[Bioc-devel] BiocCheck result

----- Original Message -----
From: "Karim Mezhoud" <kmezhoud at gmail.com>
To: bioc-devel at r-project.org
Sent: Friday, January 2, 2015 4:22:44 AM
Subject: [Bioc-devel] BiocCheck result

Dear all,

I have these comments and did not found solution for silencing them.

1 - What about Vignette?
The message (below) is saying you  need to evaluate more vignette chunks, as mentioned in the BiocCheck vignette (http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output) at least 50% of vignette chunks need to be evaluated, otherwise you get this RECOMMENDation.
2 - The version is "package.0.99.0.tar.gz"

Looks like you are running BiocCheck under Bioconductor 3.0 (the release version). You should be developing your package under the devel version of Bioconductor (currently 3.1, requires R-devel (R-3.2)). If you do that you won't see this message.
3 - In wich file can I clarify permanent objects. To avoid <<- I
create new
Environment with
myGlobalEnv <- new.env(parent = emptyenv())

I have many permanent objects because my package is a GUI. All these
objects are useful for different functions and reduce the computing
time
and the multiple running of the same function.

This is something that is best looked at during the package review process.
4- Indenting, Tabs and long lines were not found.
As mentioned in the BiocCheck output and in the vignette, the formatting suggestions are just suggestions. Some of them are more important than others, for example, most reviewers will insist on lines shorter than 80 columns, for readability's sake.
Can I submit with theses comments?
You can submit, and these issues will be looked at as part of the package review process.
Dan
Thanks
Karim

$requirements
character(0)

$recommendations
[1] "Evaluate more vignette chunks."               "y of x.y.z
version
should be even in release"

$considerations
[1] "Clarifying how objects Li, A, ttCasesGenProfs, EventTime,
Category,
Continu, Category, ttMain, CasesStudies, curselectCases, fname.GCT,
fname.CLS, ttMain, GenesDetails, CaseChoice, mSigDB_SubName,
GenesDetails,
lenght, ttCasesGenProfs, myGlobalEnv (used in canceR , dialogMut ,
dialogOptionPhenoTest, dialogOptionPhenoTest , getClinicalDataMatrix,
geteSet, getGCTCLSExample, getGeneExpMatrix, getGenesClassifier,
getGenesTree_MultipleCases, getGSEAlm_Diseases, getGSEAlm_Variables,
getMegaProfData, getMetDataMultipleGenes, getMSigDBExample ,
getMSigDBExample, GSEA, GSEA.Analyze.Sets, plot_1Gene_2GenProfs,
testCheckedCaseGenProf) were initialized. Maybe they are part of a
data set
loaded with data(), or perhaps part of an object referenced in with()
or
within()."
[2] "Shortening lines; 1227 lines (11%) are > 80 characters
long."

[3] "Replacing tabs with 4 spaces; 6 lines (0%) contain
tabs."

[4] "Indenting lines with a multiple of 4 spaces; 1752 lines (15%)
are
not."

	[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Dear Dr Dan,
Thanks,
With GUI package the vignette does not have chunks only for installation
paragraph.
Thanks
Karim

  ?__
 c/ /'_;~~~~kmezhoud
(*) \(*)   ?????  ??????
http://bioinformatics.tn/

On Fri, Jan 2, 2015 at 6:55 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

----- Original Message -----
From: "Karim Mezhoud" <kmezhoud at gmail.com>
To: bioc-devel at r-project.org
Sent: Friday, January 2, 2015 4:22:44 AM
Subject: [Bioc-devel] BiocCheck result

Dear all,

I have these comments and did not found solution for silencing them.

1 - What about Vignette?
The message (below) is saying you  need to evaluate more vignette chunks,
as mentioned in the BiocCheck vignette (
http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output)
at least 50% of vignette chunks need to be evaluated, otherwise you get
this RECOMMENDation.

2 - The version is "package.0.99.0.tar.gz"

Looks like you are running BiocCheck under Bioconductor 3.0 (the release
version). You should be developing your package under the devel version of
Bioconductor (currently 3.1, requires R-devel (R-3.2)). If you do that you
won't see this message.

3 - In wich file can I clarify permanent objects. To avoid <<- I
create new
Environment with
myGlobalEnv <- new.env(parent = emptyenv())

I have many permanent objects because my package is a GUI. All these
objects are useful for different functions and reduce the computing
time
and the multiple running of the same function.

This is something that is best looked at during the package review process.

4- Indenting, Tabs and long lines were not found.
As mentioned in the BiocCheck output and in the vignette, the formatting
suggestions are just suggestions. Some of them are more important than
others, for example, most reviewers will insist on lines shorter than 80
columns, for readability's sake.

Can I submit with theses comments?
You can submit, and these issues will be looked at as part of the package
review process.
Dan

Thanks
Karim

$requirements
character(0)

$recommendations
[1] "Evaluate more vignette chunks."               "y of x.y.z
version
should be even in release"

$considerations
[1] "Clarifying how objects Li, A, ttCasesGenProfs, EventTime,
Category,
Continu, Category, ttMain, CasesStudies, curselectCases, fname.GCT,
fname.CLS, ttMain, GenesDetails, CaseChoice, mSigDB_SubName,
GenesDetails,
lenght, ttCasesGenProfs, myGlobalEnv (used in canceR , dialogMut ,
dialogOptionPhenoTest, dialogOptionPhenoTest , getClinicalDataMatrix,
geteSet, getGCTCLSExample, getGeneExpMatrix, getGenesClassifier,
getGenesTree_MultipleCases, getGSEAlm_Diseases, getGSEAlm_Variables,
getMegaProfData, getMetDataMultipleGenes, getMSigDBExample ,
getMSigDBExample, GSEA, GSEA.Analyze.Sets, plot_1Gene_2GenProfs,
testCheckedCaseGenProf) were initialized. Maybe they are part of a
data set
loaded with data(), or perhaps part of an object referenced in with()
or
within()."
[2] "Shortening lines; 1227 lines (11%) are > 80 characters
long."

[3] "Replacing tabs with 4 spaces; 6 lines (0%) contain
tabs."

[4] "Indenting lines with a multiple of 4 spaces; 1752 lines (15%)
are
not."

      [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

----- Original Message -----
From: "Karim Mezhoud" <kmezhoud at gmail.com>
To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
Cc: bioc-devel at r-project.org
Sent: Friday, January 2, 2015 12:15:31 PM
Subject: Re: [Bioc-devel] BiocCheck result

Dear Dr Dan,
Thanks,

With GUI package the vignette does not have chunks only for
installation paragraph.

I'm not sure what you mean here, but I think you should just submit the package and these issues will be discussed during the review process.

Don't worry if your package does not pass BiocCheck the first time. We're here to help you through these things.

Thanks,
Dan
Thanks

Karim

?__
c/ /'_;~~~~kmezhoud
(*) \(*) ????? ??????
http://bioinformatics.tn/

On Fri, Jan 2, 2015 at 6:55 PM, Dan Tenenbaum <
dtenenba at fredhutch.org > wrote:

----- Original Message -----
From: "Karim Mezhoud" < kmezhoud at gmail.com >
To: bioc-devel at r-project.org
Sent: Friday, January 2, 2015 4:22:44 AM
Subject: [Bioc-devel] BiocCheck result

Dear all,

I have these comments and did not found solution for silencing
them.

1 - What about Vignette?
The message (below) is saying you need to evaluate more vignette
chunks, as mentioned in the BiocCheck vignette (
http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output
) at least 50% of vignette chunks need to be evaluated, otherwise
you get this RECOMMENDation.

2 - The version is "package.0.99.0.tar.gz"

Looks like you are running BiocCheck under Bioconductor 3.0 (the
release version). You should be developing your package under the
devel version of Bioconductor (currently 3.1, requires R-devel
(R-3.2)). If you do that you won't see this message.

3 - In wich file can I clarify permanent objects. To avoid <<- I
create new
Environment with
myGlobalEnv <- new.env(parent = emptyenv())

I have many permanent objects because my package is a GUI. All
these
objects are useful for different functions and reduce the computing
time
and the multiple running of the same function.

This is something that is best looked at during the package review
process.

4- Indenting, Tabs and long lines were not found.
As mentioned in the BiocCheck output and in the vignette, the
formatting suggestions are just suggestions. Some of them are more
important than others, for example, most reviewers will insist on
lines shorter than 80 columns, for readability's sake.

Can I submit with theses comments?
You can submit, and these issues will be looked at as part of the
package review process.
Dan

Thanks
Karim

$requirements
character(0)

$recommendations
[1] "Evaluate more vignette chunks." "y of x.y.z
version
should be even in release"

$considerations
[1] "Clarifying how objects Li, A, ttCasesGenProfs, EventTime,
Category,
Continu, Category, ttMain, CasesStudies, curselectCases, fname.GCT,
fname.CLS, ttMain, GenesDetails, CaseChoice, mSigDB_SubName,
GenesDetails,
lenght, ttCasesGenProfs, myGlobalEnv (used in canceR , dialogMut ,
dialogOptionPhenoTest, dialogOptionPhenoTest ,
getClinicalDataMatrix,
geteSet, getGCTCLSExample, getGeneExpMatrix, getGenesClassifier,
getGenesTree_MultipleCases, getGSEAlm_Diseases,
getGSEAlm_Variables,
getMegaProfData, getMetDataMultipleGenes, getMSigDBExample ,
getMSigDBExample, GSEA, GSEA.Analyze.Sets, plot_1Gene_2GenProfs,
testCheckedCaseGenProf) were initialized. Maybe they are part of a
data set
loaded with data(), or perhaps part of an object referenced in
with()
or
within()."
[2] "Shortening lines; 1227 lines (11%) are > 80 characters
long."

[3] "Replacing tabs with 4 spaces; 6 lines (0%) contain
tabs."

[4] "Indenting lines with a multiple of 4 spaces; 1752 lines (15%)
are
not."

[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel