Elana J. Fertig
| Snapshot Date: 2023-10-08 14:00:07 -0400 (Sun, 08 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/CoGAPS |
| git_branch: RELEASE_3_17 |
| git_last_commit: 6861e5b |
| git_last_commit_date: 2023-07-11 13:53:11 -0400 (Tue, 11 Jul 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-13 11:32:19 -0400 (Fri, 13 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4346 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 395/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoGAPS 3.20.0 (landing page) Elana J. Fertig
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the CoGAPS package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CoGAPS |
| Version: 3.20.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoGAPS_3.20.0.tar.gz |
| StartedAt: 2023-10-10 09:49:32 -0400 (Tue, 10 Oct 2023) |
| EndedAt: 2023-10-10 09:57:17 -0400 (Tue, 10 Oct 2023) |
| EllapsedTime: 464.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CoGAPS.Rcheck |
| Warnings: 4 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoGAPS_3.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CoGAPS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CoGAPS’ can be installed ... WARNING
Found the following significant warnings:
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CoGAPS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 21.4Mb
sub-directories of 1Mb or more:
extdata 19.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot.CogapsResult: no visible global function definition for ‘axis’
plot.CogapsResult: no visible global function definition for ‘text’
plot.CogapsResult: no visible global function definition for ‘par’
MANOVA,matrix-CogapsResult: no visible global function definition for
‘manova’
fromCSV,character: no visible global function definition for ‘read.csv’
getPatternHallmarks,CogapsResult: no visible binding for global
variable ‘.’
getPatternHallmarks,CogapsResult: no visible binding for global
variable ‘MsigDB_Hallmark’
getPatternHallmarks,CogapsResult: no visible binding for global
variable ‘padj’
plotPatternHallmarks,CogapsResult-list-numeric: no visible binding for
global variable ‘overlapGenes’
plotPatternHallmarks,CogapsResult-list-numeric: no visible binding for
global variable ‘padj’
show,CogapsParams: no visible binding for global variable
‘checkpointFile’
toCSV,CogapsResult-character: no visible global function definition for
‘write.csv’
Undefined global functions or variables:
. MsigDB_Hallmark axis checkpointFile manova overlapGenes padj par
read.csv text write.csv
Consider adding
importFrom("graphics", "axis", "par", "text")
importFrom("stats", "manova")
importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘MANOVA’ ‘fromCSV’ ‘getPatternHallmarks’ ‘plotPatternHallmarks’
‘toCSV’
Undocumented data sets:
‘ModSimBases’ ‘ModSimData’
Undocumented S4 methods:
generic 'MANOVA' and siglist 'matrix,CogapsResult'
generic 'fromCSV' and siglist 'character'
generic 'getPatternHallmarks' and siglist 'CogapsResult'
generic 'plotPatternHallmarks' and siglist
'CogapsResult,list,numeric'
generic 'toCSV' and siglist 'CogapsResult,character'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'CoGAPS':
CoGAPS
Code: function(data, params = new("CogapsParams"), nThreads = 1,
messages = TRUE, outputFrequency = 1000, uncertainty =
NULL, useCheckPoint = FALSE, checkpointOutFile =
"gaps_checkpoint.out", checkpointInterval = 0,
checkpointFile = NULL, transposeData = FALSE, BPPARAM
= NULL, workerID = 1, asynchronousUpdates = TRUE,
nSnapshots = 0, snapshotPhase = "sampling", ...)
Docs: function(data, params = new("CogapsParams"), nThreads = 1,
messages = TRUE, outputFrequency = 1000, uncertainty =
NULL, checkpointOutFile = "gaps_checkpoint.out",
checkpointInterval = 0, checkpointInFile = NULL,
transposeData = FALSE, BPPARAM = NULL, workerID = 1,
asynchronousUpdates = TRUE, nSnapshots = 0,
snapshotPhase = "sampling", ...)
Argument names in code not in docs:
useCheckPoint checkpointFile
Argument names in docs not in code:
checkpointInFile
Mismatches in argument names (first 3):
Position: 7 Code: useCheckPoint Docs: checkpointOutFile
Position: 8 Code: checkpointOutFile Docs: checkpointInterval
Position: 9 Code: checkpointInterval Docs: checkpointInFile
Codoc mismatches from documentation object 'GWCoGAPS':
GWCoGAPS
Code: function(data, params = new("CogapsParams"), nThreads = 1,
messages = TRUE, outputFrequency = 500, uncertainty =
NULL, checkpointOutFile = "gaps_checkpoint.out",
checkpointInterval = 1000, checkpointFile = NULL,
transposeData = FALSE, BPPARAM = NULL, workerID = 1,
asynchronousUpdates = FALSE, ...)
Docs: function(data, params = new("CogapsParams"), nThreads = 1,
messages = TRUE, outputFrequency = 500, uncertainty =
NULL, checkpointOutFile = "gaps_checkpoint.out",
checkpointInterval = 1000, checkpointInFile = NULL,
transposeData = FALSE, BPPARAM = NULL, workerID = 1,
asynchronousUpdates = FALSE, ...)
Argument names in code not in docs:
checkpointFile
Argument names in docs not in code:
checkpointInFile
Mismatches in argument names:
Position: 9 Code: checkpointFile Docs: checkpointInFile
Codoc mismatches from documentation object 'plotPatternMarkers':
plotPatternMarkers
Code: function(object, data, patternMarkers, patternPalette,
sampleNames, samplePalette = NULL, heatmapCol =
bluered, colDendrogram = TRUE, scale = "row", ...)
Docs: function(object, data, patternPalette, sampleNames,
samplePalette = NULL, heatmapCol = bluered,
colDenogram = TRUE, scale = "row", ...)
Argument names in code not in docs:
patternMarkers colDendrogram
Argument names in docs not in code:
colDenogram
Mismatches in argument names (first 3):
Position: 3 Code: patternMarkers Docs: patternPalette
Position: 4 Code: patternPalette Docs: sampleNames
Position: 5 Code: sampleNames Docs: samplePalette
Codoc mismatches from documentation object 'scCoGAPS':
scCoGAPS
Code: function(data, params = new("CogapsParams"), nThreads = 1,
messages = TRUE, outputFrequency = 500, uncertainty =
NULL, checkpointOutFile = "gaps_checkpoint.out",
checkpointInterval = 1000, checkpointFile = NULL,
transposeData = FALSE, BPPARAM = NULL, workerID = 1,
asynchronousUpdates = FALSE, ...)
Docs: function(data, params = new("CogapsParams"), nThreads = 1,
messages = TRUE, outputFrequency = 500, uncertainty =
NULL, checkpointOutFile = "gaps_checkpoint.out",
checkpointInterval = 1000, checkpointInFile = NULL,
transposeData = FALSE, BPPARAM = NULL, workerID = 1,
asynchronousUpdates = FALSE, ...)
Argument names in code not in docs:
checkpointFile
Argument names in docs not in code:
checkpointInFile
Mismatches in argument names:
Position: 9 Code: checkpointFile Docs: checkpointInFile
S4 class codoc mismatches from documentation object 'CogapsParams-class':
Slots for class 'CogapsParams'
Code: alphaA alphaP checkpointFile checkpointInterval
checkpointOutFile cut distributed explicitSets fixedPatterns
geneNames maxGibbsMassA maxGibbsMassP maxNS minNS nIterations
nPatterns nSets sampleNames samplingAnnotation samplingWeight
seed sparseOptimization subsetDim subsetIndices takePumpSamples
whichMatrixFixed
Docs: alphaA alphaP cut distributed explicitSets fixedPatterns
geneNames maxGibbsMassA maxGibbsMassP maxNS minNS nIterations
nPatterns nSets sampleNames samplingAnnotation samplingWeight
seed sparseOptimization subsetDim subsetIndices takePumpSamples
whichMatrixFixed
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
‘ModSimResult.Rds’ ‘ModSimResult.h5ad’
Please use e.g. ‘inst/extdata’ for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/libs/CoGAPS.so’:
Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_putchar’, possibly from ‘putchar’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CoGAPS.Rcheck/00check.log’
for details.
CoGAPS.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoGAPS
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘CoGAPS’ ...
** 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 the compiler supports GNU C++... yes
checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... yes
checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... clang++ -arch arm64 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... (cached) yes
checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... (cached) none needed
./configure: line 3246: AX_COMPILER_VENDOR: command not found
./configure: line 3247: AX_COMPILER_VERSION: command not found
./configure: line 3259: AX_OPENMP: command not found
building on compiler version
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Cogaps.cpp -o Cogaps.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GapsParameters.cpp -o GapsParameters.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GapsResult.cpp -o GapsResult.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GapsRunner.cpp -o GapsRunner.o
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^~~~~
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^~~~~
GapsRunner.cpp:70:16: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<AsynchronousGibbsSampler<SparseNormalModel>, Matrix>' requested here
return runCoGAPSAlgorithm< AsynchronousGibbsSampler<DataModel> >(data,
^
GapsRunner.cpp:85:16: note: in instantiation of function template specialization 'chooseSampler<SparseNormalModel, Matrix>' requested here
return chooseSampler<SparseNormalModel>(data, params, uncertainty, randState);
^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<Matrix>' requested here
return chooseDataModel(data, params, uncertainty, randState);
^
GapsRunner.cpp:113:12: note: in instantiation of function template specialization 'run_helper<Matrix>' requested here
return run_helper(data, params, uncertainty, randState);
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^~~~~
GapsRunner.cpp:74:12: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<SingleThreadedGibbsSampler<SparseNormalModel>, Matrix>' requested here
return runCoGAPSAlgorithm< SingleThreadedGibbsSampler<DataModel> >(data,
^
GapsRunner.cpp:85:16: note: in instantiation of function template specialization 'chooseSampler<SparseNormalModel, Matrix>' requested here
return chooseSampler<SparseNormalModel>(data, params, uncertainty, randState);
^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<Matrix>' requested here
return chooseDataModel(data, params, uncertainty, randState);
^
GapsRunner.cpp:113:12: note: in instantiation of function template specialization 'run_helper<Matrix>' requested here
return run_helper(data, params, uncertainty, randState);
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^~~~~
GapsRunner.cpp:70:16: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<AsynchronousGibbsSampler<DenseNormalModel>, Matrix>' requested here
return runCoGAPSAlgorithm< AsynchronousGibbsSampler<DataModel> >(data,
^
GapsRunner.cpp:88:12: note: in instantiation of function template specialization 'chooseSampler<DenseNormalModel, Matrix>' requested here
return chooseSampler<DenseNormalModel>(data, params, uncertainty, randState);
^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<Matrix>' requested here
return chooseDataModel(data, params, uncertainty, randState);
^
GapsRunner.cpp:113:12: note: in instantiation of function template specialization 'run_helper<Matrix>' requested here
return run_helper(data, params, uncertainty, randState);
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^~~~~
GapsRunner.cpp:74:12: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<SingleThreadedGibbsSampler<DenseNormalModel>, Matrix>' requested here
return runCoGAPSAlgorithm< SingleThreadedGibbsSampler<DataModel> >(data,
^
GapsRunner.cpp:88:12: note: in instantiation of function template specialization 'chooseSampler<DenseNormalModel, Matrix>' requested here
return chooseSampler<DenseNormalModel>(data, params, uncertainty, randState);
^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<Matrix>' requested here
return chooseDataModel(data, params, uncertainty, randState);
^
GapsRunner.cpp:113:12: note: in instantiation of function template specialization 'run_helper<Matrix>' requested here
return run_helper(data, params, uncertainty, randState);
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^~~~~
GapsRunner.cpp:70:16: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<AsynchronousGibbsSampler<SparseNormalModel>, std::basic_string<char>>' requested here
return runCoGAPSAlgorithm< AsynchronousGibbsSampler<DataModel> >(data,
^
GapsRunner.cpp:85:16: note: in instantiation of function template specialization 'chooseSampler<SparseNormalModel, std::basic_string<char>>' requested here
return chooseSampler<SparseNormalModel>(data, params, uncertainty, randState);
^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<std::basic_string<char>>' requested here
return chooseDataModel(data, params, uncertainty, randState);
^
GapsRunner.cpp:119:12: note: in instantiation of function template specialization 'run_helper<std::basic_string<char>>' requested here
return run_helper(data, params, uncertainty, randState);
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^~~~~
GapsRunner.cpp:74:12: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<SingleThreadedGibbsSampler<SparseNormalModel>, std::basic_string<char>>' requested here
return runCoGAPSAlgorithm< SingleThreadedGibbsSampler<DataModel> >(data,
^
GapsRunner.cpp:85:16: note: in instantiation of function template specialization 'chooseSampler<SparseNormalModel, std::basic_string<char>>' requested here
return chooseSampler<SparseNormalModel>(data, params, uncertainty, randState);
^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<std::basic_string<char>>' requested here
return chooseDataModel(data, params, uncertainty, randState);
^
GapsRunner.cpp:119:12: note: in instantiation of function template specialization 'run_helper<std::basic_string<char>>' requested here
return run_helper(data, params, uncertainty, randState);
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^~~~~
GapsRunner.cpp:70:16: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<AsynchronousGibbsSampler<DenseNormalModel>, std::basic_string<char>>' requested here
return runCoGAPSAlgorithm< AsynchronousGibbsSampler<DataModel> >(data,
^
GapsRunner.cpp:88:12: note: in instantiation of function template specialization 'chooseSampler<DenseNormalModel, std::basic_string<char>>' requested here
return chooseSampler<DenseNormalModel>(data, params, uncertainty, randState);
^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<std::basic_string<char>>' requested here
return chooseDataModel(data, params, uncertainty, randState);
^
GapsRunner.cpp:119:12: note: in instantiation of function template specialization 'run_helper<std::basic_string<char>>' requested here
return run_helper(data, params, uncertainty, randState);
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^~~~~
GapsRunner.cpp:74:12: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<SingleThreadedGibbsSampler<DenseNormalModel>, std::basic_string<char>>' requested here
return runCoGAPSAlgorithm< SingleThreadedGibbsSampler<DataModel> >(data,
^
GapsRunner.cpp:88:12: note: in instantiation of function template specialization 'chooseSampler<DenseNormalModel, std::basic_string<char>>' requested here
return chooseSampler<DenseNormalModel>(data, params, uncertainty, randState);
^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<std::basic_string<char>>' requested here
return chooseDataModel(data, params, uncertainty, randState);
^
GapsRunner.cpp:119:12: note: in instantiation of function template specialization 'run_helper<std::basic_string<char>>' requested here
return run_helper(data, params, uncertainty, randState);
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
9 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GapsStatistics.cpp -o GapsStatistics.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/Atom.cpp -o atomic/Atom.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/HashSets.cpp -o data_structures/HashSets.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/Matrix.cpp -o data_structures/Matrix.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/Vector.cpp -o data_structures/Vector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file_parser/FileParser.cpp -o file_parser/FileParser.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c math/Math.cpp -o math/Math.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c math/MatrixMath.cpp -o math/MatrixMath.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c math/Random.cpp -o math/Random.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c math/VectorMath.cpp -o math/VectorMath.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CoGAPS.so Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/Atom.o atomic/ConcurrentAtom.o atomic/AtomicDomain.o atomic/ConcurrentAtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CharacterDelimitedParser.o file_parser/FileParser.o file_parser/MatrixElement.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseNormalModel.o gibbs_sampler/SparseNormalModel.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-CoGAPS/00new/CoGAPS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CoGAPS)
CoGAPS.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(CoGAPS)
>
> test_check("CoGAPS")
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.20.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on GIST.matrix (1363 genes and 9 samples)
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
This is CoGAPS version 3.20.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.20.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 1 is starting!
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This is CoGAPS version 3.20.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
worker 1 is starting!
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This is CoGAPS version 3.20.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 1 is starting!
worker 2 is starting!
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This is CoGAPS version 3.20.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.gct (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on testDataFrame (9 genes and 1363 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on testMatrix (9 genes and 1363 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.gct (9 genes and 1363 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
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This is CoGAPS version 3.20.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
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This is CoGAPS version 3.20.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
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This is CoGAPS version 3.20.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
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This is CoGAPS version 3.20.0
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.20.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples) with parameters:
-- Standard Parameters --
nPatterns 3
nIterations 175
seed 42
sparseOptimization TRUE
distributed genome-wide
-- Sparsity Parameters --
alpha 0.01
maxGibbsMass 100
-- Distributed CoGAPS Parameters --
nSets 5
cut 4
minNS 3
maxNS 8
Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...
Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
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-- Equilibration Phase --
-- Sampling Phase --
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This is CoGAPS version 3.20.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples) with parameters:
-- Standard Parameters --
nPatterns 3
nIterations 175
seed 42
sparseOptimization TRUE
distributed genome-wide
-- Sparsity Parameters --
alpha 0.01
maxGibbsMass 100
-- Distributed CoGAPS Parameters --
nSets 5
cut 4
minNS 3
maxNS 8
Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...
Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
worker 1 is starting!
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-- Equilibration Phase --
-- Sampling Phase --
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[ FAIL 0 | WARN 9 | SKIP 3 | PASS 58 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_checkpoints.R:3:1', 'test_parameters.R:3:1',
'test_subset_data.R:53:1'
[ FAIL 0 | WARN 9 | SKIP 3 | PASS 58 ]
>
> proc.time()
user system elapsed
39.095 6.055 58.671
CoGAPS.Rcheck/CoGAPS-Ex.timings
| name | user | system | elapsed | |
| CoGAPS | 0.303 | 0.014 | 0.566 | |
| CogapsParams | 0.002 | 0.001 | 0.002 | |
| GWCoGAPS | 0.000 | 0.000 | 0.001 | |
| binaryA-methods | 0.025 | 0.004 | 0.054 | |
| buildReport | 0 | 0 | 0 | |
| calcZ-methods | 0.025 | 0.003 | 0.051 | |
| checkpointsEnabled | 0 | 0 | 0 | |
| compiledWithOpenMPSupport | 0 | 0 | 0 | |
| getAmplitudeMatrix-methods | 0.025 | 0.003 | 0.055 | |
| getClusteredPatterns-methods | 0.025 | 0.003 | 0.052 | |
| getCorrelationToMeanPattern-methods | 0.024 | 0.003 | 0.051 | |
| getFeatureLoadings-methods | 0.024 | 0.003 | 0.050 | |
| getMeanChiSq-methods | 0.024 | 0.003 | 0.047 | |
| getOriginalParameters-methods | 0.024 | 0.003 | 0.048 | |
| getParam-methods | 0.001 | 0.000 | 0.001 | |
| getPatternMatrix-methods | 0.025 | 0.003 | 0.052 | |
| getRetinaSubset | 1.687 | 0.261 | 3.565 | |
| getSampleFactors-methods | 0.025 | 0.003 | 0.043 | |
| getSubsets-methods | 0.025 | 0.003 | 0.049 | |
| getUnmatchedPatterns-methods | 0.024 | 0.003 | 0.050 | |
| getVersion-methods | 0.025 | 0.003 | 0.054 | |
| patternMarkers-methods | 0.062 | 0.004 | 0.122 | |
| plotResiduals-methods | 0.025 | 0.003 | 0.039 | |
| reconstructGene-methods | 0.025 | 0.003 | 0.054 | |
| scCoGAPS | 0.000 | 0.000 | 0.001 | |
| setAnnotationWeights-methods | 0.001 | 0.001 | 0.002 | |
| setDistributedParams-methods | 0.002 | 0.001 | 0.003 | |
| setFixedPatterns-methods | 0.026 | 0.004 | 0.053 | |
| setParam-methods | 0.002 | 0.000 | 0.006 | |