Closed rwbaer closed 4 years ago
mikejiang
commented
4 years ago Bioconductor builds ok for all the latest packages. Why don't you install the binary directly from there if you have trouble to build if from source? http://bioconductor.org/packages/3.12/bioc/html/cytolib.html
jacobpwagner
commented
4 years ago @rwbaer , it looks like there was an issue with quotation parsing, which should be solved by https://github.com/RGLab/cytolib/commit/48c117fffc406e6d48011af8dfd5cab317cb2d07. Now, this should succeed:
install_github("RGLab/cytolib")And you are correct that there are no longer "trunk" branches. The main branches for all RGLab repos is now "master" (which will be the default). I believe this is now updated appropriately in the instructions at https://github.com/DillonHammill/CytoExploreR/.
rwbaer
commented
4 years ago @mikejiang. Although they may be incorrect, the instructions at https://dillonhammill.github.io/CytoExploreR/ instruct me specifically that the github versions of these dependency are required. I think this cytoExploreR package is still in an early development stage and trying to track RGLab development. I understand this makes things a little dicey.
@jacobpwagner. The cytolib install is now successful, but there is still something weird about flowWorkspace install. The version number for cytolib I'm seeing in RStudio is 2.1.6. There flowworkspace install seems end with something wrong with the H5::H5File() compile. I hope supplying just these last few lines of the install is enough. If not, I can run again and supply the whole output, but that seems like overkill for now.
> remove.packages("flowWorkspace", lib="~/R/win-library/4.0")
Error in remove.packages : there is no package called ‘flowWorkspace’
> install_github("RGLab/flowWorkspace")
Downloading GitHub repo RGLab/flowWorkspace@master
Skipping 9 packages ahead of CRAN: Biobase, BiocGenerics, graph, RBGL, Rgraphviz, RProtoBufLib, ncdfFlow, Rhdf5lib, zlibbioc
√ checking for file 'C:\Users\rbaer\AppData\Local\Temp\Rtmp6TCgRX\remotes33f014f8bee\RGLab-flowWorkspace-e614305/DESCRIPTION' (641ms)
- preparing 'flowWorkspace': (2.2s)
√ checking DESCRIPTION meta-information ...
- cleaning src
- checking for LF line-endings in source and make files and shell scripts (3.3s)
- checking for empty or unneeded directories
WARNING: Removing directory 'flowWorkspace/Meta' which should only
occur in an installed package
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'flowWorkspace/tests/testthat/expect_result/empty_pop.rds'
- building 'flowWorkspace_4.1.3.tar.gz'
Installing package into ‘C:/Users/rbaer/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'flowWorkspace' ...
** using staged installation
** libs
*** arch - i386
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'C:/Users/rbaer/Documents/R/win-library/4.0/Rcpp/include' -I'C:/Users/rbaer/Documents/R/win-library/4.0/BH/include' -I'C:/Users/rbaer/Documents/R/win-library/4.0/RProtoBufLib/include' -I'C:/Users/rbaer/Documents/R/win-library/4.0/cytolib/include' -I'C:/Users/rbaer/Documents/R/win-library/4.0/Rhdf5lib/include' -I'C:/Users/rbaer/Documents/R/win-library/4.0/RcppArmadillo/include' -I'C:/Users/rbaer/Documents/R/win-library/4.0/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_API.cpp -o R_API.o
...
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: C:/Users/rbaer/Documents/R/win-library/4.0/cytolib/lib/i386/libcytolib.a(H5CytoFrame.o):H5CytoFrame.cpp:(.text.unlikely+0x5ea): undefined reference to `H5::DataSet::~DataSet()'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: C:/Users/rbaer/Documents/R/win-library/4.0/cytolib/lib/i386/libcytolib.a(H5CytoFrame.o):H5CytoFrame.cpp:(.text.unlikely+0x5f8): undefined reference to `H5::H5File::~H5File()'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'flowWorkspace'
* removing 'C:/Users/rbaer/Documents/R/win-library/4.0/flowWorkspace'
Error: Failed to install 'flowWorkspace' from GitHub:
(converted from warning) installation of package ‘C:/Users/rbaer/AppData/Local/Temp/Rtmp6TCgRX/file33f02e2d3ffe/flowWorkspace_4.1.3.tar.gz’ had non-zero exit statusThe same issue as cytolib, I've pushed fix and try again
DillonHammill
commented
4 years ago @rwbaer, I think all the required versions of RGLab packages are now available from BioC release. CytoExploreR has a minimum requirement for flowCore (>= 1.53.8), flowWorkspace (>= 3.35.8) and openCyto (>= 1.25.2). I will make sure and update the installation instructions.
mikejiang
commented
4 years ago But it is good that you caught some fresh compilation issues introduced just last weekends. It is our desire to make sure github version works for you guys as well.
DillonHammill
commented
4 years ago Thanks @mikejiang and @jacobpwagner, really appreciate your help as always.
rwbaer
commented
4 years ago Good to know @DillonHammill - Thanks. Thanks too @Mikejiang.
There may be one more of those errors in flowCore???? It stopped early when I chose menu 1 to upgrade flowCore; it compiled through when I did not (menu 3), but suffered a namespace error when reached the end without upgrading upgrading flowCore. Behavior with menu choice 3 none:
...
mkdir -p "C:/Users/rbaer/Documents/R/win-library/4.0/00LOCK-flowWorkspace/00new/flowWorkspace/lib/x64"
"C:/rtools40/mingw64/bin/"ar rs "C:/Users/rbaer/Documents/R/win-library/4.0/00LOCK-flowWorkspace/00new/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o
C:\rtools40\mingw64\bin\ar.exe: creating C:/Users/rbaer/Documents/R/win-library/4.0/00LOCK-flowWorkspace/00new/flowWorkspace/lib/x64/libflowWorkspace.a
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o -LC:/PROGRA~1/R/R-40~1.1/bin/x64 -lRlapack -LC:/PROGRA~1/R/R-40~1.1/bin/x64 -lRblas -lgfortran -lm -lquadmath C:/Users/rbaer/Documents/R/win-library/4.0/cytolib/lib/x64/libcytolib.a C:/Users/rbaer/Documents/R/win-library/4.0/RProtoBufLib/lib/x64/libprotobuf-lite.a -LC:/Users/rbaer/Documents/R/win-library/4.0/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/Users/rbaer/DOCUME~1/R/WIN-LI~1/4.0/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -lws2_32 -LC:/PROGRA~1/R/R-40~1.1/bin/x64 -lR
installing to C:/Users/rbaer/Documents/R/win-library/4.0/00LOCK-flowWorkspace/00new/flowWorkspace/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package 'flowCore' does not have a namespace
Execution halted
ERROR: lazy loading failed for package 'flowWorkspace'
* removing 'C:/Users/rbaer/Documents/R/win-library/4.0/flowWorkspace'
Error: Failed to install 'flowWorkspace' from GitHub:
(converted from warning) installation of package ‘C:/Users/rbaer/AppData/Local/Temp/RtmpeoSggd/file58286e8f15cb/flowWorkspace_4.1.3.tar.gz’ had non-zero exit statusBehavior with menu choice 1:
install_github("RGLab/flowWorkspace")
Downloading GitHub repo RGLab/flowWorkspace@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: flowCore (61bdc0413... -> 7558d2583...) [GitHub]
Enter one or more numbers, or an empty line to skip updates:
1
flowCore (61bdc0413... -> 7558d2583...) [GitHub]
Skipping 9 packages ahead of CRAN: Biobase, BiocGenerics, graph, RBGL, Rgraphviz, RProtoBufLib, ncdfFlow, Rhdf5lib, zlibbioc
Downloading GitHub repo RGLab/flowCore@master
Skipping 4 packages ahead of CRAN: Biobase, BiocGenerics, RProtoBufLib, Rhdf5lib
√ checking for file 'C:\Users\rbaer\AppData\Local\Temp\RtmpeoSggd\remotes58286d005ff9\RGLab-flowCore-7558d25/DESCRIPTION' (981ms)
- preparing 'flowCore': (12.6s)
√ checking DESCRIPTION meta-information ...
- cleaning src
- checking for LF line-endings in source and make files and shell scripts (2.3s)
- checking for empty or unneeded directories
- looking to see if a 'data/datalist' file should be added
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'flowCore/data/GvHD.rda' 'flowCore/tests/testthat/expectResults.rds' WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'flowCore/tests/testthat/ref_flowframes.rds'
- building 'flowCore_2.1.0.tar.gz'
Installing package into ‘C:/Users/rbaer/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
ERROR: failed to lock directory 'C:/Users/rbaer/Documents/R/win-library/4.0' for modifying
Try removing 'C:/Users/rbaer/Documents/R/win-library/4.0/00LOCK-flowCore'
Error: Failed to install 'flowWorkspace' from GitHub:
Failed to install 'flowCore' from GitHub:
(converted from warning) installation of package ‘C:/Users/rbaer/AppData/Local/Temp/RtmpeoSggd/file582869163c53/flowCore_2.1.0.tar.gz’ had non-zero exit status
@rwbaer , there was, but I actually just fixed it there too: https://github.com/RGLab/flowCore/commit/7558d258350d314426827e419dcdc7014f98f5ec. Try removing the lock as the error suggests and then re-try:
install_github("RGLab/flowCore")Thanks all. We have a clean compile and install. Closing this out!
Describe the bug There seems to be trouble installing a new enough cytolib to satisfy the installation of flowWorkspace. As a potential workaround, I deleted all versions from the library and tried again. I tried installing a fresh cytolib first. None of this worked. I'm presumably pulling from master after trying
My ultimate goal is to test cytoExploreR which has development versions of these packages as a dependency. This has been working fine until the last few days. However, trying to directly install flowWorkspace is not working either,
As an added note, the repository instructions suggest installing trunk, but there does not currently appear to be a "trunk"
Install console code
SessionInfo:
Additional context Add any other context about the problem here.