Multiple platform build/check report for BioC 3.9 - CHECK report for clusterExperiment on tokay2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings clusterExperiment_2.3.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clusterExperiment/DESCRIPTION' ... OK
* this is package 'clusterExperiment' version '2.3.1'
* 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 whether package 'clusterExperiment' can be installed ... WARNING
Found the following significant warnings:
  subsampleLoop.cpp:89:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  subsampleLoop.cpp:90:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  subsampleLoop.cpp:122:25: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/ClusterExperiment-class.Rd:198: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/ClusterExperiment-class.Rd:202: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/ClusterExperiment-class.Rd:235: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/RSEC.Rd:40: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/RSEC.Rd:155: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterContrasts.Rd:41: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterContrasts.Rd:41: file link 'MAST' in package 'MAST' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterDendrogram.Rd:114: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterDendrogram.Rd:117: file link 'tdata' in package 'phylobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterDendrogram.Rd:200: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterMany.Rd:38: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterMany.Rd:134: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterSingle.Rd:36: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterSingle.Rd:56: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:67: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:68: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:76: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:124: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:237: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/makeDendrogram.Rd:54: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/mergeClusters.Rd:156: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotDendrogram.Rd:113: file link 'tiplabels' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotFeatureBoxplot.Rd:40: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotFeatureScatter.Rd:39: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotHeatmap.Rd:56: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotHeatmap.Rd:127: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/reduceFunctions.Rd:94: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/reduceFunctions.Rd:178: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/reduceFunctions.Rd:289: file link 'reducedDim' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/rsecFluidigm.Rd:66: file link 'fluidigm' in package 'scRNAseq' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/transformData.Rd:40: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/updateObject.Rd:57: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/updateObject.Rd:63: file link 'nodeLabels' in package 'phylobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Foreign function calls to a different package:
  .C(ape::node_depth, ...)
  .C(ape::node_depth_edgelength, ...)
  .C(ape::node_height, ...)
  .C(ape::node_height_clado, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... WARNING
Output for data("rsecFluidigm", package = "clusterExperiment"):
  Search path was changed
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/clusterExperiment/libs/i386/clusterExperiment.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/clusterExperiment/libs/x64/clusterExperiment.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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. 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotHeatmap      21.90   0.04   21.94
plotClusters      5.86   0.03    5.89
assignUnassigned  4.25   0.79    5.03
clusterMany       4.94   0.08    5.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotHeatmap      24.52   0.10   24.64
clusterMany       6.78   0.18    6.95
assignUnassigned  6.64   0.08    6.72
plotClusters      6.72   0.00    6.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat_a-c.R'
 ERROR
Running the tests in 'tests/testthat_a-c.R' failed.
Last 13 lines of output:
  [1] "hierarchical01"
  [1] "tight"
  == testthat results  ===========================================================
  OK: 771 SKIPPED: 1 FAILED: 8
  1. Failure: RSEC works wih non default assays (@test-assays.R#85) 
  2. Failure: RSEC works wih non default assays (@test-assays.R#99) 
  3. Failure: RSEC works independent of assay order (@test-assays.R#131) 
  4. Failure: RSEC works independent of assay order (@test-assays.R#138) 
  5. Failure: RSEC works independent of assay order (@test-assays.R#147) 
  6. Failure: RSEC works independent of assay order (@test-assays.R#154) 
  7. Failure: RSEC works independent of assay order (@test-assays.R#179) 
  8. Failure: RSEC works independent of assay order (@test-assays.R#186) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat_a-c.R'
 ERROR
Running the tests in 'tests/testthat_a-c.R' failed.
Last 13 lines of output:
  [1] "hierarchical01"
  [1] "tight"
  == testthat results  ===========================================================
  OK: 771 SKIPPED: 1 FAILED: 8
  1. Failure: RSEC works wih non default assays (@test-assays.R#85) 
  2. Failure: RSEC works wih non default assays (@test-assays.R#99) 
  3. Failure: RSEC works independent of assay order (@test-assays.R#131) 
  4. Failure: RSEC works independent of assay order (@test-assays.R#138) 
  5. Failure: RSEC works independent of assay order (@test-assays.R#147) 
  6. Failure: RSEC works independent of assay order (@test-assays.R#154) 
  7. Failure: RSEC works independent of assay order (@test-assays.R#179) 
  8. Failure: RSEC works independent of assay order (@test-assays.R#186) 
  
  Error: testthat unit tests failed
  Execution halted
* 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: 2 ERRORs, 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/clusterExperiment_2.3.1.tar.gz && rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterExperiment.buildbin-libdir clusterExperiment_2.3.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL clusterExperiment_2.3.1.zip && rm clusterExperiment_2.3.1.tar.gz clusterExperiment_2.3.1.zip
###
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install for i386

* installing *source* package 'clusterExperiment' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c search_pairs.cpp -o search_pairs.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subsampleLoop.cpp -o subsampleLoop.o
subsampleLoop.cpp: In function 'Rcpp::IntegerMatrix subsampleLoop(Rcpp::List, int)':
subsampleLoop.cpp:89:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     LogicalVector clusterj = j <= indexClusterEnds & j >= indexClusterStarts;
                                ^
subsampleLoop.cpp:90:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     LogicalVector clusterk = k <= indexClusterEnds & k >= indexClusterStarts;
                                ^
subsampleLoop.cpp:122:25: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if((it->second).first>0 | (it->second).second==NA_INTEGER){
                         ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.buildbin-libdir/00LOCK-clusterExperiment/00new/clusterExperiment/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
** help
*** installing help indices
  converting help for package 'clusterExperiment'
    finding HTML links ... done
    ClusterExperiment-class                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/ClusterExperiment-class.Rd:198: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/ClusterExperiment-class.Rd:202: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/ClusterExperiment-class.Rd:235: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
    ClusterExperiment-methods               html  
    ClusterFunction-class                   html  
    ClusterFunction-methods                 html  
    RSEC                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/RSEC.Rd:40: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/RSEC.Rd:155: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    addClusterings                          html  
    assignUnassigned                        html  
    builtInClusteringFunctions              html  
    clusterContrasts                        html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterContrasts.Rd:41: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterContrasts.Rd:41: file link 'MAST' in package 'MAST' does not exist and so has been treated as a topic
    clusterDendrogram                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterDendrogram.Rd:114: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterDendrogram.Rd:117: file link 'tdata' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterDendrogram.Rd:200: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    clusterExperiment-deprecated            html  
    clusterMany                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterMany.Rd:38: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterMany.Rd:134: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    clusterSingle                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterSingle.Rd:36: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterSingle.Rd:56: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    getBestFeatures                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:67: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:68: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:76: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:124: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:237: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
    getClusterIndex                         html  
    getClusterManyParams                    html  
    mainClustering                          html  
    makeConsensus                           html  
    makeDendrogram                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/makeDendrogram.Rd:54: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    mergeClusters                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/mergeClusters.Rd:156: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    numericalAsCharacter                    html  
    plotBarplot                             html  
    plotClusters                            html  
    plotClustersTable                       html  
    plotClustersWorkflow                    html  
    plotContrastHeatmap                     html  
    plotDendrogram                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotDendrogram.Rd:113: file link 'tiplabels' in package 'ape' does not exist and so has been treated as a topic
    plotFeatureBoxplot                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotFeatureBoxplot.Rd:40: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    plotFeatureScatter                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotFeatureScatter.Rd:39: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    plotHeatmap                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotHeatmap.Rd:56: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotHeatmap.Rd:127: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    plotReducedDims                         html  
    plottingFunctions                       html  
    reduceFunctions                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/reduceFunctions.Rd:94: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/reduceFunctions.Rd:178: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/reduceFunctions.Rd:289: file link 'reducedDim' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
    renameClusters                          html  
    rsecFluidigm                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/rsecFluidigm.Rd:66: file link 'fluidigm' in package 'scRNAseq' does not exist and so has been treated as a topic
    search_pairs                            html  
    seqCluster                              html  
    simData                                 html  
    subsampleClustering                     html  
    subset                                  html  
    transformData                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/transformData.Rd:40: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    updateObject                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/updateObject.Rd:57: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/updateObject.Rd:63: file link 'nodeLabels' in package 'phylobase' does not exist and so has been treated as a topic
    workflowClusters                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'clusterExperiment' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c search_pairs.cpp -o search_pairs.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subsampleLoop.cpp -o subsampleLoop.o
subsampleLoop.cpp: In function 'Rcpp::IntegerMatrix subsampleLoop(Rcpp::List, int)':
subsampleLoop.cpp:89:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     LogicalVector clusterj = j <= indexClusterEnds & j >= indexClusterStarts;
                                ^
subsampleLoop.cpp:90:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     LogicalVector clusterk = k <= indexClusterEnds & k >= indexClusterStarts;
                                ^
subsampleLoop.cpp:122:25: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if((it->second).first>0 | (it->second).second==NA_INTEGER){
                         ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.buildbin-libdir/clusterExperiment/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterExperiment' as clusterExperiment_2.3.1.zip
* DONE (clusterExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'clusterExperiment' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)
> test_check("clusterExperiment",filter = "^[A-Ca-c]")
Loading required package: clusterExperiment
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

-- 1. Failure: RSEC works wih non default assays (@test-assays.R#85)  ----------
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .makeClusterDendro(x, cluster, type = "mat", ...) : 
  all samples have clusterIds<0



-- 2. Failure: RSEC works wih non default assays (@test-assays.R#99)  ----------
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .makeClusterDendro(x, cluster, type = "mat", ...) : 
  all samples have clusterIds<0



-- 3. Failure: RSEC works independent of assay order (@test-assays.R#131)  -----
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .makeClusterDendro(x, cluster, type = "mat", ...) : 
  all samples have clusterIds<0



-- 4. Failure: RSEC works independent of assay order (@test-assays.R#138)  -----
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .makeClusterDendro(x, cluster, type = "mat", ...) : 
  all samples have clusterIds<0



-- 5. Failure: RSEC works independent of assay order (@test-assays.R#147)  -----
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .makeClusterDendro(x, cluster, type = "mat", ...) : 
  all samples have clusterIds<0



-- 6. Failure: RSEC works independent of assay order (@test-assays.R#154)  -----
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .makeClusterDendro(x, cluster, type = "mat", ...) : 
  all samples have clusterIds<0



-- 7. Failure: RSEC works independent of assay order (@test-assays.R#179)  -----
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): var.

* Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .makeClusterDendro(x, cluster, type = "mat", ...) : 
  all samples have clusterIds<0



-- 8. Failure: RSEC works independent of assay order (@test-assays.R#186)  -----
`... <- NULL` produced unexpected messages.
Expected match: Merging will be done on
Actual values:
* Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): var.

* Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .makeClusterDendro(x, cluster, type = "mat", ...) : 
  all samples have clusterIds<0



[1] "pam"
[1] "clara"
[1] "kmeans"
[1] "hierarchicalK"
[1] "spectral"
[1] "hierarchical01"
[1] "tight"
== testthat results  ===========================================================
OK: 771 SKIPPED: 1 FAILED: 8
1. Failure: RSEC works wih non default assays (@test-assays.R#85) 
2. Failure: RSEC works wih non default assays (@test-assays.R#99) 
3. Failure: RSEC works independent of assay order (@test-assays.R#131) 
4. Failure: RSEC works independent of assay order (@test-assays.R#138) 
5. Failure: RSEC works independent of assay order (@test-assays.R#147) 
6. Failure: RSEC works independent of assay order (@test-assays.R#154) 
7. Failure: RSEC works independent of assay order (@test-assays.R#179) 
8. Failure: RSEC works independent of assay order (@test-assays.R#186) 

Error: testthat unit tests failed
Execution halted

CHECK report for clusterExperiment on tokay2

Summary

Command output

Installation output

Tests output

Example timings