 3.30.1), cqn (>= 1.28.1), edgeR (>= 3.24.3), biomaRt (>= 2.38.0), limma (>= 3.38.3), arrayQualityMetrics (>= 3.38.0), tximport (>= 1.10.1), tximportData (>= 1.10.0), rhdf5 (>= 2.26.2)

mtmorgan commented 5 years ago

Please update your vignette to include fully evaluated code chunks

```{r}
...
```

rather than

```r
```

The header also requires revision, to

KnowSeq/vignettes master$ less KnowSeq.Rmd
~/a/new_packages/KnowSeq/vignettes master$ git diff KnowSeq.Rmd
diff --git a/vignettes/KnowSeq.Rmd b/vignettes/KnowSeq.Rmd
index 5eb1249..5112a3f 100644
--- a/vignettes/KnowSeq.Rmd
+++ b/vignettes/KnowSeq.Rmd
@@ -23,8 +23,10 @@ header-includes:
 link-citations: yes
 BiocStyle::html_vignette:
   md_extensions: -autolink_bare_uris
-vignette: "%\\VignetteIndexEntry{The KnowSeq users guide} %\\VignetteEngine{knitr::rmarkdown}
-  %\\VignetteEncoding{UTF-8} \n"
+vignette: |
+  %\VignetteIndexEntry{The KnowSeq users guide}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---

Please also use the modern SummarizedExperiment rather than Biobase / ExpressionSet.

Please post a comment here when you have made these changes, and I will add your package to the review queue.

CasedUgr commented 5 years ago

Hello:

First of all, thanks for the quickly response. I have some trouble with the two requirements due to the nature of our package.

1.- Please update your vignette to include fully evaluated code chunks: Our package needs in the first step of the pipeline the user interaction. Due to this consideration, the full evaluated code chunk rais an error just at the start of the documentation that doesn't allows to continue the evaluation correctly. We can't solve it because the code needs a folders hierarchy and a set of files that are created in real time, or by the user. If you could give us some advice to solve it We would appreciate it.

2.- Please also use the modern SummarizedExperiment [1] rather than Biobase / ExpressionSet: We use internally the Bioconductor package "ArrayQualityMetrics" to perform the Quality Analysis, and this library uses ExpressionSet. It is the only appearance of ExpressionSet in our package due to the Quality analysis step require it because "ArrayQualityMetrics" doesn't allows SummarizedExperiment. The only solution if the ExpressionSet has to be removed is make again the whole quality analysis step of our package.

Thank you in advance and I'm looking forward to hear from you.

El 2019-05-15 23:27, Martin Morgan escribió:

Please update your vignette to include fully evaluated code chunks
...
rather than
Please also use the modern SummarizedExperiment [1] rather than Biobase / ExpressionSet.

Please post a comment here when you have made these changes, and I will add your package to the review queue.

-- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub [2], or mute the thread [3].

Links:

[1] https://bioconductor.org/packages/SummarizedExperiment [2]

https://github.com/Bioconductor/Contributions/issues/1121?email_source=notifications&email_token=AI3MRDO62CJ37CQQ5CIENATPVR52RA5CNFSM4HND3P42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVP73KA#issuecomment-492830120 [3]

https://github.com/notifications/unsubscribe-auth/AI3MRDJG4EH2JGUGNGXW4GLPVR52RANCNFSM4HND3P4Q

-- Daniel Castillo Secilla Deparment of Architecture and Computer Technology (ATC) ETS Ing. Informática y Telecomunicación (ETSIIT) Centro de Investigación en Tecnologías de la Información y la Comunicación (CITIC) Despacho D1-7 University of Granada, Spain

mtmorgan commented 5 years ago

One can use 'mock' data from an existing experiment data package or a SMALL dataset included in the inst/extdata folder and accessible with system.file(package="<your package>", "extdata"). Outputs can be generated in dir <- tempfile(); dir.create(dir).

Since your package uses arrayQualityMetrics, you may ignore the second requirement.

CasedUgr commented 5 years ago

Hello:

The fully evaluated code chunk has been added to the documentation. There are only three pieces of code at the start of the documentation without the evaluation because the user interaction in command line is required, and it is imposible to achieved it in the markdown compiler. Concretely, the function rawAlignment but, the rest of the package can be evaluated in real time in the documentation. Furthermore, to carry out this goal, a new folder with 10 limited count files has been added to the extdata folder.

We hope that all would be fine now for the evaluation of our package but if you need more requirement just tell us.

Thank you in advance and I'm looking forward to hear from you.

bioc-issue-bot commented 5 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

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.

bioc-issue-bot commented 5 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.

bioc-issue-bot commented 5 years ago

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

5b8a736 KnowSeq V0.99.0ç

bioc-issue-bot commented 5 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.

bioc-issue-bot commented 5 years ago

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

b9c5911 KnowSeqV0.99.1

bioc-issue-bot commented 5 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.

bioc-issue-bot commented 5 years ago

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

d27fbd1 KnowSeqV0.99.2

bioc-issue-bot commented 5 years ago

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

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Kayla-Morrell commented 5 years ago

Hello @CasedUgr - Thank you for your submission to Bioconductor. I see that this is considered a workflow package based on the biocViews tag used in the DESCRIPTION file but then you also introduce some functionality within the package (much like a software package). My suggestion would be to put all the functionality into a separate software package and then have the workflow package be just an in-depth vignette walking through the functions. The software package can be added to this thread using 'Additional package:' with the github repo url. Please let me know if you have any questions.

Best, Kayla

CasedUgr commented 5 years ago

Dear Kayla. First of all, thanks for your message. We would like to note that we do not understand well the reasons to create two different packages (Software & Workflow). We see the package as you pointed out as a set of powerful functions with a workflow that can be followed from a source data to relevant knowledge that can be extracted from it.

So please if possible specify a little bit more why should be provide two different packages and how to organize them so that we can succesfully understand and apply the changes you require.

bioc-issue-bot commented 5 years ago

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

45f62e2 KnowSeq V0.99.4

bioc-issue-bot commented 5 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.

bioc-issue-bot commented 5 years ago

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

3090c45 KnowSeq V0.99.5

bioc-issue-bot commented 5 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.

bioc-issue-bot commented 5 years ago

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

4c08920 KnowSeq V0.99.6

bioc-issue-bot commented 5 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.

CasedUgr commented 5 years ago

Hello, We made tonight a new build changing the biocViews tag to tags related with a Software package. We thought that KnowSeq has better relation with this category. However, if you note that its also required another package with the workflow, we would do it.

Thank you in advance.

Best,

Daniel

Kayla-Morrell commented 5 years ago

Hello @CasedUgr - Thank you for making the changes. Since this package is now a software package then the additional workflow package is not needed. The idea of having a workflow package is to accompany a software package by demonstrating a pipeline through a more in-depth vignette, it's normally lighter weight and contains little to no actual R code. What you currently have is sufficient and I will continue with my review.

Best, Kayla

Kayla-Morrell commented 5 years ago

Hello @CasedUgr,

Thank you for your submission to Bioconductor. Please see the initial review of 'KnowSeq' below. Comment back here with updates that have been made and when the package is ready for re-review.

DESCRIPTION

[ ] REQUIRED: Malformed Title field: should not end in a period.
[ ] REQUIRED: Since you are using a standard license you don't need to include the 'LICENSE' file in the repository.
[ ] REQUIRED: 'LazyData:' should be set to false.
[ ] REQUIRED: The relation fields ('Depends', 'Imports', and 'Suggests') should be reworked. The 'Depends' should only include packages that provide essential functionality for your package. There usually isn't more than 3 packages listed here. 'R' is okay to be included but most of the other packages should be put elsewhere. The 'Imports' is for packages that provide functions, methods or classes that are used inside your package. Most packages are listed here. The 'Suggests' should be for packages not needed in order to load and use your package, it's mainly for packages used in vignettes or examples.
[ ] SUGGESTION: We suggest including the relevant link to a GitHub for reporting Issues.

NAMESPACE

[ ] SUGGESTION: Consider adding to NAMESPACE:
- importFrom("grDevices", "colorRampPalette", "dev.off", "hsv", "pdf", "png")
- importFrom("graphics", "abline", "axis", "box", "boxplot", "image", "layout", "lines", "par", "text", "title")
- importFrom("stats", "kmeans", "model.matrix", "p.adjust", "setNames")
- importFrom("utils", "download.file", "read.csv", "untar", "write.csv", "write.table")
[ ] SUGGESTION: Consider using importFrom() instead of import() if only using a few functions from a package.

NEWS

[ ] REQUIRED: It is good to include a NEWS file to keep track of changes but the file you have is not formatted correctly. For formatting help see this link https://bioconductor.org/developers/package-guidelines/#news.

data

[ ] REQUIRED: Be sure that the data in 'inst/extdata' is documented in the 'inst/script/' directory. It must be documented very clearly how the data was generated. It should also include source urls and any important information regarding filtering or processing. It can be executable code, sudo code or text description. The user should be able to download and be able to roughly reproduce the file or object that is present as data. (I believe this is the purpose of your 'examples.R' file, just rename if this is the case.)

Vignettes

[ ] REQUIRED: Line 39 is not needed and doesn't render correctly in the built vignette.
[ ] CLARIFIATION: After your section headers, I'm not sure what the purpose of '\<a name="">\<\a>' is after the header. I don't think they are rendering the way you intended them too.
[ ] REQUIRED: Add an “Installation” section that show to users how to download and load the package from Bioconductor.
[ ] SUGGESTION: We strongly encourage the use of table of contents.
[ ] REQUIRED: The link in line 60 does not work. Please fix this.
[ ] REQUIRED: All R code chunks need to contain '{}' so that the code is evaluated as R code. There are many code chunks that do not contain these curly braces, please correct this (line 76, 86, 146, 194, etc.).
[ ] REQUIRED: Line 76-82, when running this code locally I get the following error, please fix this:
```
downloadSamples = TRUE,  : 
formal argument "fromGDC" matched by multiple actual arguments
```
[ ] REQUIRED: Line 86-98, I get the same error as above when running this section of code.
[ ] CLARIFICATION: Line 146-151, the error message for this section of code indicates that the function is only suppported by GNU/Linux. Is this just when downloading raw data from the GDC portal or the rawAlignment function as a whole?
[ ] REQUIRED: Line 194-203, this section of code does not work properly. I think line 195 needs to be, dir <- system.file("examples", package="KnowSeq").
[ ] REQUIRED: Line 244 and 245, I got an error when running these lines of code. It seems to be an issue with biomaRt but I would just be sure the function is correct since I didn't get the error when running line 241. It very well could be from my end (or biomaRt) but I just wanted to bring your attention to a possible problem. See the error below:
```
values = values,  :
The query to the BioMart webservice returned an invalid result: biomaRt 
expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
```
[ ] CLARIFICATION: Line 259, towards the end of this line you explain that "in order to see the expression boxplot of each sample, the function has to be called with the parameter method equal to 'boxplot'...", I think the text should be 'mode' not 'method', since this is the paramet in the function that is set to 'boxplot'. This seems to be the case else where, like in line 279 and line 294.
[ ] REQUIRED: Line 306-315, this code does not work because there is an error produced in lines 309 and 310. In order for the rest of the code to work these lines should be fixed. The error is below:
```
stdev.coef.lim = stdev.coef.lim,  :
No residual degrees of freedom in linear model fits
```
[ ] REQUIRED: Line 370, this line of code produces an error:
```
object 'rfRankingPrueba' not found
```
[ ] REQUIRED: Line 375, this line of code doesn't work because of the error when creating 'rfRanking'.
[ ] REQUIRED: Line 429 and 430, these lines of code don't work because of the error when creating 'rfRanking'.
[ ] REQUIRED: Line 442 and 443, these lines don't work because of the error when creating 'results_test_svm'.
[ ] SUGGESTION: Line 455-463, for this section in particular (and maybe other sections of code) it may be helpful to set message to FALSE so that all of the messages for the function geneOntologyEnrichment does not get printed in the vignette. This can be done by adding {r Retrieving_GOs, message=FALSE} to the current code chunk.

[ ] REQUIRED: Line 480-482, I'm running into another issue with biomaRt. Please see the error below and try to fix it since the rest of the code relies on 'allMyAnnotation'.

values = values,  :
The query to the BioMart webservice returned an invalid result: biomaRt 
expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org

[ ] REQUIRED: The last section (before References) should be titled 'Session Info' and should include SessionInfo().
[ ] REQUIRED: Only the vignette file (.Rnw or .Rmd), any necessary static images, and bibliography information should be in the vignette directory. No intermediate files (such as R files) should be present.

man pages

[ ] REQUIRED: Add runnable examples to the following man pages which document exported objects:
- gdcClientDownload
- rawAlignment
- sraToFastq
[ ] SUGGESTION: For 'hisatAlignment', 'hallistoAlignment', 'rawAlignment', 'salmonAlignment', and 'tophapAlignment' I would suggest at least adding some example code so that when a user looks up the man page they will know how to perform the certain functions. You could add '\dontrun{}' around the code if need be since the functions are (or will be) pretty well tested in the vignette.

Unit tests

[ ] SUGGESTION: Consider adding unit tests. We strongly encourage them.

R code

[ ] REQUIRED: Use various apply functions, such as vapply() instead of for loops were applicable.
[ ] REQUIRED: Use system2() instead of system().
[ ] REQUIRED: Avoid sapply(), use vapply() instead. Found in files:
- svm_CV.R, line 72
- svm_CV.R, line 73
- svm_CV.R, line 97
- svm_CV.R, line 98
[ ] SUGGESTION: Consider shorter lines, 992 lines (18%) are > 80 characters long.
[ ] SUGGESTION: Consider multiples of 4 spaces for line indents, 1087 lines (20%) are not.

Best, Kayla

bioc-issue-bot commented 5 years ago

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

8713792 KnowSeqV0.99.7

bioc-issue-bot commented 5 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.

CasedUgr commented 5 years ago

Dear @Kayla-Morrell :

We have upload the new built with the revision requirements. In this sense, I am going to response each point in bold and italic. We hope that the package accomplish now the bioconductor guidelines, but if we have to perform more changes just tell us.

Thanks in advance for your revision.

DESCRIPTION

[x] REQUIRED: Malformed Title field: should not end in a period. Done.
[x] REQUIRED: Since you are using a standard license you don't need to include the 'LICENSE' file in the repository. The LICENSE file has been removed.
[x] REQUIRED: 'LazyData:' should be set to false. Done.
[x] REQUIRED: The relation fields ('Depends', 'Imports', and 'Suggests') should be reworked. The 'Depends' should only include packages that provide essential functionality for your package. There usually isn't more than 3 packages listed here. 'R' is okay to be included but most of the other packages should be put elsewhere. The 'Imports' is for packages that provide functions, methods or classes that are used inside your package. Most packages are listed here. The 'Suggests' should be for packages not needed in order to load and use your package, it's mainly for packages used in vignettes or examples. The packages mclust and quantreg does not well imported if we put them in imports with the importfrom in the namespace file. These packages are dependencies of other packages used by KnowSeq. Furthermore, if the package topGO is not included in the depends, the group go terms environments are not built and the gos enrichment fail. The rest of the packages have been moved to imports.
[x] SUGGESTION: We suggest including the relevant link to a GitHub for reporting Issues. The link to the github has been added.

NAMESPACE
[x] SUGGESTION: Consider adding to NAMESPACE:
- importFrom("grDevices", "colorRampPalette", "dev.off", "hsv", "pdf", "png")
- importFrom("graphics", "abline", "axis", "box", "boxplot", "image", "layout", "lines", "par", "text", "title")
- importFrom("stats", "kmeans", "model.matrix", "p.adjust", "setNames")
- importFrom("utils", "download.file", "read.csv", "untar", "write.csv", "write.table") Done.
[x] SUGGESTION: Consider using importFrom() instead of import() if only using a few functions from a package. Done.

NEWS
[x] REQUIRED: It is good to include a NEWS file to keep track of changes but the file you have is not formatted correctly. For formatting help see this link https://bioconductor.org/developers/package-guidelines/#news. The NEWS file has been formated correctly

data
[x] REQUIRED: Be sure that the data in 'inst/extdata' is documented in the 'inst/script/' directory. It must be documented very clearly how the data was generated. It should also include source urls and any important information regarding filtering or processing. It can be executable code, sudo code or text description. The user should be able to download and be able to roughly reproduce the file or object that is present as data. (I believe this is the purpose of your 'examples.R' file, just rename if this is the case.) You are right. Now the folder examples is named script.

Vignettes
[x] REQUIRED: Line 39 is not needed and doesn't render correctly in the built vignette. The line 39 has been removed.
[x] CLARIFIATION: After your section headers, I'm not sure what the purpose of '<\a>' is after the header. I don't think they are rendering the way you intended them too. These header was added to represent manually the Table of contents, but we have removed the headers and we have added the toc automatically.

[x] REQUIRED: Add an “Installation” section that show to users how to download and load the package from Bioconductor. Done.

[x] SUGGESTION: We strongly encourage the use of table of contents. Done.

[x] REQUIRED: The link in line 60 does not work. Please fix this. The link has been fixed

[x] REQUIRED: All R code chunks need to contain '{}' so that the code is evaluated as R code. There are many code chunks that do not contain these curly braces, please correct this (line 76, 86, 146, 194, etc.). These pieces of code are related to the alignment step. This step requires the user interaction and the download of a precompiled tools. Due to that considerations, it is not possible to evaluated these pieces of code in the vignette. The rest of the code, when the count files are available, can be evaluated without problems. However, the example code includes the alignment step to execute it.

[x] REQUIRED: Line 76-82, when running this code locally I get the following error, please fix this:

downloadSamples = TRUE,  : 
formal argument "fromGDC" matched by multiple actual arguments

Done.

[x] REQUIRED: Line 86-98, I get the same error as above when running this section of code. Done.

[x] CLARIFICATION: Line 146-151, the error message for this section of code indicates that the function is only suppported by GNU/Linux. Is this just when downloading raw data from the GDC portal or the rawAlignment function as a whole? _The alignment step makes use of a set of precompiled tools that are not available for Windows. Now, we are working on the MACOS version that will be included in the next official release. This step is the only limited step in KnowSeq. If the user has the count files, the rest of the pipeline can be executed no matter the OS.

[x] REQUIRED: Line 194-203, this section of code does not work properly. I think line 195 needs to be, dir <- system.file("examples", package="KnowSeq"). Done.

[x] REQUIRED: Line 244 and 245, I got an error when running these lines of code. It seems to be an issue with biomaRt but I would just be sure the function is correct since I didn't get the error when running line 241. It very well could be from my end (or biomaRt) but I just wanted to bring your attention to a possible problem. See the error below:

values = values,  :
The query to the BioMart webservice returned an invalid result: biomaRt 
expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org

This error has to be a punctual fail in the biomaRt servers. Maybe, in that moment the servers were overloaded because we cannot reproduce the error and the R check and BiocCheck tests pass without problems.

[x] CLARIFICATION: Line 259, towards the end of this line you explain that "in order to see the expression boxplot of each sample, the function has to be called with the parameter method equal to 'boxplot'...", I think the text should be 'mode' not 'method', since this is the paramet in the function that is set to 'boxplot'. This seems to be the case else where, like in line 279 and line 294. You are right. Done.

[x] REQUIRED: Line 306-315, this code does not work because there is an error produced in lines 309 and 310. In order for the rest of the code to work these lines should be fixed. The error is below:

stdev.coef.lim = stdev.coef.lim,  :
No residual degrees of freedom in linear model fits

This error could come from the previous biomaRt error. In our simulations and tests, the code is executed successfully for the three OS and for the R check and biocCheck functions.

[x] REQUIRED: Line 370, this line of code produces an error:

object 'rfRankingPrueba' not found

Done.

[x] REQUIRED: Line 375, this line of code doesn't work because of the error when creating 'rfRanking'. Done.

[x] REQUIRED: Line 429 and 430, these lines of code don't work because of the error when creating 'rfRanking'. Done.

[x] REQUIRED: Line 442 and 443, these lines don't work because of the error when creating 'results_test_svm'. Done.

[x] SUGGESTION: Line 455-463, for this section in particular (and maybe other sections of code) it may be helpful to set message to FALSE so that all of the messages for the function geneOntologyEnrichment does not get printed in the vignette. This can be done by adding {r Retrieving_GOs, message=FALSE} to the current code chunk. Done.

[x] REQUIRED: Line 480-482, I'm running into another issue with biomaRt. Please see the error below and try to fix it since the rest of the code relies on 'allMyAnnotation'.

values = values,  :
The query to the BioMart webservice returned an invalid result: biomaRt 
expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org

This error has to be a punctual fail just like the error above.

[x] REQUIRED: The last section (before References) should be titled 'Session Info' and should include SessionInfo(). Done.

[x] REQUIRED: Only the vignette file (.Rnw or .Rmd), any necessary static images, and bibliography information should be in the vignette directory. No intermediate files (such as R files) should be present. Done.

man pages

[x] REQUIRED: Add runnable examples to the following man pages which document exported objects:

gdcClientDownload
rawAlignment
sraToFastq For the rawAlignment, an example has been added with the \dontrun command due to the rawAlignment is the super-function to call the 'hisatAlignment', 'hallistoAlignment', 'rawAlignment', 'salmonAlignment', and 'tophapAlignment' just changing one parameter. For the gdcClientDownload, it is not possible to add a real example because it necessary to have the token file supply by GDC portal that grant authorization. Finally, it is not possible to add a real example to sraToFastq, due to this function needs one of the precompiled tools.

[x] SUGGESTION: For 'hisatAlignment', 'hallistoAlignment', 'rawAlignment', 'salmonAlignment', and 'tophapAlignment' I would suggest at least adding some example code so that when a user looks up the man page they will know how to perform the certain functions. You could add '\dontrun{}' around the code if need be since the functions are (or will be) pretty well tested in the vignette.

Done.

Unit tests

[x] SUGGESTION: Consider adding unit tests. We strongly encourage them. The unit tests have not been included in this release, but we are planning to add them in next releases when we planned them.

R code
[x] REQUIRED: Use various apply functions, such as vapply() instead of for loops were applicable. Done. Around 8 loops for was changed by vapply.
[x] REQUIRED: Use system2() instead of system(). Done.
[x] REQUIRED: Avoid sapply(), use vapply() instead. Found in files:
- svm_CV.R, line 72
- svm_CV.R, line 73
- svm_CV.R, line 97
- svm_CV.R, line 98

Done.

[x] SUGGESTION: Consider shorter lines, 992 lines (18%) are > 80 characters long. This change has not been applied.
[x] SUGGESTION: Consider multiples of 4 spaces for line indents, 1087 lines (20%) are not. This change has not been applied.

Best,

Daniel

Kayla-Morrell commented 5 years ago

Hello @CasedUgr - Thank you for making the necessary changes. I just have a couple more points and then your package should be ready to be accepted. Please comment back here when you are ready for me to look at the changes.

vignette

[ ] CLARIFICATION: You said that Table of Contents were added to the file, but when I build the vignette I don't see it. Since it is just a suggestion, it isn't needed but I thought I would point it out since you said you made the change.
- [ ] REQUIRED: All R code chunks need to contain '{}' so that the code is evaluated as R code. There are many code chunks that do not contain these curly braces, please correct this (line 76, 86, 146, 194, etc.). These pieces of code are related to the alignment step. This step requires the user interaction and the download of a precompiled tools. Due to that considerations, it is not possible to evaluated these pieces of code in the vignette. The rest of the code, when the count files are available, can be evaluated without problems. However, the example code includes the alignment step to execute it. If the chunks of R code shouldn't be evaluated then you should add 'eval = FALSE' but they still need to contain '{ }' so they are recognized as R code and not just text.

Best, Kayla

bioc-issue-bot commented 5 years ago

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

46811c3 KnowSeq V0.99.8

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

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

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

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

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

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Bioconductor / Contributions

KnowSeq R package #1121

Links:

DESCRIPTION

NAMESPACE

NEWS

data

Vignettes

man pages

Unit tests

R code

DESCRIPTION

NAMESPACE

NEWS

data

Vignettes

man pages

Unit tests

R code

vignette