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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:43:42 -0400 (Wed, 17 Oct 2018).
| Package 336/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cydar 1.4.0 Aaron Lun
| 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 | |
| Package: cydar |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cydar.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cydar_1.4.0.tar.gz |
| StartedAt: 2018-10-17 01:25:51 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:34:33 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 522.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cydar.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cydar.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cydar_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/cydar.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'cydar/DESCRIPTION' ... OK * this is package 'cydar' version '1.4.0' * 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 'cydar' can be installed ... WARNING Found the following significant warnings: 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 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 See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/cydar.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 ... NOTE Unexported objects imported by ':::' calls: 'S4Vectors:::selectSome' 'SummarizedExperiment:::.SummarizedExperiment.charbound' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * 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 line endings in C/C++/Fortran sources/headers ... 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-3.7-bioc/R/library/cydar/libs/i386/cydar.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 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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: 1 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/cydar.Rcheck/00check.log' for details.
cydar.Rcheck/00install.out
##############################################################################
##############################################################################
###
### 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
|
cydar.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(cydar)
Loading required package: BiocParallel
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, lengths, 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
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
> test_check("cydar")
Estimating landmarks for channel X1 ...
Registering curves for parameter X1 ...
Estimating landmarks for channel X2 ...
Registering curves for parameter X2 ...
== testthat results ===========================================================
OK: 8229 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
114.17 1.40 116.25
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cydar.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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)
> library(cydar)
Loading required package: BiocParallel
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, lengths, 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
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
> test_check("cydar")
Estimating landmarks for channel X1 ...
Registering curves for parameter X1 ...
Estimating landmarks for channel X2 ...
Registering curves for parameter X2 ...
== testthat results ===========================================================
OK: 8229 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
135.78 0.96 136.75
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cydar.Rcheck/examples_i386/cydar-Ex.timings
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cydar.Rcheck/examples_x64/cydar-Ex.timings
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