Fix to readJunctionSeqCounts() countdata handling#22
Open
ALysaght wants to merge 1 commit intohartleys:masterfrom
Open
Fix to readJunctionSeqCounts() countdata handling#22ALysaght wants to merge 1 commit intohartleys:masterfrom
ALysaght wants to merge 1 commit intohartleys:masterfrom
Conversation
Formal `countdata` is expected to be a list of data.frames which is passed to `lf` in line 608. In line 611, the code segment `x$V1 == lf[1]$V1` attempted to confirm that the order of all feature ids was the same in the current and first input data.frames. However, `lf[1]` returns a list containing 1 data.frame instead of the data.frame itself, so `lf[1]$V1` returns `NULL` and throws the following warning:
```
> if (!all(sapply(lf[-1], function(x) all(x$V1 == lf[1]$V1))))
+ stop("Count files have differing gene ID column.")
Warning message:
In is.na(e2) : is.na() applied to non-(list or vector) of type 'NULL'
```
Owner
|
This looks like something specific to a new version of R that changed basic
functons.
What versions of R have you tried this with?
On May 19, 2017 2:54 PM, "Andrew" <notifications@github.com> wrote:
Formal countdata is expected to be a list of data.frames which is passed to
lf in line 608. In line 611, the code segment x$V1 == lf[1]$V1 attempted to
confirm that the order of all feature ids was the same in the current and
first input data.frames. However, lf[1] returns a list containing 1
data.frame instead of the data.frame itself, so lf[1]$V1 returns NULL and
throws the following warning:
if (!all(sapply(lf[-1], function(x) all(x$V1 == lf[1]$V1))))
+ stop("Count files have differing gene ID column.")
Warning message:
In is.na(e2) : is.na() applied to non-(list or vector) of type 'NULL'
…------------------------------
You can view, comment on, or merge this pull request online at:
#22
Commit Summary
- Fix to readJunctionSeqCounts() countdata handling
File Changes
- *M* JunctionSeq/R/func.R
<https://github.com/hartleys/JunctionSeq/pull/22/files#diff-0> (2)
Patch Links:
- https://github.com/hartleys/JunctionSeq/pull/22.patch
- https://github.com/hartleys/JunctionSeq/pull/22.diff
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#22>, or mute the thread
<https://github.com/notifications/unsubscribe-auth/ACwu7KtlDiaz3c1djJf6jEd_AZipO7SUks5r7eVLgaJpZM4Ng4_o>
.
|
Author
|
Hi, thanks for the quick reply!
As I understand it, `[` returns a subset of the original list, and `[[`
returns the contents of a specified list element:
"Lists
Subsetting a list works in the same way as subsetting an atomic vector.
Using [ will always return a list; [[ and $, as described below, let you
pull out the components of the list." (source
<http://adv-r.had.co.nz/Subsetting.html>)
sessionInfo()R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
…On Fri, May 19, 2017 at 6:10 PM, hartleys ***@***.***> wrote:
This looks like something specific to a new version of R that changed basic
functons.
What versions of R have you tried this with?
On May 19, 2017 2:54 PM, "Andrew" ***@***.***> wrote:
Formal countdata is expected to be a list of data.frames which is passed to
lf in line 608. In line 611, the code segment x$V1 == lf[1]$V1 attempted to
confirm that the order of all feature ids was the same in the current and
first input data.frames. However, lf[1] returns a list containing 1
data.frame instead of the data.frame itself, so lf[1]$V1 returns NULL and
throws the following warning:
> if (!all(sapply(lf[-1], function(x) all(x$V1 == lf[1]$V1))))
+ stop("Count files have differing gene ID column.")
Warning message:
In is.na(e2) : is.na() applied to non-(list or vector) of type 'NULL'
------------------------------
You can view, comment on, or merge this pull request online at:
#22
Commit Summary
- Fix to readJunctionSeqCounts() countdata handling
File Changes
- *M* JunctionSeq/R/func.R
<https://github.com/hartleys/JunctionSeq/pull/22/files#diff-0> (2)
Patch Links:
- https://github.com/hartleys/JunctionSeq/pull/22.patch
- https://github.com/hartleys/JunctionSeq/pull/22.diff
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#22>, or mute the thread
<https://github.com/notifications/unsubscribe-
auth/ACwu7KtlDiaz3c1djJf6jEd_AZipO7SUks5r7eVLgaJpZM4Ng4_o>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#22 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AKfF1NOtzhNzUlX2qY5B9aHEn4FDgmj1ks5r7hNCgaJpZM4Ng4_o>
.
--
Andrew Lysaght
andrewlysaght@gmail.com
|
Owner
|
That code is legacy code from (an old version of) DEXSeq. How have I not
seen this error before?
Heck, this function gets called in the build. According to the doc i'm
reading, it shouldn't even build...
On May 19, 2017 6:35 PM, "Andrew" <notifications@github.com> wrote:
Hi, thanks for the quick reply!
As I understand it, `[` returns a subset of the original list, and `[[`
returns the contents of a specified list element:
"Lists
Subsetting a list works in the same way as subsetting an atomic vector.
Using [ will always return a list; [[ and $, as described below, let you
pull out the components of the list." (source
<http://adv-r.had.co.nz/Subsetting.html>)
sessionInfo()R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
On Fri, May 19, 2017 at 6:10 PM, hartleys ***@***.***> wrote:
This looks like something specific to a new version of R that changed
basic
functons.
What versions of R have you tried this with?
On May 19, 2017 2:54 PM, "Andrew" ***@***.***> wrote:
Formal countdata is expected to be a list of data.frames which is passed
to
lf in line 608. In line 611, the code segment x$V1 == lf[1]$V1 attempted
to
confirm that the order of all feature ids was the same in the current and
first input data.frames. However, lf[1] returns a list containing 1
data.frame instead of the data.frame itself, so lf[1]$V1 returns NULL and
throws the following warning:
> if (!all(sapply(lf[-1], function(x) all(x$V1 == lf[1]$V1))))
+ stop("Count files have differing gene ID column.")
Warning message:
In is.na(e2) : is.na() applied to non-(list or vector) of type 'NULL'
------------------------------
You can view, comment on, or merge this pull request online at:
#22
Commit Summary
- Fix to readJunctionSeqCounts() countdata handling
File Changes
- *M* JunctionSeq/R/func.R
<https://github.com/hartleys/JunctionSeq/pull/22/files#diff-0> (2)
Patch Links:
- https://github.com/hartleys/JunctionSeq/pull/22.patch
- https://github.com/hartleys/JunctionSeq/pull/22.diff
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#22>, or mute the thread
<https://github.com/notifications/unsubscribe-
auth/ACwu7KtlDiaz3c1djJf6jEd_AZipO7SUks5r7eVLgaJpZM4Ng4_o>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#22 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/
AKfF1NOtzhNzUlX2qY5B9aHEn4FDgmj1ks5r7hNCgaJpZM4Ng4_o>
… .
--
Andrew Lysaght
andrewlysaght@gmail.com
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#22 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ACwu7J-EtfvfxKTY-2WgtU6Wxv0GYoN8ks5r7hkvgaJpZM4Ng4_o>
.
|
Author
|
It's throwing a warning not an error, so I don't know if that would cause a build to fail. I was just trying to find the source of the warning and realized the test was not accomplishing what it was intended to do.
Wasn't trying to create a headache for you, just help out a little.
Best,
Andrew
… On May 19, 2017, at 7:39 PM, hartleys ***@***.***> wrote:
That code is legacy code from (an old version of) DEXSeq. How have I not
seen this error before?
Heck, this function gets called in the build. According to the doc i'm
reading, it shouldn't even build...
On May 19, 2017 6:35 PM, "Andrew" ***@***.***> wrote:
Hi, thanks for the quick reply!
As I understand it, `[` returns a subset of the original list, and `[[`
returns the contents of a specified list element:
"Lists
Subsetting a list works in the same way as subsetting an atomic vector.
Using [ will always return a list; [[ and $, as described below, let you
pull out the components of the list." (source
<http://adv-r.had.co.nz/Subsetting.html>)
> sessionInfo()R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
On Fri, May 19, 2017 at 6:10 PM, hartleys ***@***.***> wrote:
> This looks like something specific to a new version of R that changed
basic
> functons.
>
> What versions of R have you tried this with?
>
> On May 19, 2017 2:54 PM, "Andrew" ***@***.***> wrote:
>
> Formal countdata is expected to be a list of data.frames which is passed
to
> lf in line 608. In line 611, the code segment x$V1 == lf[1]$V1 attempted
to
> confirm that the order of all feature ids was the same in the current and
> first input data.frames. However, lf[1] returns a list containing 1
> data.frame instead of the data.frame itself, so lf[1]$V1 returns NULL and
> throws the following warning:
>
> > if (!all(sapply(lf[-1], function(x) all(x$V1 == lf[1]$V1))))
> + stop("Count files have differing gene ID column.")
> Warning message:
> In is.na(e2) : is.na() applied to non-(list or vector) of type 'NULL'
>
> ------------------------------
> You can view, comment on, or merge this pull request online at:
>
> #22
> Commit Summary
>
> - Fix to readJunctionSeqCounts() countdata handling
>
> File Changes
>
> - *M* JunctionSeq/R/func.R
> <https://github.com/hartleys/JunctionSeq/pull/22/files#diff-0> (2)
>
> Patch Links:
>
> - https://github.com/hartleys/JunctionSeq/pull/22.patch
> - https://github.com/hartleys/JunctionSeq/pull/22.diff
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#22>, or mute the thread
> <https://github.com/notifications/unsubscribe-
> auth/ACwu7KtlDiaz3c1djJf6jEd_AZipO7SUks5r7eVLgaJpZM4Ng4_o>
> .
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#22 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/
AKfF1NOtzhNzUlX2qY5B9aHEn4FDgmj1ks5r7hNCgaJpZM4Ng4_o>
> .
>
--
Andrew Lysaght
***@***.***
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#22 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ACwu7J-EtfvfxKTY-2WgtU6Wxv0GYoN8ks5r7hkvgaJpZM4Ng4_o>
.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or mute the thread.
|
Owner
|
Ah! Gotcha. I thought the stop was being triggered, hence the confusion.
In any event. I'll merge in the patch.
Thanks for the catch! Always appreciated!
…On May 19, 2017 10:59 PM, "Andrew" ***@***.***> wrote:
It's throwing a warning not an error, so I don't know if that would cause
a build to fail. I was just trying to find the source of the warning and
realized the test was not accomplishing what it was intended to do.
Wasn't trying to create a headache for you, just help out a little.
Best,
Andrew
> On May 19, 2017, at 7:39 PM, hartleys ***@***.***> wrote:
>
> That code is legacy code from (an old version of) DEXSeq. How have I not
> seen this error before?
>
> Heck, this function gets called in the build. According to the doc i'm
> reading, it shouldn't even build...
>
>
> On May 19, 2017 6:35 PM, "Andrew" ***@***.***> wrote:
>
> Hi, thanks for the quick reply!
>
> As I understand it, `[` returns a subset of the original list, and `[[`
> returns the contents of a specified list element:
>
> "Lists
>
> Subsetting a list works in the same way as subsetting an atomic vector.
> Using [ will always return a list; [[ and $, as described below, let you
> pull out the components of the list." (source
> <http://adv-r.had.co.nz/Subsetting.html>)
>
>
>
> > sessionInfo()R version 3.4.0 (2017-04-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.1 LTS
>
> Matrix products: default
> BLAS: /usr/lib/libblas/libblas.so.3.6.0
> LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
>
>
>
>
>
> On Fri, May 19, 2017 at 6:10 PM, hartleys ***@***.***>
wrote:
>
> > This looks like something specific to a new version of R that changed
> basic
> > functons.
> >
> > What versions of R have you tried this with?
> >
> > On May 19, 2017 2:54 PM, "Andrew" ***@***.***> wrote:
> >
> > Formal countdata is expected to be a list of data.frames which is
passed
> to
> > lf in line 608. In line 611, the code segment x$V1 == lf[1]$V1
attempted
> to
> > confirm that the order of all feature ids was the same in the current
and
> > first input data.frames. However, lf[1] returns a list containing 1
> > data.frame instead of the data.frame itself, so lf[1]$V1 returns NULL
and
> > throws the following warning:
> >
> > > if (!all(sapply(lf[-1], function(x) all(x$V1 == lf[1]$V1))))
> > + stop("Count files have differing gene ID column.")
> > Warning message:
> > In is.na(e2) : is.na() applied to non-(list or vector) of type 'NULL'
> >
> > ------------------------------
>
> > You can view, comment on, or merge this pull request online at:
> >
> > #22
> > Commit Summary
> >
> > - Fix to readJunctionSeqCounts() countdata handling
> >
> > File Changes
> >
> > - *M* JunctionSeq/R/func.R
> > <https://github.com/hartleys/JunctionSeq/pull/22/files#diff-0> (2)
> >
> > Patch Links:
> >
> > - https://github.com/hartleys/JunctionSeq/pull/22.patch
> > - https://github.com/hartleys/JunctionSeq/pull/22.diff
>
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub
> > <#22>, or mute the thread
> > <https://github.com/notifications/unsubscribe-
> > auth/ACwu7KtlDiaz3c1djJf6jEd_AZipO7SUks5r7eVLgaJpZM4Ng4_o>
> > .
> >
> > —
> > You are receiving this because you authored the thread.
>
> > Reply to this email directly, view it on GitHub
> > <#22#
issuecomment-302822817>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/
> AKfF1NOtzhNzUlX2qY5B9aHEn4FDgmj1ks5r7hNCgaJpZM4Ng4_o>
> > .
> >
>
>
>
> --
> Andrew Lysaght
> ***@***.***
>
> —
> You are receiving this because you commented.
>
> Reply to this email directly, view it on GitHub
> <#22 (comment)
>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/ACwu7J-EtfvfxKTY-
2WgtU6Wxv0GYoN8ks5r7hkvgaJpZM4Ng4_o>
> .
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
>
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#22 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/ACwu7OnCjmA4UTEbud1oQPQqBfEUSth7ks5r7lcOgaJpZM4Ng4_o>
.
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Formal
countdatais expected to be a list of data.frames which is passed tolfin line 608. In line 611, the code segmentx$V1 == lf[1]$V1attempted to confirm that the order of all feature ids was the same in the current and first input data.frames. However,lf[1]returns a list containing 1 data.frame instead of the data.frame itself, solf[1]$V1returnsNULLand throws the following warning: