parse_gctx Error: segfault from C stack overflow

[FogatoHub]

Hi, i need help to use the parsing function of cmapR

I was testing the cmapR library by following the tutorial

and i have problems with the function parse_gctx when i try to parse the small 77kb "modzs_n25x50.gctx" file provided with the cmapR library.

ds_path <- system.file("extdata", "modzs_n25x50.gctx", package="cmapR")
my_ds <- parse_gctx(ds_path)
reading /home/usr/R/x86_64-pc-linux-gnu-library/4.0/cmapR/extdata/modzs_n25x50.gctx
Error: segfault from C stack overflow

same error if i try to parse a subset of the file as described in the tutorial
my_ds_10_columns <- parse_gctx(ds_path, cid=1:10)

I checked my memory usage and it's all set to infinity,

> library(unix)
> rlimit_all() 
$cur
      as     core      cpu     data    fsize  memlock   nofile    nproc    stack 
     Inf        0      Inf      Inf      Inf 67108864     8192    63355  8388608 

$max
      as     core      cpu     data    fsize  memlock   nofile    nproc    stack 
     Inf      Inf      Inf      Inf      Inf 67108864  1048576    63355      Inf 

my operative system is Ubuntu 20.04
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

Thank you

[innesbre]

Same problem here:

> library(cmapR)
> lvl4_data <- parse_gctx("~/Data_LINCS/2020beta/level4_beta_trt_misc_n26428x12328.gctx")
reading ~/Data_LINCS/2020beta/level4_beta_trt_misc_n26428x12328.gctx
Error: segfault from C stack overflow
> R.version
               _                           
platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          4                           
minor          0.3                         
year           2020                        
month          10                          
day            10                          
svn rev        79318                       
language       R                           
version.string R version 4.0.3 (2020-10-10)
nickname       Bunny-Wunnies Freak Out 
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] cmapR_1.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6                  XVector_0.30.0             
 [3] GenomicRanges_1.42.0        BiocGenerics_0.36.0        
 [5] zlibbioc_1.36.0             IRanges_2.24.1             
 [7] flowCore_2.2.0              lattice_0.20-41            
 [9] GenomeInfoDb_1.26.2         tools_4.0.3                
[11] SummarizedExperiment_1.20.0 parallel_4.0.3             
[13] grid_4.0.3                  rhdf5_2.34.0               
[15] Biobase_2.50.0              matrixStats_0.58.0         
[17] RcppParallel_5.0.2          Matrix_1.3-2               
[19] GenomeInfoDbData_1.2.4      Rhdf5lib_1.12.1            
[21] cytolib_2.2.1               RProtoBufLib_2.2.0         
[23] rhdf5filters_1.2.0          S4Vectors_0.28.1           
[25] bitops_1.0-6                RCurl_1.98-1.2             
[27] DelayedArray_0.16.1         compiler_4.0.3             
[29] MatrixGenerics_1.2.1        stats4_4.0.3 

[innesbre]

I used cmapR::parse.gctx() just fine with R4.0.2 last spring, so its must be a relatively new bug.

[RussBainer]

I'm also catching this bug- any ideas about workarounds?

> ds_10_columns <- parse_gctx(ds_path, cid=1:10, rid= 1:10)
reading GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx
Error: segfault from C stack overflow

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] cmapR_1.2.1         ckanr_0.6.0         DBI_1.1.1
[4] BiocManager_1.30.10

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6                  cytolib_2.2.1
 [3] XVector_0.30.0              pillar_1.5.1
 [5] compiler_4.0.3              dbplyr_2.1.0
 [7] GenomeInfoDb_1.26.4         rhdf5filters_1.2.0
 [9] zlibbioc_1.36.0             MatrixGenerics_1.2.1
[11] bitops_1.0-6                tools_4.0.3
[13] rhdf5_2.34.0                lattice_0.20-41
[15] jsonlite_1.7.2              lifecycle_1.0.0
[17] tibble_3.1.0                debugme_1.1.0
[19] pkgconfig_2.0.3             rlang_0.4.10
[21] Matrix_1.3-2                DelayedArray_0.16.2
[23] crul_1.1.0                  curl_4.3
[25] parallel_4.0.3              GenomeInfoDbData_1.2.4
[27] dplyr_1.0.5                 generics_0.1.0
[29] vctrs_0.3.6                 S4Vectors_0.28.1
[31] IRanges_2.24.1              grid_4.0.3
[33] stats4_4.0.3                tidyselect_1.1.0
[35] Biobase_2.50.0              glue_1.4.2
[37] httpcode_0.3.0              R6_2.5.0
[39] fansi_0.4.2                 Rhdf5lib_1.12.1
[41] RProtoBufLib_2.2.0          purrr_0.3.4
[43] magrittr_2.0.1              ellipsis_0.3.1
[45] matrixStats_0.58.0          BiocGenerics_0.36.0
[47] GenomicRanges_1.42.0        assertthat_0.2.1
[49] SummarizedExperiment_1.20.0 flowCore_2.2.0
[51] utf8_1.2.1                  RcppParallel_5.0.3
[53] RCurl_1.98-1.2              crayon_1.4.1

[rajivnarayan]

I ran into similar segfaulting with R-4.0.3. and the latest cmapR package. Noticed that pre-loading the rhdf5 library before cmapR seems to work for me i.e

library(rhdf5)
library(cmapR)
gctx_file <- system.file('extdata', 'modzs_n25x50.gctx', package='cmapR') 
x <- parse_gctx(gctx_file)

Equivalently rebuilding the cmapR package after adding rhdf5 as a dependency instead of an import in the DESCRIPTION file also works.

Version info:
R-4.0.3
cmapR-1.2.1
rhdf5 2.34.4
rhdf5lib 1.10.1

[tnat1031]

Hi all, Thanks for the detailed descriptions and my apologies for the late reply. I am actually having trouble reproducing this issue, though admittedly I'm on a Mac running an Ubuntu docker image (rocker/tidyverse:4.0.3) and installing cmapR from Bioconductor. ``` $ docker run --rm -p 8787:8787 -e PASSWORD=somepassword rocker/tidyverse:4.0.3 # within RStudio on the docker container if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("cmapR") library(cmapR) example("parse_gctx") # runs without errors ``` It also works fine installing directly onto my local Mac (running R version 4.0.3) from Bioconductor. So I'm a bit puzzled. I'd prefer not to make rhdf5 a dependency for cmapR, as that could potentially lead to namespace conflicts with other packages, but I'm not immediately sure of a better fix. Let me look into it a bit more. I'm of course open to other suggestions. Thanks a lot, Ted

…

On Mon, Mar 15, 2021 at 10:17 PM rajivnarayan ***@***.***> wrote: I ran into similar segfaulting with R-4.0.3. and the latest cmapR package. Noticed that pre-loading the rhdf5 library before cmapR seems to work for me i.e library(rhdf5) library(cmapR)gctx_file <- system.file('extdata', 'modzs_n25x50.gctx', package='cmapR') x <- parse_gctx(gctx_file) Equivalently rebuilding the cmapR package after adding rhdf5 as a dependency instead of an import in the DESCRIPTION file also works. Version info: R-4.0.3 cmapR-1.2.1 rhdf5 2.34.4 rhdf5lib 1.10.1 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#65 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAO6F3Y2K7I7A2RG3LFA5ZDTD25UJANCNFSM4XL4JMKQ> .

[RussBainer]

Following up, I tried the rhdf5 workaround suggested by @rajivnarayan and I continue to get the segfault, but I notice that I am getting a slightly older version from Bioconductor (2.34.0 vs 2.34.4).

Sadly, the current github build of rhdf5 is erroring out on install, so I haven't been able to test further.

[tnat1031]

Hi Russell, Sorry to hear you're having trouble with the github source code. I am able to install that successfully on the same ubuntu docker (rocker/tidyverse:4.0.3). Could you please share the error message you're getting? Thanks a lot, Ted

…

On Tue, Mar 16, 2021 at 3:47 PM Russell Bainer ***@***.***> wrote: Following up, I tried the rhdf5 workaround suggested by @rajivnarayan <https://github.com/rajivnarayan> and I continue to get the segfault, but I notice that I am getting a slightly older version from Bioconductor (2.34.0 vs 2.34.4). Sadly, the current github build is erroring out on install, so I haven't been able to test further. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#65 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAO6F35ASORLJBD2FMXESH3TD6YURANCNFSM4XL4JMKQ> .

[RussBainer]

Hi Ted,

Here's the error I get from an devtools::install_github() call:

[Many lines of compiler output]

** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘rhdf5’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/site-library/00LOCK-rhdf5/00new/rhdf5/libs/rhdf5.so':
  /usr/local/lib/R/site-library/00LOCK-rhdf5/00new/rhdf5/libs/rhdf5.so: undefined symbol: H5Scombine_select
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/rhdf5’
Error: Failed to install 'rhdf5' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpscBSTb/file261c4a49497f/rhdf5_2.35.2.tar.gz’ had non-zero exit status

Will try installing into the docker container that you suggest as a workaround. Thanks!

[tnat1031]

Hi Russell, Ok, thanks for sharing that error log. I simply ran `devtools::install_github()` on that docker image and it worked fine. Looks like the issue you're hitting has something to do with the rhdf5 library. Does that package install successfully if you try to install it by itself using `BiocManager::install("rhdf5")` ? Thanks a lot, Ted

…

On Wed, Mar 17, 2021 at 3:15 PM Russell Bainer ***@***.***> wrote: Hi Ted, Here's the error I get from an devtools::install_github() call: [Many lines of compiler output] ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘rhdf5’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib/R/site-library/00LOCK-rhdf5/00new/rhdf5/libs/rhdf5.so': /usr/local/lib/R/site-library/00LOCK-rhdf5/00new/rhdf5/libs/rhdf5.so: undefined symbol: H5Scombine_select Error: loading failed Execution halted ERROR: loading failed * removing ‘/usr/local/lib/R/site-library/rhdf5’ Error: Failed to install 'rhdf5' from GitHub: (converted from warning) installation of package ‘/tmp/RtmpscBSTb/file261c4a49497f/rhdf5_2.35.2.tar.gz’ had non-zero exit status Will try installing into the docker container that you suggest as a workaround. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#65 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAO6F37PG2EEYS6N2RIR7TTTED5TRANCNFSM4XL4JMKQ> .

[RussBainer]

No, I'm sorry if my previous note was ambiguous- the github error is derived from the `rhdf5` library install, not cmapR. I'll update when I have had time to try the docker container install- sorry, juggling a lot of things at the moment.

-R

________________________________ From: Ted Natoli ***@***.***> Sent: Thursday, March 18, 2021 5:58 AM To: cmap/cmapR ***@***.***> Cc: Russell Bainer ***@***.***>; Comment ***@***.***> Subject: Re: [cmap/cmapR] parse_gctx Error: segfault from C stack overflow (#65) Hi Russell, Ok, thanks for sharing that error log. I simply ran `devtools::install_github()` on that docker image and it worked fine. Looks like the issue you're hitting has something to do with the rhdf5 library. Does that package install successfully if you try to install it by itself using `BiocManager::install("rhdf5")` ? Thanks a lot, Ted

On Wed, Mar 17, 2021 at 3:15 PM Russell Bainer ***@***.***> wrote: Hi Ted, Here's the error I get from an devtools::install_github() call: [Many lines of compiler output] ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘rhdf5’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib/R/site-library/00LOCK-rhdf5/00new/rhdf5/libs/rhdf5.so': /usr/local/lib/R/site-library/00LOCK-rhdf5/00new/rhdf5/libs/rhdf5.so: undefined symbol: H5Scombine_select Error: loading failed Execution halted ERROR: loading failed * removing ‘/usr/local/lib/R/site-library/rhdf5’ Error: Failed to install 'rhdf5' from GitHub: (converted from warning) installation of package ‘/tmp/RtmpscBSTb/file261c4a49497f/rhdf5_2.35.2.tar.gz’ had non-zero exit status Will try installing into the docker container that you suggest as a workaround. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#65 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAO6F37PG2EEYS6N2RIR7TTTED5TRANCNFSM4XL4JMKQ> .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub<#65 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AL7CZQLJXBB3KCBURTMMATDTEH2HVANCNFSM4XL4JMKQ>. This email and any attachments may contain CONFIDENTIAL or PRIVILEGED information and is a private communication between the intended addressee and Maze Therapeutics, Inc. If you have received this email in error, reading, copying, using or disclosing its contents to others is prohibited. Please notify us of the delivery error by replying to this message and then delete it from your system. Thank you.

[tnat1031]

Ok thanks for the clarification and no worries at all. Best of luck and please let me know if I can help in any way. Best, Ted On Thu, Mar 18, 2021 at 11:58 AM Russell Bainer ***@***.***> wrote:

…

No, I'm sorry if my previous note was ambiguous- the github error is derived from the `rhdf5` library install, not cmapR. I'll update when I have had time to try the docker container install- sorry, juggling a lot of things at the moment. -R ________________________________ From: Ted Natoli ***@***.***> Sent: Thursday, March 18, 2021 5:58 AM To: cmap/cmapR ***@***.***> Cc: Russell Bainer ***@***.***>; Comment ***@***.***> Subject: Re: [cmap/cmapR] parse_gctx Error: segfault from C stack overflow (#65) Hi Russell, Ok, thanks for sharing that error log. I simply ran `devtools::install_github()` on that docker image and it worked fine. Looks like the issue you're hitting has something to do with the rhdf5 library. Does that package install successfully if you try to install it by itself using `BiocManager::install("rhdf5")` ? Thanks a lot, Ted On Wed, Mar 17, 2021 at 3:15 PM Russell Bainer ***@***.***> wrote: > Hi Ted, > > Here's the error I get from an devtools::install_github() call: > > [Many lines of compiler output] > > > > ** R > > ** inst > > ** byte-compile and prepare package for lazy loading > > ** help > > *** installing help indices > > ** building package indices > > ** installing vignettes > > ** testing if installed package can be loaded from temporary location > > Error: package or namespace load failed for ‘rhdf5’ in dyn.load(file, DLLpath = DLLpath, ...): > > unable to load shared object '/usr/local/lib/R/site-library/00LOCK-rhdf5/00new/rhdf5/libs/rhdf5.so': > > /usr/local/lib/R/site-library/00LOCK-rhdf5/00new/rhdf5/libs/rhdf5.so: undefined symbol: H5Scombine_select > > Error: loading failed > > Execution halted > > ERROR: loading failed > > * removing ‘/usr/local/lib/R/site-library/rhdf5’ > > Error: Failed to install 'rhdf5' from GitHub: > > (converted from warning) installation of package ‘/tmp/RtmpscBSTb/file261c4a49497f/rhdf5_2.35.2.tar.gz’ had non-zero exit status > > > Will try installing into the docker container that you suggest as a > workaround. Thanks! > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#65 (comment)>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAO6F37PG2EEYS6N2RIR7TTTED5TRANCNFSM4XL4JMKQ > > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub< #65 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AL7CZQLJXBB3KCBURTMMATDTEH2HVANCNFSM4XL4JMKQ >. This email and any attachments may contain CONFIDENTIAL or PRIVILEGED information and is a private communication between the intended addressee and Maze Therapeutics, Inc. If you have received this email in error, reading, copying, using or disclosing its contents to others is prohibited. Please notify us of the delivery error by replying to this message and then delete it from your system. Thank you. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#65 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAO6F325BVWV3UJCEXL2RBDTEIPJTANCNFSM4XL4JMKQ> .

[RussBainer]

Can confirm that the install and run works as promised in the specified docker container; this is a fine workaround IMHO.

Not sure how interested you are in tracking down architecture-specific bugs, but I'm running this on an AWS EC2 instance:

uname -a
Linux 4.15.0-1045-aws #47-Ubuntu SMP Fri Aug 2 13:50:30 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

[tnat1031]

Hi Russell, Ok great, glad the docker container works for you. Thanks for the details on the EC2 instance. If I have time I'll see if I can figure out what's causing the problem. Best, Ted

…

On Mon, Mar 22, 2021 at 1:39 PM Russell Bainer ***@***.***> wrote: Can confirm that the install and run works as promised in the specified docker container; this is a fine workaround IMHO. Not sure how interested you are in tracking down architecture-specific bugs, but I'm running this on an AWS EC2 instance: uname -a Linux 4.15.0-1045-aws #47-Ubuntu SMP Fri Aug 2 13:50:30 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#65 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAO6F36PMFUHU2I4UEZ7KK3TE56FJANCNFSM4XL4JMKQ> .