scater 1.6.3
Davis McCarthy
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_6 |
| Last Commit: 964effb |
| Last Changed Date: 2018-02-13 08:43:57 -0400 (Tue, 13 Feb 2018) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/scater_1.6.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=scater.buildbin-libdir --merge-multiarch scater_1.6.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL scater_1.6.3.zip && rm scater_1.6.3.tar.gz scater_1.6.3.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:125:120: required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sfIt->size() != ncells) {
^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sf_to_use.size()!=ngenes) {
^
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:128:123: required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sfIt->size() != ncells) {
^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sf_to_use.size()!=ngenes) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c calc_top_features.cpp -o calc_top_features.o
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:83:91: required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (x<=target_index && x<survivors.size()) {
^
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:86:94: required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (x<=target_index && x<survivors.size()) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c calc_variance.cpp -o calc_variance.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c downsample_matrix.cpp -o downsample_matrix.o
downsample_matrix.cpp: In instantiation of 'void downsample_matrix_internal(M, O, Rcpp::NumericVector) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; O = beachmat::lin_output<int>*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
downsample_matrix.cpp:72:62: required from here
downsample_matrix.cpp:9:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (prop.size()!=ncells) {
^
downsample_matrix.cpp: In instantiation of 'void downsample_matrix_internal(M, O, Rcpp::NumericVector) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; O = beachmat::lin_output<double>*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
downsample_matrix.cpp:77:62: required from here
downsample_matrix.cpp:9:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c margin_summary.cpp -o margin_summary.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o calc_top_features.o calc_variance.o downsample_matrix.o init.o margin_summary.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/beachmat/lib/i386 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/scater.buildbin-libdir/scater/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for 'mutate' in package 'scater'
Creating a new generic function for 'filter' in package 'scater'
** help
*** installing help indices
converting help for package 'scater'
finding HTML links ... done
SCESet html
accessors html
finding level-2 HTML links ... done
areSizeFactorsCentred html
arrange html
bootstraps html
calcAverage html
calcIsExprs html
calculateCPM html
calculateFPKM html
calculateQCMetrics html
calculateTPM html
deprecated html
downsampleCounts html
filter html
findImportantPCs html
getBMFeatureAnnos html
isOutlier html
kallisto-wrapper html
multiplot html
mutate html
newSCESet html
nexprs html
normaliseExprs html
normalize html
plotDiffusionMap html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgDEDF/R.INSTALLb982b28433c/scater/man/plotDiffusionMap.Rd:64: missing file link 'DiffusionMap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgDEDF/R.INSTALLb982b28433c/scater/man/plotDiffusionMap.Rd:66: missing file link 'DiffusionMap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgDEDF/R.INSTALLb982b28433c/scater/man/plotDiffusionMap.Rd:68: missing file link 'DiffusionMap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWgDEDF/R.INSTALLb982b28433c/scater/man/plotDiffusionMap.Rd:107: missing file link 'DiffusionMap'
plotExplanatoryVariables html
plotExpression html
plotExprsFreqVsMean html
plotExprsVsTxLength html
plotFeatureData html
plotHighestExprs html
plotMDS html
plotMetadata html
plotPCA html
plotPhenoData html
plotPlatePosition html
plotQC html
plotRLE html
plotReducedDim html
plotScater html
plotTSNE html
read10XResults html
readTxResults html
rename html
salmon-wrapper html
sc_example_cell_info html
sc_example_counts html
scater-package html
scater_gui html
summariseExprsAcrossFeatures html
toSingleCellExperiment html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'scater' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:125:120: required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sfIt->size() != ncells) {
^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sf_to_use.size()!=ngenes) {
^
calc_exprs.cpp: In instantiation of 'Rcpp::RObject calc_exprs_internal(M, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]':
calc_exprs.cpp:128:123: required from here
calc_exprs.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sfIt->size() != ncells) {
^
calc_exprs.cpp:30:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (sf_to_use.size()!=ngenes) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c calc_top_features.cpp -o calc_top_features.o
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = int; V = Rcpp::Vector<13>; M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:83:91: required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (x<=target_index && x<survivors.size()) {
^
calc_top_features.cpp: In instantiation of 'Rcpp::RObject calc_top_features_internal(M, Rcpp::RObject, Rcpp::RObject) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]':
calc_top_features.cpp:86:94: required from here
calc_top_features.cpp:27:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ntop && (top[0] < 1 || top[ntop-1] > used_genes)) {
^
calc_top_features.cpp:61:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (x<=target_index && x<survivors.size()) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c calc_variance.cpp -o calc_variance.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c downsample_matrix.cpp -o downsample_matrix.o
downsample_matrix.cpp: In instantiation of 'void downsample_matrix_internal(M, O, Rcpp::NumericVector) [with M = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; O = beachmat::lin_output<int>*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
downsample_matrix.cpp:72:62: required from here
downsample_matrix.cpp:9:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (prop.size()!=ncells) {
^
downsample_matrix.cpp: In instantiation of 'void downsample_matrix_internal(M, O, Rcpp::NumericVector) [with M = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; O = beachmat::lin_output<double>*; Rcpp::NumericVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]':
downsample_matrix.cpp:77:62: required from here
downsample_matrix.cpp:9:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/beachmat/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c margin_summary.cpp -o margin_summary.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o calc_top_features.o calc_variance.o downsample_matrix.o init.o margin_summary.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/beachmat/lib/x64 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.6.3.zip
* DONE (scater)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'scater' successfully unpacked and MD5 sums checked
In R CMD INSTALL