diva_to_gatingset: option required to *not* use compensation matrix from xml #128
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yeah, send the link or data to [email protected]. Thanks! |
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No problem, I've sent it over just now. Please let me know if the link didn't work for some reason. Thank you! |
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There is currently no elegant way to decide whether xml compensation should/can be used since I've pushed the easy workaround as you suggested, i.e. optionally disable it |
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Awesome, that does the job. Look forward to using CytoML! |
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I also have a dummy compensation issue in my xml file. I tried setting xml_compensation_enabled to either TRUE or FALSE and both times I received the same error. Are there alternative solutions to this problem?
I am wondering if it might be easier to create a function that removes dummy compensation data from diva xml files. I tried removing the code listed above from my xml file but I received the following error. |
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Can you show the error and traceback() output when you set |
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I don't know much about these functions, but it seems like diva_to_gatingset is not passing |
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You may need to pull the latest version from github. |
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I am currently having trouble running the diva_to_gatingset function from the CytoML package I am using CytoML version 2.4.0. available through biocManager > library(flowWorkspace)
> library(CytoML)
> setwd("/Users/user1/Desktop/DummyProject_Folder/DummyExp")
> flowData <- getwd()
> gatingFile <- list.files(flowData, pattern=".xml",full = TRUE)
> ws <- open_diva_xml(gatingFile)
> ws
> diva_get_sample_groups(ws)
> gs <- diva_to_gatingset(ws)
> sampleNames(gs)
> gs_get_pop_paths(gs)
> plotGate(gs[[1]])
> sessionInfo()
Diva Workspace Version Version 9.1.2
File location: /Users/user1/Desktop/DummyProject_Folder/DummyExp
File name: DummyExp.xml
Workspace is open.
Groups in Workspace
> diva_get_sample_groups(ws)
> gs <- diva_to_gatingset(ws)
Choose which group of samples to import:
1: DummySpecimen1
> Selection: 1
Parsing 2 samples
loading data: /Users/nvannest/Desktop/ACE openCyto Test/DummyProject_Folder/DummyExp_Exp_Export/DummyExp_DummySpecimen1_DummyTube1.fcs
swap cols: FSC-H:FSC-W
swap cols: SSC-H:SSC-W
Compensating
Error in solve.default(comp) : 'a' (7 x 14) must be square )
When I try to install the version of CytoML available through github I get an installation error > devtools::install_github("RGLab/CytoML")
Downloading GitHub repo RGLab/CytoML@HEAD
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: robustbase (0.93-7 -> 0.93-8) [CRAN]
5: matrixStats (0.58.0 -> 0.59.0) [CRAN]
6: ks (1.13.0 -> 1.13.1) [CRAN]
> Enter one or more numbers, or an empty line to skip updates: 1
robustbase (0.93-7 -> 0.93-8) [CRAN]
matrixStats (0.58.0 -> 0.59.0) [CRAN]
ks (1.13.0 -> 1.13.1) [CRAN]
Installing 3 packages: robustbase, matrixStats, ks
There are binary versions available but the source versions are later:
binary source needs_compilation
robustbase 0.93-7 0.93-8 TRUE
matrixStats 0.58.0 0.59.0 TRUE
ks 1.13.0 1.13.1 TRUE
> Do you want to install from sources the packages which need compilation? (Yes/no/cancel) no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/robustbase_0.93-7.tgz'
Content type 'application/x-gzip' length 3123297 bytes (3.0 MB)
==================================================
downloaded 3.0 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/matrixStats_0.58.0.tgz'
Content type 'application/x-gzip' length 2019790 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ks_1.13.0.tgz'
Content type 'application/x-gzip' length 1851632 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
The downloaded binary packages are in
/var/folders/_g/xp8hp7mn02z122v2092lzw499zps22/T//RtmpcPvBBy/downloaded_packages
✓ checking for file ‘/private/var/folders/_g/xp8hp7mn02z122v2092lzw499zps22/T/RtmpcPvBBy/remotes132e432e8405d/RGLab-CytoML-d544a00/DESCRIPTION’ ...
─ preparing ‘CytoML’:
✓ 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
Omitted ‘LazyData’ from DESCRIPTION
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:
‘CytoML/tests/testthat/expect_result/flowJoWorkspace_expect.rds’
─ building ‘CytoML_2.5.1.tar.gz’
Warning in sprintf(gettext(fmt, domain = domain), ...) :
one argument not used by format 'invalid uid value replaced by that for user 'nobody''
Warning: invalid uid value replaced by that for user 'nobody'
Warning in sprintf(gettext(fmt, domain = domain), ...) :
one argument not used by format 'invalid gid value replaced by that for user 'nobody''
Warning: invalid gid value replaced by that for user 'nobody'
* installing *source* package ‘CytoML’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes
checking for gcc... clang -mmacosx-version-min=10.13
checking whether we are using the GNU C compiler... yes
checking whether clang -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: setting cytolib-ml commandline tool path...
configure: Using the following compilation and linking flags
configure: PKG_CPPFLAGS=-I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -ftemplate-depth=900
configure: PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm
configure: CYTOLIBML_BIN=/usr/local/bin
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/cytolibml_bin_path.R
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/flowWorkspace/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/CytoML.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/flowWorkspace/include/flowWorkspace.h:5:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include/cytolib/populationTree.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use <iterator> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<iterator>")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
^
<scratch space>:12:2: note: expanded from here
message("This header is deprecated. Use " "<iterator>" " instead.")
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/CytoML.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/flowWorkspace/include/flowWorkspace.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/flowWorkspace/include/flowWorkspace/pairVectorRcppWrap.h:15:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/CytoML.h:5:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: '/*' within block comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
../inst/include/CytoML/winFlowJoWorkspace.hpp:866:18: error: no member named 'setDataOnlyFlag' in 'cytolib::scaleTrans'
curTran->setDataOnlyFlag(true);
~~~~~~~ ^
../inst/include/CytoML/winFlowJoWorkspace.hpp:882:16: error: no member named 'setDataOnlyFlag' in 'cytolib::scaleTrans'
curTran->setDataOnlyFlag(false);
~~~~~~~ ^
3 warnings and 2 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘CytoML’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/CytoML’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/CytoML’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/_g/xp8hp7mn02z122v2092lzw499zps22/T//RtmpcPvBBy/file132e439dffd5e/CytoML_2.5.1.tar.gz’ had non-zero exit statusHere is additional information about my setup: R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
BiocManager version 1.30.15
> tools:::.BioC_version_associated_with_R_version()
[1] ‘3.13’Any help would be very appreciated. Thanks! |
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try to update cytolib and flowWorkspace from github first |
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I've updated cytolib and flowWorkspace directly from github and continue to get the same error Input: Output: |
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how about set xml_compensation_enabled = F? |
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Success!! Wow what a relief. Thanks so much for your help! |
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Hi,
In cases where a compensation matrix was not created in Diva, diva_to_gatingset attempts to find one in the xml file and returns an error:
Error in solve.default(comp) : 'a' (2 x 4) must be square.This makes importing xml gates from Diva impossible in many situations. Let me know if you require an example xlm / fcs set.
The text was updated successfully, but these errors were encountered: