[Bioc-devel] chimera Attempts to Open Non-existent File

2016-11-02 Thread Dario Strbenac 
Good day,

The importFusionData function fails trying to open a file that doesn't exist.

> fd = importFusionData("star", 
> "/verona/nobackup/biostat/datasets/melanoma/AAHChimeric.out.junction")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'Thu_Nov_3_13-46-27_2016': No such file or directory

The section of code where the error occurs seems to be in the .starImport 
function.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

2016-11-02 Thread Kevin RUE 
Me again :)

Please find attached the first patch to print the first 6 lines over 80
characters long. (I'll get to the tabulation offenders next).

Note that all the offending lines are stored in the "df.length" data.frame.
How about an option like "fullReport=c(FALSE, TRUE)" that print *all* the
offending lines?
The data.frame also stores the content of the lines for the record, but
does not print them. I think Kasper is right: filename and line should be
enough to track down the line.

All the best,
Kevin



On Wed, Nov 2, 2016 at 8:08 PM, Kevin RUE  wrote:

> Thanks for the feedback!
>
> I also tend to prefer *all* the lines being reported (or to be honest,
> that was really true when I had lots of them; a problem that I largely
> mitigated by fixing all of them once and subsequently paying more attention
> while developing).
>
> Printing the content of the offending line somewhat helps me spot the line
> faster (more so for tab issues). But I must admit that showing the whole
> line is somewhat "overkill". I just started thinking of a compromise being
> to only show the first N characters of the line, with N being 80 minus the
> number of characters necessary to print the filename and line number.
>
> Thanks Martin for pointing out the lines in BiocCheck. (Now I feel bad for
> not having checked sooner.. hehe!)
> I think the idea of BiocCheck showing the first 6 offenders in BiocCheck
> quite nice, as I rarely have more since I use using the RStudio "Tools >
> Global Options > Code > Display > Show Margin > Margin column: 80" feature.
>
> I'll give a go at both approaches (developing BiocCheck and my own scripts)
>
> Cheers,
> Kevin
>
>
> On Wed, Nov 2, 2016 at 7:41 PM, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
>
>> I would prefer all line numbers reported, but on the other hand I am
>> indifferent wrt. the content of the line, unless (say) TABs are marked up
>> somehow.
>>
>> Kasper
>>
>> On Wed, Nov 2, 2016 at 3:17 PM, Martin Morgan <
>> martin.mor...@roswellpark.org> wrote:
>>
>>> On 11/02/2016 02:49 PM, Kevin RUE wrote:
>>>
 Dear all,

 Just thought I'd share a handful of scripts that I wrote to follow up on
 certain NOTE messages thrown by R CMD BiocCheck.

 https://github.com/kevinrue/BiocCheckTools

 They're very simple, but I occasionally find them quite convenient.
 Apologies if something similar already exists somewhere :)

>>>
>>> Maybe consider creating a diff against the source code that, e.g.,
>>> reported the first 6 offenders? The relevant lines are near
>>>
>>> https://github.com/Bioconductor-mirror/BiocCheck/blob/master
>>> /R/checks.R#L1081
>>>
>>> Martin
>>>
>>>
 All the best,
 Kevin

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>>>
>>> This email message may contain legally privileged and/or...{{dropped:2}}
>>>
>>>
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>>
>>
>
diff --git a/R/checks.R b/R/checks.R
index f0b5844..9b1f273 100644
--- a/R/checks.R
+++ b/R/checks.R
@@ -1057,14 +1057,12 @@ checkFormatting <- function(pkgdir)
 tablines <- 0L
 badindentlines <- 0L
 ok <- TRUE
-
-df.length <- data.frame(stringsAsFactors=FALSE)
-df.i <- 1
+
 for (file in files)
 {
-pkgname <- getPkgNameFromPkgDir(pkgdir)
 if (file.exists(file) && file.info(file)$size == 0)
 {
+pkgname <- getPkgNameFromPkgDir(pkgdir)
 handleNote(sprintf("Add content to the empty file %s.",
 mungeName(file, pkgname)))
 }
@@ -1074,23 +1072,14 @@ checkFormatting <- function(pkgdir)
 lines <- readLines(file, warn=FALSE)
 totallines <- totallines + length(lines)
 n <- nchar(lines, allowNA=TRUE)
-n <- n[!is.na(n)]; lines <- lines[!is.na(n)]
+n <- n[!is.na(n)]
 
 names(n) <- seq_along(1:length(n))
-long <- which(n > 80)
-
+long <- n[n > 80]
 if (length(long))
 {
 ## TODO/FIXME We could tell the user here which lines are long
 ## in which files.
-for (i in long){
-df.length[df.i,1] <- mungeName(file, pkgname) # filename
-df.length[df.i,2] <- names(n)[i] # line number
-df.length[df.i,3] <- lines[i] # content
-df.length[df.i,4] <- n[i] # length
-df.i <- df.i + 1
-}
-
 longlines <- longlines + length(long)
 }
 
@@ -,22 +1100,12 @@ checkFormatting <- function(pkgdir)
 
 }
 }
-colnames(df.length) <- c("File",

Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

2016-11-02 Thread Kevin RUE 
Thanks for the feedback!

I also tend to prefer *all* the lines being reported (or to be honest, that
was really true when I had lots of them; a problem that I largely mitigated
by fixing all of them once and subsequently paying more attention while
developing).

Printing the content of the offending line somewhat helps me spot the line
faster (more so for tab issues). But I must admit that showing the whole
line is somewhat "overkill". I just started thinking of a compromise being
to only show the first N characters of the line, with N being 80 minus the
number of characters necessary to print the filename and line number.

Thanks Martin for pointing out the lines in BiocCheck. (Now I feel bad for
not having checked sooner.. hehe!)
I think the idea of BiocCheck showing the first 6 offenders in BiocCheck
quite nice, as I rarely have more since I use using the RStudio "Tools >
Global Options > Code > Display > Show Margin > Margin column: 80" feature.

I'll give a go at both approaches (developing BiocCheck and my own scripts)

Cheers,
Kevin


On Wed, Nov 2, 2016 at 7:41 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> I would prefer all line numbers reported, but on the other hand I am
> indifferent wrt. the content of the line, unless (say) TABs are marked up
> somehow.
>
> Kasper
>
> On Wed, Nov 2, 2016 at 3:17 PM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
>> On 11/02/2016 02:49 PM, Kevin RUE wrote:
>>
>>> Dear all,
>>>
>>> Just thought I'd share a handful of scripts that I wrote to follow up on
>>> certain NOTE messages thrown by R CMD BiocCheck.
>>>
>>> https://github.com/kevinrue/BiocCheckTools
>>>
>>> They're very simple, but I occasionally find them quite convenient.
>>> Apologies if something similar already exists somewhere :)
>>>
>>
>> Maybe consider creating a diff against the source code that, e.g.,
>> reported the first 6 offenders? The relevant lines are near
>>
>> https://github.com/Bioconductor-mirror/BiocCheck/blob/master
>> /R/checks.R#L1081
>>
>> Martin
>>
>>
>>> All the best,
>>> Kevin
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>> This email message may contain legally privileged and/or...{{dropped:2}}
>>
>>
>> ___
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>>
>
>

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Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

2016-11-02 Thread Martin Morgan 

On 11/02/2016 02:49 PM, Kevin RUE wrote:

Dear all,

Just thought I'd share a handful of scripts that I wrote to follow up on
certain NOTE messages thrown by R CMD BiocCheck.

https://github.com/kevinrue/BiocCheckTools

They're very simple, but I occasionally find them quite convenient.
Apologies if something similar already exists somewhere :)


Maybe consider creating a diff against the source code that, e.g., 
reported the first 6 offenders? The relevant lines are near


https://github.com/Bioconductor-mirror/BiocCheck/blob/master/R/checks.R#L1081

Martin



All the best,
Kevin

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Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

2016-11-02 Thread Kasper Daniel Hansen 
seems pretty useful.  Would be improved by a single master file which runs
everything and gives a report.

On Wed, Nov 2, 2016 at 2:49 PM, Kevin RUE  wrote:

> Dear all,
>
> Just thought I'd share a handful of scripts that I wrote to follow up on
> certain NOTE messages thrown by R CMD BiocCheck.
>
> https://github.com/kevinrue/BiocCheckTools
>
> They're very simple, but I occasionally find them quite convenient.
> Apologies if something similar already exists somewhere :)
>
> All the best,
> Kevin
>
> [[alternative HTML version deleted]]
>
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> Bioc-devel@r-project.org mailing list
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>

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[Bioc-devel] A handful of check to follow up on R CMD BiocCheck

2016-11-02 Thread Kevin RUE 
Dear all,

Just thought I'd share a handful of scripts that I wrote to follow up on
certain NOTE messages thrown by R CMD BiocCheck.

https://github.com/kevinrue/BiocCheckTools

They're very simple, but I occasionally find them quite convenient.
Apologies if something similar already exists somewhere :)

All the best,
Kevin

[[alternative HTML version deleted]]

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