Re: [Bioc-devel] Issues with GenomicRanges updates
Hi Herve,
Never mind, I see now I am still a day old, looks like I was looking at
your sessionInfo paste and thought it was mine, whoops. I'll give it
another try tomorrow with the new versions.
other attached packages:
[1] GenomicRanges_1.31.18 GenomeInfoDb_1.15.5 IRanges_2.13.24
[4] S4Vectors_0.17.31 BiocGenerics_0.25.3
-Nathan
On 02/10/2018 07:33 PM, Nathan Sheffield wrote:
According to my `sessionInfo` (see below), those are the versions I
had been using:
other attached packages:
[1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5 IRanges_2.13.25
[4] S4Vectors_0.17.31 BiocGenerics_0.25.3
And I had pulled them from biocLite...what's going on?
-Nathan
On 02/10/2018 06:19 PM, Hervé Pagès wrote:
Hi Nathan,
I can't reproduce this with the latest versions of S4Vectors (0.17.31),
IRanges (2.13.25), and GenomicRanges (1.31.19). Note that these versions
will only become available via biocLite() tomorrow but you can get them
directly from git.bioconductor.org.
With these versions, as.list, lapply, and mclapply work for on userSets:
> library(GenomicRanges)
> data("sample_input", package="LOLA")
> as.list(userSets)
$setA
GRanges object with 3142 ranges and 0 metadata columns:
seqnames ranges strand
[1] chr1 [ 437151, 438164] *
[2] chr1 [ 875730, 878363] *
[3] chr1 [ 933387, 937410] *
[4] chr1 [ 967966, 970238] *
[5] chr1 [1016863, 1017439] *
... ... ... ...
[3138] chrY [ 9364545, 9364859] *
[3139] chrY [ 9385471, 9385777] *
[3140] chrY [14532115, 14533600] *
[3141] chrY [23696580, 23696878] *
[3142] chrY [26959489, 26959716] *
---
seqinfo: 69 sequences from an unspecified genome; no seqlengths
$setB
GRanges object with 5831 ranges and 0 metadata columns:
seqnames ranges strand
[1] chr1 [ 28735, 29810] *
[2] chr1 [544738, 546649] *
[3] chr1 [713984, 714547] *
[4] chr1 [762416, 763445] *
[5] chr1 [805198, 805628] *
... ... ... ...
[5827] chrY [20508190, 20508452] *
[5828] chrY [21154603, 21155040] *
[5829] chrY [21238448, 21240005] *
[5830] chrY [26979889, 26980116] *
[5831] chrY [28773315, 28773544] *
---
seqinfo: 69 sequences from an unspecified genome; no seqlengths
> lapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
> mclapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
Note that you should not need to call as.list() on a GRangesList object
before passing it to lapply() or mclapply().
Let me know if the problem persist after you update.
Best,
H.
> sessionInfo()
R Under development (unstable) (2017-12-11 r73889)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS
Matrix products: default
BLAS: /home/hpages/R/R-3.5.r73889/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.5.r73889/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5 IRanges_2.13.25
[4] S4Vectors_0.17.31 BiocGenerics_0.25.3
loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0 compiler_3.5.0 tools_3.5.0
[4] XVector_0.19.8 GenomeInfoDbData_1.1.0 RCurl_1.95-4.10
[7] bitops_1.0-6
On 02/10/2018 02:48 PM, Nathan Sheffield wrote:
I'm having some issues getting my package LOLA to pass R CMD check
using the updated dev versions of GenomicRanges et al.
It seems like any time I try to apply something across a
"CompressedGRangesList" object, it's giving errors when I use
mclapply from parallel. Here's a reproducible example:
data("sample_input", package="LOLA")
library(parallel)
mclapply(userSets, length)
(loads packages...)
Error in lapply_CompressedList(X, FUN, ...) :
invalid output element of class "GRanges"
It works with regular lapply:
> lapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
This is running on the bioconductor docker devel_core2 container,
and I've then gone and updated to the latest dev versions of these
packages with `biocLite()`.
I earlier ran into issues using `as.list()` on these same
CompressedGRangesList objects. It used to be that I had to call
as.list when they were just GRangesList objects, but now that's
failing,
Re: [Bioc-devel] Issues with GenomicRanges updates
According to my `sessionInfo` (see below), those are the versions I had
been using:
other attached packages:
[1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5 IRanges_2.13.25
[4] S4Vectors_0.17.31 BiocGenerics_0.25.3
And I had pulled them from biocLite...what's going on?
-Nathan
On 02/10/2018 06:19 PM, Hervé Pagès wrote:
Hi Nathan,
I can't reproduce this with the latest versions of S4Vectors (0.17.31),
IRanges (2.13.25), and GenomicRanges (1.31.19). Note that these versions
will only become available via biocLite() tomorrow but you can get them
directly from git.bioconductor.org.
With these versions, as.list, lapply, and mclapply work for on userSets:
> library(GenomicRanges)
> data("sample_input", package="LOLA")
> as.list(userSets)
$setA
GRanges object with 3142 ranges and 0 metadata columns:
seqnames ranges strand
[1] chr1 [ 437151, 438164] *
[2] chr1 [ 875730, 878363] *
[3] chr1 [ 933387, 937410] *
[4] chr1 [ 967966, 970238] *
[5] chr1 [1016863, 1017439] *
... ... ... ...
[3138] chrY [ 9364545, 9364859] *
[3139] chrY [ 9385471, 9385777] *
[3140] chrY [14532115, 14533600] *
[3141] chrY [23696580, 23696878] *
[3142] chrY [26959489, 26959716] *
---
seqinfo: 69 sequences from an unspecified genome; no seqlengths
$setB
GRanges object with 5831 ranges and 0 metadata columns:
seqnames ranges strand
[1] chr1 [ 28735, 29810] *
[2] chr1 [544738, 546649] *
[3] chr1 [713984, 714547] *
[4] chr1 [762416, 763445] *
[5] chr1 [805198, 805628] *
... ... ... ...
[5827] chrY [20508190, 20508452] *
[5828] chrY [21154603, 21155040] *
[5829] chrY [21238448, 21240005] *
[5830] chrY [26979889, 26980116] *
[5831] chrY [28773315, 28773544] *
---
seqinfo: 69 sequences from an unspecified genome; no seqlengths
> lapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
> mclapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
Note that you should not need to call as.list() on a GRangesList object
before passing it to lapply() or mclapply().
Let me know if the problem persist after you update.
Best,
H.
> sessionInfo()
R Under development (unstable) (2017-12-11 r73889)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS
Matrix products: default
BLAS: /home/hpages/R/R-3.5.r73889/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.5.r73889/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5 IRanges_2.13.25
[4] S4Vectors_0.17.31 BiocGenerics_0.25.3
loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0 compiler_3.5.0 tools_3.5.0
[4] XVector_0.19.8 GenomeInfoDbData_1.1.0 RCurl_1.95-4.10
[7] bitops_1.0-6
On 02/10/2018 02:48 PM, Nathan Sheffield wrote:
I'm having some issues getting my package LOLA to pass R CMD check
using the updated dev versions of GenomicRanges et al.
It seems like any time I try to apply something across a
"CompressedGRangesList" object, it's giving errors when I use
mclapply from parallel. Here's a reproducible example:
data("sample_input", package="LOLA")
library(parallel)
mclapply(userSets, length)
(loads packages...)
Error in lapply_CompressedList(X, FUN, ...) :
invalid output element of class "GRanges"
It works with regular lapply:
> lapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
This is running on the bioconductor docker devel_core2 container, and
I've then gone and updated to the latest dev versions of these
packages with `biocLite()`.
I earlier ran into issues using `as.list()` on these same
CompressedGRangesList objects. It used to be that I had to call
as.list when they were just GRangesList objects, but now that's
failing, and so I've had to go take all calls to as.list out of my
code. This has solved that issue (I guess the updates made the
as.list calls unnecessary), but you can see it's still causing errors:
as.list(userSets)
Error in lapply_CompressedList(X, FUN, ...) :
invalid output element of class "GRanges"
-Nathan
```
> sessionInfo()
R Under development (unstable) (2018-02-04 r74204)
Re: [Bioc-devel] Issues with GenomicRanges updates
Hi Nathan,
I can't reproduce this with the latest versions of S4Vectors (0.17.31),
IRanges (2.13.25), and GenomicRanges (1.31.19). Note that these versions
will only become available via biocLite() tomorrow but you can get them
directly from git.bioconductor.org.
With these versions, as.list, lapply, and mclapply work for on userSets:
> library(GenomicRanges)
> data("sample_input", package="LOLA")
> as.list(userSets)
$setA
GRanges object with 3142 ranges and 0 metadata columns:
seqnames ranges strand
[1] chr1 [ 437151, 438164] *
[2] chr1 [ 875730, 878363] *
[3] chr1 [ 933387, 937410] *
[4] chr1 [ 967966, 970238] *
[5] chr1 [1016863, 1017439] *
... ... ......
[3138] chrY [ 9364545, 9364859] *
[3139] chrY [ 9385471, 9385777] *
[3140] chrY [14532115, 14533600] *
[3141] chrY [23696580, 23696878] *
[3142] chrY [26959489, 26959716] *
---
seqinfo: 69 sequences from an unspecified genome; no seqlengths
$setB
GRanges object with 5831 ranges and 0 metadata columns:
seqnames ranges strand
[1] chr1 [ 28735, 29810] *
[2] chr1 [544738, 546649] *
[3] chr1 [713984, 714547] *
[4] chr1 [762416, 763445] *
[5] chr1 [805198, 805628] *
... ... ......
[5827] chrY [20508190, 20508452] *
[5828] chrY [21154603, 21155040] *
[5829] chrY [21238448, 21240005] *
[5830] chrY [26979889, 26980116] *
[5831] chrY [28773315, 28773544] *
---
seqinfo: 69 sequences from an unspecified genome; no seqlengths
> lapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
> mclapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
Note that you should not need to call as.list() on a GRangesList object
before passing it to lapply() or mclapply().
Let me know if the problem persist after you update.
Best,
H.
> sessionInfo()
R Under development (unstable) (2017-12-11 r73889)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS
Matrix products: default
BLAS: /home/hpages/R/R-3.5.r73889/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.5.r73889/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5 IRanges_2.13.25
[4] S4Vectors_0.17.31 BiocGenerics_0.25.3
loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0compiler_3.5.0 tools_3.5.0
[4] XVector_0.19.8 GenomeInfoDbData_1.1.0 RCurl_1.95-4.10
[7] bitops_1.0-6
On 02/10/2018 02:48 PM, Nathan Sheffield wrote:
I'm having some issues getting my package LOLA to pass R CMD check using
the updated dev versions of GenomicRanges et al.
It seems like any time I try to apply something across a
"CompressedGRangesList" object, it's giving errors when I use mclapply
from parallel. Here's a reproducible example:
data("sample_input", package="LOLA")
library(parallel)
mclapply(userSets, length)
(loads packages...)
Error in lapply_CompressedList(X, FUN, ...) :
invalid output element of class "GRanges"
It works with regular lapply:
> lapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
This is running on the bioconductor docker devel_core2 container, and
I've then gone and updated to the latest dev versions of these packages
with `biocLite()`.
I earlier ran into issues using `as.list()` on these same
CompressedGRangesList objects. It used to be that I had to call as.list
when they were just GRangesList objects, but now that's failing, and so
I've had to go take all calls to as.list out of my code. This has solved
that issue (I guess the updates made the as.list calls unnecessary), but
you can see it's still causing errors:
as.list(userSets)
Error in lapply_CompressedList(X, FUN, ...) :
invalid output element of class "GRanges"
-Nathan
```
> sessionInfo()
R Under development (unstable) (2018-02-04 r74204)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5]
[Bioc-devel] Issues with GenomicRanges updates
I'm having some issues getting my package LOLA to pass R CMD check using
the updated dev versions of GenomicRanges et al.
It seems like any time I try to apply something across a
"CompressedGRangesList" object, it's giving errors when I use mclapply
from parallel. Here's a reproducible example:
data("sample_input", package="LOLA")
library(parallel)
mclapply(userSets, length)
(loads packages...)
Error in lapply_CompressedList(X, FUN, ...) :
invalid output element of class "GRanges"
It works with regular lapply:
> lapply(userSets, length)
$setA
[1] 3142
$setB
[1] 5831
This is running on the bioconductor docker devel_core2 container, and
I've then gone and updated to the latest dev versions of these packages
with `biocLite()`.
I earlier ran into issues using `as.list()` on these same
CompressedGRangesList objects. It used to be that I had to call as.list
when they were just GRangesList objects, but now that's failing, and so
I've had to go take all calls to as.list out of my code. This has solved
that issue (I guess the updates made the as.list calls unnecessary), but
you can see it's still causing errors:
as.list(userSets)
Error in lapply_CompressedList(X, FUN, ...) :
invalid output element of class "GRanges"
-Nathan
```
> sessionInfo()
R Under development (unstable) (2018-02-04 r74204)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.31.18 GenomeInfoDb_1.15.5 IRanges_2.13.24
[4] S4Vectors_0.17.31 BiocGenerics_0.25.3
loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0 compiler_3.5.0 XVector_0.19.8
[4] tools_3.5.0 GenomeInfoDbData_1.1.0 RCurl_1.95-4.10
[7] bitops_1.0-6
```
___
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