Loading FlowSOM package fails

[JPGranizo]

Hi,

when I try to load the FlowSOM package, then I receive an error message:

> library(FlowSOM) Error: package or namespace load failed for ‘FlowSOM’: object ‘compute_timestep’ is not exported by 'namespace:flowWorkspace'

I am running macOS Catalina 10.15.7 and R version 4.0.3. FlowSOM was installed via "BiocManager::install("FlowSOM")" and the installed FlowSOM version is 1.20.0 I tried to install FlowSOM via devtools::install_github("SofieVG/FlowSOM") or devtools::install_github("SofieVG/FlowSOM", ref = "devel") in case there is a more recent version. But the FlowSOM installation from github fails in both cases (see the error messages copied below).

I tried to load FlowSOM in combination with two different flowWorkspace versions: Version 4.0.6 installed via BiocManager and Version 4.1.12 installed from github. The flowWorkspace version does not have an effect on the error while loading FlowSOM.

Can you please advice how to fix loading FlowSOM? Thank you very much in advance!

Error messages during the installation of FlowSOM from github:

devtools::install_github("SofieVG/FlowSOM") Downloading GitHub repo SofieVG/FlowSOM@HEAD ✓ checking for file ‘/private/var/folders/sl/6h6dh39d2p3617w8h3sf2bsm0000gn/T/RtmpR2sVJa/remotes10cf62afa7f5e/SofieVG-FlowSOM-6f79b8b/DESCRIPTION’ ... ─ preparing ‘FlowSOM’: ✓ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘FlowSOM_1.19.4.tar.gz’

• installing source package ‘FlowSOM’ ... using staged installation libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c som.c -o som.o som.c:37:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] xdist += abs(tmp); ^ som.c:37:18: note: use function 'fabs' instead xdist += abs(tmp); ^~~ fabs som.c:47:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] tmp = abs(tmp); ^ som.c:47:15: note: use function 'fabs' instead tmp = abs(tmp); ^~~ fabs som.c:134:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value] change += abs(tmp); ^ som.c:134:27: note: use function 'fabs' instead change += abs(tmp); ^~~ fabs 3 warnings generated. clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-FlowSOM/00new/FlowSOM/libs R inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/libs/flowWorkspace.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/libs/flowWorkspace.so, 6): Symbol not found: ZN7cytolib11H5CytoFrameC1ERKNSt3112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_14FCS_READ_PARAMES9_b Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/libs/flowWorkspace.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/libs/flowWorkspace.so Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘FlowSOM’
• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/FlowSOM’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/FlowSOM’ Error: Failed to install 'FlowSOM' from GitHub: (converted from warning) installation of package ‘/var/folders/sl/6h6dh39d2p3617w8h3sf2bsm0000gn/T//RtmpR2sVJa/file10cf623c00a5d/FlowSOM_1.19.4.tar.gz’ had non-zero exit status

[yuhuisunnyluo]

Hi, I use flowSOM via Rstudio, and don't have this problem

[JPGranizo]

Hi, I use flowSOM via Rstudio, and don't have this problem

Hi, which R version and which FlowSOM / flowWorkspace versions have you installed?

[SofieVG]

Hi,

I haven't encountered this issue and do not think we call this compute_timestep function anywhere in the FlowSOM code. The compute_timestep function seems to be from an older version of flowWorkspace though. Maybe try to update all packages, that another dependency of FlowSOM used this older function and gets loaded when trying to load FlowSOM?

All the best, Sofie

On Mon, 19 Oct 2020 at 23:22, JPGranizo notifications@github.com wrote:

Hi, I use flowSOM via Rstudio, and don't have this problem

Hi, which R version and which FlowSOM / flowWorkspace versions have you installed?

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[SofieVG]

Hi @JPGranizo,

As I could not replicate this error and a newer version of the FlowSOM package has been pushed to github in the meantime, I will close this issue for now. If updating the packages didn't work and you're still encountering issues with the newest FlowSOM version, feel free to reopen this issue or start a new one.