cydar 1.4.0
Aaron Lun
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/cydar |
| Branch: RELEASE_3_7 |
| Last Commit: bdb0b16 |
| Last Changed Date: 2018-04-30 10:35:45 -0400 (Mon, 30 Apr 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/cydar_1.4.0.tar.gz && rm -rf cydar.buildbin-libdir && mkdir cydar.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cydar.buildbin-libdir cydar_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL cydar_1.4.0.zip && rm cydar_1.4.0.tar.gz cydar_1.4.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 67039 100 67039 0 0 1024k 0 --:--:-- --:--:-- --:--:-- 1109k
install for i386
* installing *source* package 'cydar' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_density.cpp -o compute_density.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_hyperstats.cpp -o compute_hyperstats.o
compute_hyperstats.cpp: In function 'SEXPREC* compute_hyperstats(SEXP, SEXP, SEXP, SEXP)':
compute_hyperstats.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (_sample_id.size()!=ncells) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_median_int.cpp -o compute_median_int.o
compute_median_int.cpp: In function 'SEXPREC* compute_median_int(SEXP, SEXP, SEXP, SEXP)':
compute_median_int.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (_sample_id.size()!=ncells) {
^
compute_median_int.cpp:46:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex < 0 || curdex >= ncells) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c count_cells.cpp -o count_cells.o
In file included from count_cells.cpp:2:0:
packer.h: In instantiation of 'void pack_index_vector(std::deque<int>&, Iter, Iter) [with Iter = std::_Deque_iterator<unsigned int, unsigned int&, unsigned int*>]':
count_cells.cpp:38:73: required from here
packer.h:28:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ((*previous)+1!=sorted_ids.back()) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c drop_redundant.cpp -o drop_redundant.o
drop_redundant.cpp: In function 'SEXPREC* drop_redundant(SEXP, SEXP, SEXP, SEXP, SEXP)':
drop_redundant.cpp:15:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ordering.size()!=nhyper) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c find_knn.cpp -o find_knn.o
find_knn.cpp: In function 'SEXPREC* find_knn(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
find_knn.cpp:20:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (_query.nrow()!=nmarkers) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c get_nndist.cpp -o get_nndist.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c objects.cpp -o objects.o
objects.cpp: In member function 'void naive_holder::find_neighbors(size_t, double, bool)':
objects.cpp:31:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (cell >= exprs.ncol()) { throw std::runtime_error("cell index out of range"); }
^
objects.cpp: In member function 'void naive_holder::find_nearest_neighbors(size_t, size_t, bool)':
objects.cpp:43:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (cell >= exprs.ncol()) { throw std::runtime_error("cell index out of range"); }
^
objects.cpp: In member function 'double naive_holder::compute_marker_sqdist(const double*, const double*) const':
objects.cpp:66:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t m=0; m<exprs.nrow(); ++m) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pack_indices.cpp -o pack_indices.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c recount.cpp -o recount.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cydar.dll tmp.def compute_density.o compute_hyperstats.o compute_median_int.o count_cells.o drop_redundant.o find_knn.o get_nndist.o init.o objects.o pack_indices.o recount.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/cydar.buildbin-libdir/cydar/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cydar'
finding HTML links ... done
countCells html
cyData-class html
cyData-getset html
cyData-subset html
diffIntDistr html
dnaGate html
finding level-2 HTML links ... done
expandRadius html
findFirstSphere html
intensityRanges html
interpretSpheres html
labelSpheres html
medIntensities html
multiIntHist html
neighborDistances html
normalizeBatch html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyEOROh/R.INSTALL1e0433494833/cydar/man/normalizeBatch.Rd:95: file link 'normalization' in package 'flowCore' does not exist and so has been treated as a topic
outlierGate html
packIndices html
pickBestMarkers html
plotCells html
poolCells html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyEOROh/R.INSTALL1e0433494833/cydar/man/poolCells.Rd:26: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyEOROh/R.INSTALL1e0433494833/cydar/man/poolCells.Rd:36: file link 'flowFrame' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpyEOROh/R.INSTALL1e0433494833/cydar/man/poolCells.Rd:38: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
prepareCellData html
recountCells html
spatialFDR html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'cydar' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_density.cpp -o compute_density.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_hyperstats.cpp -o compute_hyperstats.o
compute_hyperstats.cpp: In function 'SEXPREC* compute_hyperstats(SEXP, SEXP, SEXP, SEXP)':
compute_hyperstats.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (_sample_id.size()!=ncells) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_median_int.cpp -o compute_median_int.o
compute_median_int.cpp: In function 'SEXPREC* compute_median_int(SEXP, SEXP, SEXP, SEXP)':
compute_median_int.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (_sample_id.size()!=ncells) {
^
compute_median_int.cpp:46:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curdex < 0 || curdex >= ncells) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c count_cells.cpp -o count_cells.o
In file included from count_cells.cpp:2:0:
packer.h: In instantiation of 'void pack_index_vector(std::deque<int>&, Iter, Iter) [with Iter = std::_Deque_iterator<long long unsigned int, long long unsigned int&, long long unsigned int*>]':
count_cells.cpp:38:73: required from here
packer.h:28:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ((*previous)+1!=sorted_ids.back()) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c drop_redundant.cpp -o drop_redundant.o
drop_redundant.cpp: In function 'SEXPREC* drop_redundant(SEXP, SEXP, SEXP, SEXP, SEXP)':
drop_redundant.cpp:15:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ordering.size()!=nhyper) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c find_knn.cpp -o find_knn.o
find_knn.cpp: In function 'SEXPREC* find_knn(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
find_knn.cpp:20:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (_query.nrow()!=nmarkers) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c get_nndist.cpp -o get_nndist.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c objects.cpp -o objects.o
objects.cpp: In member function 'void naive_holder::find_neighbors(size_t, double, bool)':
objects.cpp:31:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (cell >= exprs.ncol()) { throw std::runtime_error("cell index out of range"); }
^
objects.cpp: In member function 'void naive_holder::find_nearest_neighbors(size_t, size_t, bool)':
objects.cpp:43:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (cell >= exprs.ncol()) { throw std::runtime_error("cell index out of range"); }
^
objects.cpp: In member function 'double naive_holder::compute_marker_sqdist(const double*, const double*) const':
objects.cpp:66:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t m=0; m<exprs.nrow(); ++m) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pack_indices.cpp -o pack_indices.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c recount.cpp -o recount.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cydar.dll tmp.def compute_density.o compute_hyperstats.o compute_median_int.o count_cells.o drop_redundant.o find_knn.o get_nndist.o init.o objects.o pack_indices.o recount.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/cydar.buildbin-libdir/cydar/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cydar' as cydar_1.4.0.zip
* DONE (cydar)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'cydar' successfully unpacked and MD5 sums checked
In R CMD INSTALL