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mojaveazure / seurat-disk

Interfaces for HDF5-based Single Cell File Formats
https://mojaveazure.github.io/seurat-disk
GNU General Public License v3.0
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When installing seurat-disk, there is a bug, which says "ERROR: lazy loading failed for package 'SeuratDisk' * removing 'C:/Users/user/Documents/R/win-library/4.0/SeuratDisk'" #63

Open zhangleiju opened 3 years ago

zhangleiju commented 3 years ago

My code is as follows install.packages("remotes") remotes::install_github("mojaveazure/seurat-disk")

error is as follows 停止执行 ERROR: lazy loading failed for package 'SeuratDisk'

zhangleiju commented 3 years ago

Restart R studio and reinstall packages seurat-disk

wolf5996 commented 3 years ago

I have restarted Rstudio as well as my entire system, and I have tried to install seurat-disk multiple times afterwards to no avail. Can someone please help?

My error message is as follows:

Downloading GitHub repo mojaveazure/seurat-disk@HEAD
✓  checking for file ‘/private/var/folders/_x/n9zx11j17db4km3_34pd3w5h0000gn/T/Rtmp4H6ax5/remotes8f5724e3c8f/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:  3364 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//Rtmp7RloW7/filed1d125b5b66'
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’
Warning in i.p(...) :
  installation of package ‘/var/folders/_x/n9zx11j17db4km3_34pd3w5h0000gn/T//Rtmp4H6ax5/file8f573f27fa0/SeuratDisk_0.0.0.9019.tar.gz’ had non-zero exit status

My session info is as follows:

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
lstankiewicz15 commented 3 years ago

I have the same issue. I have restarted R with no avail. These are the errors I get:

Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/BoolToInt.Rd:39: missing link 'WriteH5Seurat' CheckMatrix html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/CheckMatrix.Rd:10: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic ChunkPoints html
ClosestVersion html
CompoundToGroup html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/CompoundToGroup.Rd:17: file link 'H5D' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/CompoundToGroup.Rd:18: file link 'H5T_COMPOUND' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/CompoundToGroup.Rd:20: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/CompoundToGroup.Rd:21: file link 'H5Group' in package 'hdf5r' does not exist and so has been treated as a topic Connect html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Connect.Rd:25: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Convert html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Convert.Rd:48: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Convert.Rd:96: missing file link 'SeuratDisk.dtype.dataframe_as_group' Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Convert.Rd:179: file link 'IsGlobal' in package 'Seurat' does not exist and so has been treated as a topic Dims html
FileType html
FixFeatures html
GetClass html
GetMargin html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GetMargin.Rd:14: missing file link 'SeuratDisk.chunking.MARGIN' Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GetMargin.Rd:29: missing file link 'SeuratDisk.chunking.MARGIN' GetObject html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GetObject.Rd:42: file link 'IsGlobal' in package 'Seurat' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GetObject.Rd:46: file link 'IsGlobal' in package 'Seurat' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GetObject.Rd:61: file link 'IsGlobal' in package 'Seurat' does not exist and so has been treated as a topic GetParent html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GetParent.Rd:13: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GetParent.Rd:13: file link 'H5Group' in package 'hdf5r' does not exist and so has been treated as a topic GuessDType html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GuessDType.Rd:38: file link 'H5T_INTEGER' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GuessDType.Rd:38: file link 'H5T_LOGICAL' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GuessDType.Rd:23: file link 'H5T_ARRAY' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GuessDType.Rd:25: file link 'H5T_ARRAY' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/GuessDType.Rd:32: file link 'H5T' in package 'hdf5r' does not exist and so has been treated as a topic H5ADToH5Seurat html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/H5ADToH5Seurat.Rd:66: missing file link 'SeuratDisk.dtype.dataframe_as_group' H5Exists html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/H5Exists.Rd:15: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/H5Exists.Rd:15: file link 'H5Group' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/H5Exists.Rd:16: file link 'H5D' in package 'hdf5r' does not exist and so has been treated as a topic H5Path html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/H5Path.Rd:13: file link 'NAcharacter' in package 'base' does not exist and so has been treated as a topic H5SeuratToH5AD html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/H5SeuratToH5AD.Rd:28: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/H5SeuratToH5AD.Rd:60: file link 'IsGlobal' in package 'Seurat' does not exist and so has been treated as a topic ImageWrite html
IsDType html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/IsDType.Rd:10: file link 'H5D' in package 'hdf5r' does not exist and so has been treated as a topic IsMatrixEmpty html
IsSCDisk html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/IsSCDisk.Rd:10: missing file link ':R6Class' LoadH5Seurat html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/LoadH5Seurat.Rd:93: file link 'IsGlobal' in package 'Seurat' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/LoadH5Seurat.Rd:97: file link 'IsGlobal' in package 'Seurat' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/LoadH5Seurat.Rd:119: file link 'IsGlobal' in package 'Seurat' does not exist and so has been treated as a topic LoadLoom html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/LoadLoom.Rd:71: file link 'Seurat' in package 'Seurat' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/LoadLoom.Rd:68: file link 'Seurat' in package 'Seurat' does not exist and so has been treated as a topic LoomLoading html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/LoomLoading.Rd:55: file link 'Seurat' in package 'Seurat' does not exist and so has been treated as a topic MakeSpace html
PB html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/PB.Rd:33: file link 'stderr' in package 'base' does not exist and so has been treated as a topic PadMatrix html
PadNames html
RandomName html
ReadH5 html
RegisterSCDisk html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/RegisterSCDisk.Rd:13: missing file link ':R6Class' Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/RegisterSCDisk.Rd:38: missing file link ':ns-hooks' Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/RegisterSCDisk.Rd:19: missing file link ':R6Class' SaveH5Seurat html
SaveLoom html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/SaveLoom.Rd:11: file link 'Seurat' in package 'Seurat' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/SaveLoom.Rd:58: file link 'Seurat' in package 'Seurat' does not exist and so has been treated as a topic Scalar html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Scalar.Rd:10: file link 'H5S' in package 'hdf5r' does not exist and so has been treated as a topic SeuratDisk-package html
SparsePointers html
SparseWrite html
StringType html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/StringType.Rd:20: file link 'H5T_STRING' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/StringType.Rd:17: file link 'H5T_STRING' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/StringType.Rd:31: file link 'H5T_STRING' in package 'hdf5r' does not exist and so has been treated as a topic TestH5 html
TestObject html
Timestamp html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Timestamp.Rd:19: file link 'Sys.timezone' in package 'base' does not exist and so has been treated as a topic Transpose html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Transpose.Rd:45: missing file link 'dgCMatrix' Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Transpose.Rd:46: missing file link 'dgCMatrix' Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Transpose.Rd:48: file link 'H5D' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Transpose.Rd:48: file link 'H5Group' in package 'hdf5r' does not exist and so has been treated as a topic UpdateKey html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/UpdateKey.Rd:32: file link 'Key' in package 'Seurat' does not exist and so has been treated as a topic UpdateSlots html
ValidateLoom html
WriteAttribute html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/WriteAttribute.Rd:12: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/WriteAttribute.Rd:12: file link 'H5Group' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/WriteAttribute.Rd:13: file link 'H5D' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/WriteAttribute.Rd:23: file link 'H5S' in package 'hdf5r' does not exist and so has been treated as a topic WriteH5Group html
WriteMode html
Writeable html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Writeable.Rd:10: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Writeable.Rd:10: file link 'H5Group' in package 'hdf5r' does not exist and so has been treated as a topic h5SI html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/h5SI.Rd:25: file link 'DefaultAssay' in package 'Seurat' does not exist and so has been treated as a topic h5Seurat-bindings html
h5Seurat-class html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/h5Seurat-class.Rd:20: file link 'H5RefClass' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/h5Seurat-class.Rd:20: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/h5Seurat-class.Rd:20: file link 'scdisk' in package 'SeuratDisk' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/h5Seurat-class.Rd:17: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic loom-bindings html
loom-class html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/loom-class.Rd:20: file link 'H5RefClass' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/loom-class.Rd:20: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/loom-class.Rd:20: file link 'scdisk' in package 'SeuratDisk' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/loom-class.Rd:17: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic scdisk-class html
Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/scdisk-class.Rd:20: file link 'H5RefClass' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/scdisk-class.Rd:20: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/scdisk-class.Rd:17: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic building package indices installing vignettes testing if installed package can be loaded from temporary location ** arch - i386 Error: package or namespace load failed for 'SeuratDisk' in library.dynam(lib, package, package.lib): DLL 'RANN' not found: maybe not installed for this architecture? Error: loading failed Execution halted arch - x64 ERROR: loading failed for 'i386'

wolf5996 commented 3 years ago

@lstankiewicz15 Would you mind posting the results of your sessioninfo() as well to see the versions of the different packages you have loaded on your system?

I was able to solve my problem by downgrading to a lower version of R. Initially, I was on R 4.1.0, so I downgraded to R 4.0.5 and that solved my issue. Note that downgrading to any 3rd version of R (such R 3.6) is not a good idea because sueratDisk was developed for the 4th version of R.

lstankiewicz15 commented 3 years ago

@wolf5996 Thanks for your help! Please see below.

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 [4] LC_NUMERIC=C LC_TIME=English_Canada.1252

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

other attached packages: [1] SeuratObject_4.0.2 Seurat_4.0.2

loaded via a namespace (and not attached): [1] Rtsne_0.15 colorspace_2.0-1 deldir_0.2-10 ellipsis_0.3.2
[5] ggridges_0.5.3 rprojroot_2.0.2 rstudioapi_0.13 spatstat.data_2.1-0
[9] leiden_0.3.8 listenv_0.8.0 remotes_2.4.0 ggrepel_0.9.1
[13] fansi_0.4.2 codetools_0.2-16 splines_4.0.3 knitr_1.33
[17] polyclip_1.10-0 jsonlite_1.7.2 ica_1.0-2 cluster_2.1.0
[21] png_0.1-7 pheatmap_1.0.12 uwot_0.1.10 shiny_1.6.0
[25] sctransform_0.3.2 spatstat.sparse_2.0-0 BiocManager_1.30.16 compiler_4.0.3
[29] httr_1.4.2 assertthat_0.2.1 Matrix_1.3-3 fastmap_1.1.0
[33] lazyeval_0.2.2 cli_3.0.1 later_1.2.0 htmltools_0.5.1.1
[37] prettyunits_1.1.1 tools_4.0.3 igraph_1.2.6 gtable_0.3.0
[41] glue_1.4.2 RANN_2.6.1 reshape2_1.4.4 dplyr_1.0.6
[45] Rcpp_1.0.7 scattermore_0.7 vctrs_0.3.8 nlme_3.1-149
[49] lmtest_0.9-38 xfun_0.23 stringr_1.4.0 globals_0.14.0
[53] ps_1.6.0 mime_0.11 miniUI_0.1.1.1 lifecycle_1.0.0
[57] irlba_2.3.3 goftest_1.2-2 future_1.21.0 MASS_7.3-53
[61] zoo_1.8-9 scales_1.1.1 spatstat.core_2.3-0 promises_1.2.0.1
[65] spatstat.utils_2.2-0 parallel_4.0.3 RColorBrewer_1.1-2 curl_4.3.2
[69] reticulate_1.20 pbapply_1.4-3 gridExtra_2.3 ggplot2_3.3.5
[73] rpart_4.1-15 stringi_1.6.2 pkgbuild_1.2.0 rlang_0.4.11
[77] pkgconfig_2.0.3 matrixStats_0.59.0 lattice_0.20-41 ROCR_1.0-11
[81] purrr_0.3.4 tensor_1.5 patchwork_1.1.1 htmlwidgets_1.5.3
[85] cowplot_1.1.1 tidyselect_1.1.1 processx_3.5.2 parallelly_1.27.0
[89] RcppAnnoy_0.0.18 plyr_1.8.6 magrittr_2.0.1 R6_2.5.0
[93] generics_0.1.0 DBI_1.1.1 withr_2.4.2 pillar_1.6.1
[97] mgcv_1.8-33 fitdistrplus_1.1-5 survival_3.2-7 abind_1.4-5
[101] tibble_3.1.1 future.apply_1.7.0 crayon_1.4.1 KernSmooth_2.23-17
[105] utf8_1.2.1 spatstat.geom_2.2-2 plotly_4.9.4.1 grid_4.0.3
[109] data.table_1.14.0 callr_3.7.0 digest_0.6.27 xtable_1.8-4
[113] tidyr_1.1.3 httpuv_1.6.1 munsell_0.5.0 viridisLite_0.4.0

Some packages: fansi (0.4.2) colorspace (2.0-1) stringi (1.6.2) tibble (3.1.1) dplyr (1.0.6) Seurat (4.0.2)

lstankiewicz15 commented 3 years ago

Update: I upgraded to R v 4.1.0 and SeuratDisk now installs. @wolf5996 thanks for your help

wolf5996 commented 3 years ago

@lstankiewicz15 I am glad I could assist you. To be honest, I don't think the issue is in the R version you are using; I think the general solution for this issue is a clean install of R (R 4.0.5 worked for me and R 4.1.0 worked for you, so we can't say that the problem is version related), which usually fixes whatever dependency error that was causing SeuratDisk to malfunction. In your case, switching to the latest version of R solved it, and in my case downgrading to a slightly lower version solved it (I donwgraded since I was already on the latest version).

saulvegasauceda commented 2 years ago

Hi, I'm running into the same issue Lazy Loading Error but I'm running R from the shell. I've tried downloading using conda and install_github function. Is there any way of fixing this while avoiding a downgrade?

R version info:

platform       x86_64-conda-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          4
minor          1.3
year           2022
month          03
day            10
svn rev        81868
language       R
version.string R version 4.1.3 (2022-03-10)
nickname       One Push-Up
andrei-stoica26 commented 1 year ago

What worked for me was updating vctrs. Try to have the prerequisite packages up to date, then I think the error should disappear.

wingszewendyyue commented 1 year ago

I got the "lazy loading failed" problem. I re-installed R v4.3.0 and Seurat. The problem was resolved.