wolf5996
commented
3 years ago Have you managed to find a fix for this issue? I am trying to get SeuratDisk to work on Rstudio, but I am getting the same error with my install. My error message is:
Downloading GitHub repo mojaveazure/seurat-disk@HEAD
✓ checking for file ‘/private/var/folders/_x/n9zx11j17db4km3_34pd3w5h0000gn/T/RtmpLeq73X/remotes342651b6c9/mojaveazure-seurat-disk-163f1aa/DESCRIPTION’ ...
─ preparing ‘SeuratDisk’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘SeuratDisk_0.0.0.9019.tar.gz’
* installing *source* package ‘SeuratDisk’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
sh: line 1: 1060 Abort trap: 6 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/_x/n9zx11j17db4km3_34pd3w5h0000gn/T//RtmpZolrQz/file41c29adf35b'
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.12.0, library is 1.12.1
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.12.1
Configured on: Mon Jul 12 08:05:03 BST 2021
Configured by: brew@BigSur
Host system: x86_64-apple-darwin20.4.0
Uname information: Darwin BigSur 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64
Byte sex: little-endian
Installation point: /usr/local/Cellar/hdf5/1.12.1
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: static, shared
Statically Linked Executables:
LDFLAGS:
H5_LDFLAGS: -Wl,-commons,use_dylibs
AM_LDFLAGS: -L/usr/local/opt/szip/lib
Extra libraries: -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib
Languages:
----------
C: yes
C Compiler: /usr/bin/clang ( Apple clang version 12.0.5 )
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/usr/local/opt/szip/include
C Flags:
H5 C Flags: -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wno-c++-compat -Wno-format-nonliteral -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-missing-noreturn -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -O3
AM C Flags:
Shared C Library: yes
Static C Library: yes
Fortran: yes
Fortran Compiler: /usr/local/opt/gcc/bin/gfortran ( GNU Fortran (Homebrew GCC 11.1.0_1) 11.1.0)
Fortran Flags:
H5 Fortran Flags: -std=f2008 -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Wuse-without-only -Winteger-division -Wfrontend-loop-interchange -fdiagnostics-urls=never -fno-diagnostics-color -s -O3
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: yes
C++ Compiler: /usr/bin/clang++ ( Apple clang version 12.0.5 )
C++ Flags:
H5 C++ Flags: -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wno-c++-compat -Wno-format-nonliteral -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -O3
AM C++ Flags: -DOLD_HEADER_FILENAME -DHDF_NO_NAMESPACE -DNO_STATIC_CAST
Shared C++ Library: yes
Static C++ Library: yes
Java: no
Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Build HDF5 Tests: yes
Build HDF5 Tools: yes
Threadsafety: no (recursive RW locks: no)
Default API mapping: v112
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(no encoder)
MPE: no
Map (H5M) API: no
Direct VFD: no
Mirror VFD: no
(Read-Only) S3 VFD: no
(Read-Only) HDFS VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Function stack tracing: no
Use file locking: best-effort
Strict file format checks: no
Optimization instrumentation: no
Bye...
ERROR: lazy loading failed for package ‘SeuratDisk’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/SeuratDisk’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/SeuratDisk’
Warning in i.p(...) :
installation of package ‘/var/folders/_x/n9zx11j17db4km3_34pd3w5h0000gn/T//RtmpLeq73X/file34253316798/SeuratDisk_0.0.0.9019.tar.gz’ had non-zero exit statusMy R session info is:
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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
loaded via a namespace (and not attached):
[1] bitops_1.0-7 bit64_4.0.5 httr_1.4.2 rprojroot_2.0.2 GenomeInfoDb_1.28.1 tools_4.1.0
[7] utf8_1.2.1 R6_2.5.0 DBI_1.1.1 BiocGenerics_0.38.0 colorspace_2.0-2 withr_2.4.2
[13] tidyselect_1.1.1 gridExtra_2.3 prettyunits_1.1.1 processx_3.5.2 bit_4.0.4 curl_4.3.2
[19] compiler_4.1.0 cli_3.0.0 Biobase_2.52.0 scales_1.1.1 callr_3.7.0 digest_0.6.27
[25] rmarkdown_2.9 XVector_0.32.0 pkgconfig_2.0.3 htmltools_0.5.1.1 fastmap_1.1.0 rlang_0.4.11
[31] rstudioapi_0.13 RSQLite_2.2.7 shiny_1.6.0 farver_2.1.0 generics_0.1.0 jsonlite_1.7.2
[37] dplyr_1.0.7 RCurl_1.98-1.3 magrittr_2.0.1 GenomeInfoDbData_1.2.6 Matrix_1.3-4 Rcpp_1.0.7
[43] munsell_0.5.0 S4Vectors_0.30.0 fansi_0.5.0 reticulate_1.20-9001 viridis_0.6.1 lifecycle_1.0.0
[49] yaml_2.2.1 ggraph_2.0.5 MASS_7.3-54 zlibbioc_1.38.0 pkgbuild_1.2.0 grid_4.1.0
[55] blob_1.2.1 parallel_4.1.0 promises_1.2.0.1 ggrepel_0.9.1 crayon_1.4.1 lattice_0.20-44
[61] graphlayouts_0.7.1 Biostrings_2.60.1 KEGGREST_1.32.0 knitr_1.33 clustree_0.4.3 ps_1.6.0
[67] pillar_1.6.1 igraph_1.2.6 stats4_4.1.0 glue_1.4.2 evaluate_0.14 remotes_2.4.0
[73] png_0.1-7 vctrs_0.3.8 tweenr_1.0.2 httpuv_1.6.1 gtable_0.3.0 purrr_0.3.4
[79] polyclip_1.10-0 tidyr_1.1.3 assertthat_0.2.1 cachem_1.0.5 ggplot2_3.3.5 xfun_0.24
[85] ggforce_0.3.3 mime_0.11 xtable_1.8-4 tidygraph_1.2.0 later_1.2.0 viridisLite_0.4.0
[91] tibble_3.1.2 AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0 ellipsis_0.3.2
Dear all,
I seem to have an issue installing the seuratdisk can anyone maybe help me?
thank you so so much
i used:
but i get the error below
with my R info