Comments (19)
bjreisman
commented on August 15, 2024
2
@rcannood Thank you for taking the time to troubleshoot this, I can confirm that worked!
> library(dyno)
> data("fibroblast_reprogramming_treutlein")
> model <- infer_trajectory(fibroblast_reprogramming_treutlein, "dynverse/ti_slingshot:dynwrapv2")
> plot_graph(model)
Coloring by milestone
Using milestone_percentages from trajectory
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rcannood
commented on August 15, 2024
1
Got round to installing Win10 again, at the very least I can already replicate the problem. I'll work on finding a solution.
Error: Error during trajectory inference
HDF5-API Errors:
error #000: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5Tget_native_type(): line 119: cannot retrieve native type
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #001: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5T_get_native_type(): line 400: cannot get member value
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #002: C:\pkg\hdf5-1.8.14\src\H5T.c in H5T_convert(): line 4816: data type conversion failed
class: HDF5
major: Attribute
minor: Unable to encode value
error #003: C:\pkg\hdf5-1.8.14\src\H5Tconv.c in H5T__conv_i_i(): line 3639: can't find property list for ID
class: HDF5
major: Object atom
minor: Unable to find atom information (already closed?)
error #004: C:\pkg\hdf5-1.8.14\src\H5Pint.c in H5P_object_verify(): line 3381: property list is no
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bjreisman
commented on August 15, 2024
1
Thank you, I can see that took a lot of work! The examples are running great on my machine. 🏆
I'm running into another issue with PAGA which I've posted here, but it looks to be an easier fix😄
dynverse/ti_paga#3
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bjreisman
commented on August 15, 2024
Sorry, realized that I forgot to pass the data through wrap_expression() which would have been an easy fix. Unfortunately, still running into the same error.
> library(dyno)
> library(tidyverse)
Registered S3 method overwritten by 'rvest':
method from
read_xml.response xml2
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 3.1.0 v purrr 0.3.0
v tibble 2.0.1 v dplyr 0.8.0.1
v tidyr 0.8.2 v stringr 1.4.0
v readr 1.3.1 v forcats 0.4.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x purrr::flatten_df() masks hdf5r::flatten_df()
x dplyr::lag() masks stats::lag()
> dataset <- wrap_expression(
+ counts = example_dataset$counts,
+ expression = example_dataset$expression
+ )
> model <- infer_trajectory(dataset, ti_comp1())
Error: Error during trajectory inference
HDF5-API Errors:
error #000: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5Tget_native_type(): line 119: cannot retrieve native type
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #001: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5T_get_native_type(): line 400: cannot get member value
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #002: C:\pkg\hdf5-1.8.14\src\H5T.c in H5T_convert(): line 4816: data type conversion failed
class: HDF5
major: Attribute
minor: Unable to encode value
error #003: C:\pkg\hdf5-1.8.14\src\H5Tconv.c in H5T__conv_i_i(): line 3639: can't find property list for ID
class: HDF5
major: Object atom
minor: Unable to find atom information (already closed?)
error #004: C:\pkg\hdf5-1.8.14\src\H5Pint.c in H5P_object_verify(): line 3381: property list is no
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rcannood
commented on August 15, 2024
Thanks Benjamin, we're looking into it.
Could you check whether a output.h5 was generated at /c/Users/reismab/AppData/Local/Temp/RtmpOK0ZZ0/file19089056d27/ti/ (or whatever folder is being printed). The error is probably being generated when calling dynutils::read_h5(file). If you find a file like this, could you send it to us?
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bjreisman
commented on August 15, 2024
Thanks for looking into this! The folder was empty once the error was thrown, but I was able to find the files by stopping the script just after it loaded dynutils.
See below:
input_output_h5.zip
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zouter
commented on August 15, 2024
Hi Benjamin, thanks! I can load in your output & input just fine. I have a hunch that this might be caused by an outdated version of HDF5. This will probably be fixed once you update to more recent versions (i.e. 1.10.5 or 1.8.21). I hope this is possible for you?
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zouter
commented on August 15, 2024
You might have to reinstall hdf5r if you do
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bjreisman
commented on August 15, 2024
Thanks! I had 1.10.5 installed previously and tried it again after uninstall and reinstalling 1.8.21, but ran into the same error with both versions.
If it's helpful, I also tried reading in the output.h5 file directly and it seemed to work? I was also able to run the examples from the hdf5r vignette successfully.
> library(hdf5r)
> hdf5r::is_hdf5("output.h5")
[1] TRUE
> output <- H5File$new("output.h5")
> names(output)
[1] "class" "data" "names"
> data <- output[["data"]]
> data
Class: H5Group
Filename: C:\Users\reismab\OneDrive\Vanderbilt\Bachmann Lab\Notebook\2019\April 2019\Dyno\output.h5
Group: /data
Listing:
name obj_type dataset.dims dataset.type_class
cell_ids H5I_GROUP <NA> <NA>
cell_info H5I_GROUP <NA> <NA>
dimred H5I_GROUP <NA> <NA>
dimred_milestones H5I_GROUP <NA> <NA>
dimred_segment_points H5I_GROUP <NA> <NA>
dimred_segment_progressions H5I_GROUP <NA> <NA>
directed H5I_GROUP <NA> <NA>
divergence_regions H5I_GROUP <NA> <NA>
id H5I_GROUP <NA> <NA>
milestone_ids H5I_GROUP <NA> <NA>
< Printed 10, out of 16>
> version
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 5.3
year 2019
month 03
day 11
svn rev 76217
language R
version.string R version 3.5.3 (2019-03-11)
nickname Great Truth
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bjreisman
commented on August 15, 2024
I noticed that C:\pkg\hdf5-1.8.14\src\H5Tnative.c is not a valid path, there's no pkg directory in C:\, could that be the problem?
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bjreisman
commented on August 15, 2024
Ah ha!
I was able to reproduce the error here, just as you had suspected:
> dynutils <- dynutils::read_h5("output.h5")
Error in standalone_H5D_get_type(h5d_id = self$id, native = TRUE) :
HDF5-API Errors:
error #000: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5Tget_native_type(): line 119: cannot retrieve native type
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #001: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5T_get_native_type(): line 400: cannot get member value
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #002: C:\pkg\hdf5-1.8.14\src\H5T.c in H5T_convert(): line 4816: data type conversion failed
class: HDF5
major: Attribute
minor: Unable to encode value
error #003: C:\pkg\hdf5-1.8.14\src\H5Tconv.c in H5T__conv_i_i(): line 3639: can't find property list for ID
class: HDF5
major: Object atom
minor: Unable to find atom information (already closed?)
error #004: C:\pkg\hdf5-1.8.14\src\H5Pint.c in H5P_object_verify(): line 3381: property list is not a member of the class
class
When I changed line 4 in dynutils::read_h5
file_h5 <- hdf5r::H5File$new(path, "r")
to
file_h5 <- hdf5r::H5File$new(path)
at line 4 in read_h5, it was able to make it past this point.
Unfortunately it threw the same error when called read_h5_, at which point it failed at line 76 as follows:
Browse[3]> n
debug: out <- map(colnames, ~.read_h5_vec(data[[.]])) %>% data.frame(check.names = FALSE,
stringsAsFactors = FALSE)
Browse[3]> n
Error: Error during trajectory inference
HDF5-API Errors:
error #000: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5Tget_native_type(): line 119: cannot retrieve native type
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #001: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5T_get_native_type(): line 400: cannot get member value
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #002: C:\pkg\hdf5-1.8.14\src\H5T.c in H5T_convert(): line 4816: data type conversion failed
class: HDF5
major: Attribute
minor: Unable to encode value
error #003: C:\pkg\hdf5-1.8.14\src\H5Tconv.c in H5T__conv_i_i(): line 3639: can't find property list for ID
class: HDF5
major: Object atom
minor: Unable to find atom information (already closed?)
error #004: C:\pkg\hdf5-1.8.14\src\H5Pint.c in H5P_object_verify(): line 3381: property list is no
I might keep working at it if I can, but I thought I'd provide a partial update before it got too late on that side of the world 🌝.
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zouter
commented on August 15, 2024
Wow, great debugging so far! 🥇
I'm just wondering why it says C:\pkg\hdf5-1.8.14 even though you have installed a more recent version of HDF5. I think this is the version of hdf5 that is installed by the hdf5r library (which is indeed 1.8.14 -> https://github.com/mannau/h5-libwin ). There is still an issue open for updating the windows version that is installed with CRAN hdf5r: hhoeflin/hdf5r#60 .
This will probably be solved if you install hdf5r from source (e.g. by doing devtools::install_github("hhoeflin/hdf5r") because this won't use the pre-build binaries but rather the ones installed on your system. This could be a temporary workaround for you until we find a more permanent solution 😉
PS: It's never too late on this side of the world to answer issues 😃
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bjreisman
commented on August 15, 2024
I think you're right.
> hdf5r::h5version()
hdf5r version 1.1.1 with C-library HDF5 Version 1.8.14
[1] "1.8.14"
While trying to troubleshoot this I noticed there's another package called rhdf5, which does seem to use the newer versions:
> rhdf5::h5version()
This is Bioconductor rhdf5 2.27.15 linking to C-library HDF5 1.10.3
I tried installing the development version of hdf5r via devtools::install_github() as well as by downloading it and trying to install it locally, but it still insisted on connecting to the 1.8.14 version. I suspect there is a way to get it to run a different version, but it looks like it would be very involved (altering the config.win file).
Do you think this is an issue with windows installations in general or something about my set-up specifically? I've tried it on two computers, but both were running windows 10.
Before I started messing with HDF5, I also dug a bit deeper into the read_h5 function. In debug mode hdf5r::H5File$new(path, "r") actually works just fine. The error seems to be thrown at line 60, as follows:
Browse[3]> map(nms, ~read_h5_(subfile[[.]]))
Error in standalone_H5D_get_type(h5d_id = self$id, native = TRUE) :
HDF5-API Errors:
error #000: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5Tget_native_type(): line 119: cannot retrieve native type
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #001: C:\pkg\hdf5-1.8.14\src\H5Tnative.c in H5T_get_native_type(): line 400: cannot get member value
class: HDF5
major: Invalid arguments to routine
minor: Inappropriate type
error #002: C:\pkg\hdf5-1.8.14\src\H5T.c in H5T_convert(): line 4816: data type conversion failed
class: HDF5
major: Attribute
minor: Unable to encode value
error #003: C:\pkg\hdf5-1.8.14\src\H5Tconv.c in H5T__conv_i_i(): line 3639: can't find property list for ID
class: HDF5
major: Object atom
minor: Unable to find atom information (already closed?)
error #004: C:\pkg\hdf5-1.8.14\src\H5Pint.c in H5P_object_verify(): line 3381: property list is not a member of the class
class
If I go through and call read_h5_(subfile[[nms[i]]]) for each i = 1:16, it fails on nms[5], nms[6], and nms[10], corresponding to "milestone_network", "divergence_regions", "directed."
On a related note, I saw you added a test_h5_installation() function. I tried it out and it passed 😃🙃
> dynutils::test_h5_installation(detailed = TRUE)
<U+2714> HDF5 files can be written
<U+2714> HDF5 files can be read
<U+2714> An R object that is written and read with HDF5 is the same
<U+2714> HDF5 test successful -------------------------------------------------------------------
[1] TRUE
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zouter
commented on August 15, 2024
Hmmmm yeah I think this is something that is general for Windows and hdf5r... Everyone using hdf5r on windows is going to have this problem. We're trying to find a solution, which will probably involve updating the version in hdf5r.. I don't have a lot of time today/tomorrow though, perhaps @rcannood can help.
And thanks for testing the test_h5_installation(), it clearly doesn't test enough 🤣
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zouter
commented on August 15, 2024
@rcannood Looking at the excellent debugging of Benjamin, I think this has something to do with booleans being saved by hdf5, given that these are present inside the "milestone_network", "divergence_regions" and "directed"
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rcannood
commented on August 15, 2024
👍 I can confirm this as well. I can read/write a trajectory to files without a problem, but when they're produced by HDF5 1.10 I run into problems. A good solution would be to have h5-libwin update itself. For now, I'll try to find a workaround for writing h5 files with 1.10 that 1.8 is able to read. The downside is that all the containers will have to be updated.
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rcannood
commented on August 15, 2024
@bjreisman I implemented a workaround for now (I hope that h5-libwin will still be updated). All of the containers will need to be rebuilt, however. Before I start the rebuild procedure, could you verify that this version of slingshot works for you as well?
library(dyno)
data("fibroblast_reprogramming_treutlein")
model <- infer_trajectory(fibroblast_reprogramming_treutlein, "dynverse/ti_slingshot:dynwrapv2")
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zouter
commented on August 15, 2024
Great! Feel free to open another issue if you have any other... issues 😁
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rcannood
commented on August 15, 2024
Just to follow up on this issue; all of the containers have been rebuilt and the workaround has been merged into the dynmethods and dyno packages. If you reinstall dyno (and make sure to upgrade all the dependencies as well), you should be able to run each of the methods now.
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