problem parsing kallisto abundance.h5 #56
Description
This issue seems to be unrelated to #55 .
EDIT:
If any users out there experience this error, please let us know. As is, I am unable to pinpoint the cause of it. I only know it is not caused by RATs.
/EDIT
h5read('./kallisto_quant/Hs_GRCh37.67.1/abundance.h5', '/aux/ids/') succeeds on my mac but fails on both the login node and the HPC nodes.
Mac session:
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rhdf5_2.22.0 data.table_1.10.4-3
loaded via a namespace (and not attached):
[1] zlibbioc_1.24.0 compiler_3.4.1 tools_3.4.1
Ningal session:
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)
Matrix products: default
BLAS: /homes/kfroussios/local_installs/miniconda3/envs/mybasics/lib/R/lib/libRblas.so
LAPACK: /homes/kfroussios/local_installs/miniconda3/envs/mybasics/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rhdf5_2.22.0 data.table_1.10.4-3 RevoUtils_10.0.8
[4] RevoUtilsMath_10.0.1
loaded via a namespace (and not attached):
[1] zlibbioc_1.24.0 compiler_3.4.3
HPC session:
R version 3.4.3 (2017-11-30)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /homes/kfroussios/local_installs/miniconda3/envs/nodebasics/lib/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rhdf5_2.22.0 data.table_1.11.0
loaded via a namespace (and not attached):
[1] zlibbioc_1.24.0 compiler_3.4.3