flowcore install

[antoine4ucsd]

Hello I am trying to install CytoExploreR on my Mac (catalina) but the flowcore install seems problematic...

tryCatch(library(devtools), error = function(e){ install.packages("devtools") library(devtools) }) install_github("RGLab/flowCore") it seems to be 'ok'... (...) testing if installed package keeps a record of temporary installation path DONE (flowCore)

but then I get this error and I cannot proceed with the CtyExploreR install

Error: package or namespace load failed for ‘flowCore’ in get(Info[i, 1], envir = env): lazy-load database '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowCore/R/flowCore.rdb' is corrupt

any suggestions? thank you!

[DillonHammill]

This should sort itself out if you remove the current installation and reinstall flowCore. Note: dependencies can now be installed from BioConductor.

remove.packages("flowCore")
# restart R
BiocManager::install("flowCore")

[antoine4ucsd]

thank you! trying now

[antoine4ucsd]

I wish it were more simple...sorry running into another problem

The downloaded binary packages are in /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T//RtmpuNhbOV/downloaded_packages Old packages: 'sf' Update all/some/none? [a/s/n]: a

There is a binary version available but the source version is later: binary source needs_compilation sf 0.9-7 0.9-8 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel)

if I start from the source, it failed so I answer no.

but then I get into this error (really sorry):

_Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no trying URL https://cran.rstudio.com/bin/macosx/contrib/4.0/sf_0.9-7.tgz Content type 'application/x-gzip' length 89143896 bytes (85.0 MB) downloaded 85.0 MB_

The downloaded binary packages are in /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T//RtmpuNhbOV/downloaded_packages

_library(flowCore) Error: package or namespace load failed for ‘flowCore’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowCore/libs/flowCore.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowCore/libs/flowCore.so, 6): Symbol not found: ZN7cytolib10in_polygonEPdS0_RKNSt316vectorINS_10CYTO_POINTENS1_9allocatorIS3_EEEERNS2_IjNS4IjEEEEbSB Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowCore/libs/flowCore.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowCore/libs/flowCore.so_

[DillonHammill]

Have you installed all the packages in the right order?

BiocManger::install(c("cytolib", "flowCore", "flowWorkspace", "openCyto"))

All the binaries are available so whenever it asks to install these from source, say no.

[antoine4ucsd]

ok.trying again thank you!

[antoine4ucsd]

does not work. Seems to be related to sf package

BiocManager::install(cytolib) Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10) Installing package(s) 'cytolib' trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/macosx/contrib/4.0/cytolib_2.2.1.tgz' Content type 'application/x-gzip' length 2537325 bytes (2.4 MB) downloaded 2.4 MB

The downloaded binary packages are in /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T//RtmpZtBfrb/downloaded_packages Old packages: 'sf' Update all/some/none? [a/s/n]: a

There is a binary version available but the source version is later: binary source needs_compilation sf 0.9-7 0.9-8 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no trying URL https://cran.rstudio.com/bin/macosx/contrib/4.0/sf_0.9-7.tgz Content type 'application/x-gzip' length 89143896 bytes (85.0 MB) downloaded 85.0 MB

The downloaded binary packages are in /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T//RtmpZtBfrb/downloaded_packages

library(cytolib) Error: package or namespace load failed for ‘cytolib’: .onLoad failed in loadNamespace() for 'cytolib', details: call: dyn.load(cytolib, local = FALSE, now = TRUE) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/libs/cytolib.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/libs/cytolib.so, 10): Symbol not found: __ZN6google8protobuf8internal17UnknownFieldParseEjPNS1_29InternalMetadataWithArenaLiteEPKcPNS1_12ParseContextE Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/libs/cytolib.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/libs/cytolib.so

[DillonHammill]

Is RProtoBufLib installed?

BiocManager::install("RProtoBufLib")

[antoine4ucsd]

I just did it: install.packages("sf") library(sf) Linking to GEOS 3.8.1, GDAL 3.1.4, PROJ 6.3.1

but still

BiocManager::install("cytolib") Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10) Installing package(s) 'cytolib' trying URL https://bioconductor.org/packages/3.12/bioc/bin/macosx/contrib/4.0/cytolib_2.2.1.tgz Content type 'application/x-gzip' length 2537325 bytes (2.4 MB) downloaded 2.4 MB

The downloaded binary packages are in /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T//Rtmp8BEecG/downloaded_packages Old packages: 'sf' Update all/some/none? [a/s/n]:

reply all: There is a binary version available but the source version is later: binary source needs_compilation sf 0.9-7 0.9-8 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel)

reply:no

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/sf_0.9-7.tgz' Content type 'application/x-gzip' length 89143896 bytes (85.0 MB) downloaded 85.0 MB

The downloaded binary packages are in /var/folders/r3/y359df552hg8krxm_3lr1f1r0000gr/T//Rtmp8BEecG/downloaded_packages

but I am back again with the same issue...

library(cytolib) Error: package or namespace load failed for ‘cytolib’: .onLoad failed in loadNamespace() for 'cytolib', details: call: dyn.load(cytolib, local = FALSE, now = TRUE) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/libs/cytolib.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/libs/cytolib.so, 10): Symbol not found: __ZN6google8protobuf8internal17UnknownFieldParseEjPNS1_29InternalMetadataWithArenaLiteEPKcPNS1_12ParseContextE Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/libs/cytolib.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/libs/cytolib.so

[DillonHammill]

@antoine4ucsd, sorry for not getting back to you sooner. Did you manage to get everything installed correctly?

[ghost]

Writing this here in case someone encounters the same issue, which seems to be linked to Bioconductor installation.

To solve it, before running the following command line 'devtools::install_github("DillonHammill/CytoExploreR")', I manually downloaded the following libraries in this order:

remotes::install_github("RGLab/cytolib", force = TRUE) remotes::install_github("RGLab/flowCore”, force = TRUE) remotes::install_github("RGLab/ncdfFlow”, force = TRUE) remotes::install_github("RGLab/flowWorkspace”, force = TRUE) remotes::install_github("RGLab/flowClust", force = TRUE) remotes::install_github("RGLab/flowStats”, force = TRUE) remotes::install_github("RGLab/openCyto”, force = TRUE)

(in case the problem appears with any other library, using the same command lines should work too)