Aaron Lun
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DropletUtils |
| Branch: RELEASE_3_8 |
| Last Commit: 1424ff5 |
| Last Changed Date: 2019-01-04 13:09:29 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:28:43 -0400 (Sat, 13 Apr 2019).
| Package 436/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DropletUtils 1.2.2 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: DropletUtils |
| Version: 1.2.2 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DropletUtils.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DropletUtils_1.2.2.tar.gz |
| StartedAt: 2019-04-13 01:54:48 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:03:28 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 519.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DropletUtils.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DropletUtils.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DropletUtils_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DropletUtils.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DropletUtils/DESCRIPTION' ... OK
* this is package 'DropletUtils' version '1.2.2'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'DropletUtils' can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.0Mb
sub-directories of 1Mb or more:
libs 10.8Mb
* 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 ... 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 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-3.8-bioc/R/library/DropletUtils/libs/i386/DropletUtils.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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' ... WARNING
Found the following significant warnings:
Warning: 'read10xMatrix' is deprecated.
Warning: 'read10xMatrix' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
emptyDrops 6.52 0.22 6.74
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
Warning: 'read10xMatrix' is deprecated.
Warning: 'read10xMatrix' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/DropletUtils.Rcheck/00check.log'
for details.
DropletUtils.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DropletUtils_1.2.2.tar.gz && rm -rf DropletUtils.buildbin-libdir && mkdir DropletUtils.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DropletUtils.buildbin-libdir DropletUtils_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DropletUtils_1.2.2.zip && rm DropletUtils_1.2.2.tar.gz DropletUtils_1.2.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 47506 100 47506 0 0 1220k 0 --:--:-- --:--:-- --:--:-- 1364k
install for i386
* installing *source* package 'DropletUtils' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_multinom.cpp -o compute_multinom.o
compute_multinom.cpp: In instantiation of 'SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_multinom.cpp:45:85: required from here
compute_multinom.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ambient.size()!=NR) {
^
compute_multinom.cpp: In instantiation of 'SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_multinom.cpp:48:85: required from here
compute_multinom.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from DropletUtils.h:5,
from compute_multinom.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:77:56: required from 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]'
compute_multinom.cpp:22:61: required from 'SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]'
compute_multinom.cpp:45:85: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:77:56: required from 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]'
compute_multinom.cpp:22:61: required from 'SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]'
compute_multinom.cpp:48:85: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c downsample_counts.cpp -o downsample_counts.o
downsample_counts.cpp: In function 'bool check_downsampling_mode(size_t, Rcpp::NumericVector, Rcpp::LogicalVector)':
downsample_counts.cpp:78:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (prop.size()!=ncells) {
^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from DropletUtils.h:5,
from downsample_counts.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, double*>; typename V::iterator = double*; size_t = unsigned int; typename V::iterator = double*]':
downsample_counts.cpp:205:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<unsigned int, int*, int*>; typename V::iterator = int*; size_t = unsigned int; typename V::iterator = int*]':
downsample_counts.cpp:205:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function 'SEXPREC* encode_sequences(SEXP)':
encode_sequences.cpp:8:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=0; i<output.size(); ++i) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c find_swapped.cpp -o find_swapped.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c get_cell_barcodes.cpp -o get_cell_barcodes.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function 'SEXPREC* group_cells(SEXP, SEXP)':
group_cells.cpp:34:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=1; i<output.size(); ++i) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c load_tenx_to_hdf5.cpp -o load_tenx_to_hdf5.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c montecarlo_pval.cpp -o montecarlo_pval.o
montecarlo_pval.cpp: In function 'SEXPREC* montecarlo_pval(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
montecarlo_pval.cpp:76:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (chosen >= ngenes) {
^
montecarlo_pval.cpp:92:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (higher<curlen) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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 DropletUtils.dll tmp.def compute_multinom.o downsample_counts.o encode_sequences.o find_swapped.o get_cell_barcodes.o group_cells.o init.o load_tenx_to_hdf5.o montecarlo_pval.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/beachmat/lib/i386 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/DropletUtils.buildbin-libdir/DropletUtils/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DropletUtils'
finding HTML links ... done
barcodeRanks html
defaultDrops html
downsampleMatrix html
downsampleReads html
emptyDrops html
finding level-2 HTML links ... done
encodeSequences html
get10xMolInfoStats html
makeCountMatrix html
read10xCounts html
read10xMatrix html
read10xMolInfo html
swappedDrops html
write10xCounts html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'DropletUtils' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c compute_multinom.cpp -o compute_multinom.o
compute_multinom.cpp: In instantiation of 'SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]':
compute_multinom.cpp:45:85: required from here
compute_multinom.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ambient.size()!=NR) {
^
compute_multinom.cpp: In instantiation of 'SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]':
compute_multinom.cpp:48:85: required from here
compute_multinom.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from DropletUtils.h:5,
from compute_multinom.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:77:56: required from 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]'
compute_multinom.cpp:22:61: required from 'SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<13>; MAT = beachmat::lin_matrix<int, Rcpp::Vector<13> >*; SEXP = SEXPREC*]'
compute_multinom.cpp:45:85: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:77:56: required from 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]'
compute_multinom.cpp:22:61: required from 'SEXPREC* compute_multinom_internal(MAT, SEXP, SEXP) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; MAT = beachmat::lin_matrix<double, Rcpp::Vector<14, Rcpp::PreserveStorage> >*; SEXP = SEXPREC*]'
compute_multinom.cpp:48:85: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c downsample_counts.cpp -o downsample_counts.o
downsample_counts.cpp: In function 'bool check_downsampling_mode(size_t, Rcpp::NumericVector, Rcpp::LogicalVector)':
downsample_counts.cpp:78:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (prop.size()!=ncells) {
^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_matrix.h:238:0,
from C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/integer_matrix.h:4,
from DropletUtils.h:5,
from downsample_counts.cpp:1:
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = double; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, double*>; typename V::iterator = double*; size_t = long long unsigned int; typename V::iterator = double*]':
downsample_counts.cpp:205:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (indices.size()!=this->get_nrow()) {
^
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h: In instantiation of 'beachmat::const_col_indexed_info<V> beachmat::lin_matrix<T, V>::get_const_col_indexed(size_t, typename V::iterator, size_t, size_t) [with T = int; V = Rcpp::Vector<13>; beachmat::const_col_indexed_info<V> = std::tuple<long long unsigned int, int*, int*>; typename V::iterator = int*; size_t = long long unsigned int; typename V::iterator = int*]':
downsample_counts.cpp:205:1: required from here
C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include/beachmat/LIN_methods_read.h:82:23: 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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c encode_sequences.cpp -o encode_sequences.o
encode_sequences.cpp: In function 'SEXPREC* encode_sequences(SEXP)':
encode_sequences.cpp:8:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=0; i<output.size(); ++i) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c find_swapped.cpp -o find_swapped.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c get_cell_barcodes.cpp -o get_cell_barcodes.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c group_cells.cpp -o group_cells.o
group_cells.cpp: In function 'SEXPREC* group_cells(SEXP, SEXP)':
group_cells.cpp:34:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i=1; i<output.size(); ++i) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c load_tenx_to_hdf5.cpp -o load_tenx_to_hdf5.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c montecarlo_pval.cpp -o montecarlo_pval.o
montecarlo_pval.cpp: In function 'SEXPREC* montecarlo_pval(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
montecarlo_pval.cpp:76:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (chosen >= ngenes) {
^
montecarlo_pval.cpp:92:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (higher<curlen) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/beachmat/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/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 DropletUtils.dll tmp.def compute_multinom.o downsample_counts.o encode_sequences.o find_swapped.o get_cell_barcodes.o group_cells.o init.o load_tenx_to_hdf5.o montecarlo_pval.o utils.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/beachmat/lib/x64 -lbeachmat -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/DropletUtils.buildbin-libdir/DropletUtils/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DropletUtils' as DropletUtils_1.2.2.zip
* DONE (DropletUtils)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DropletUtils' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
DropletUtils.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(DropletUtils)
Loading required package: BiocParallel
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, 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("DropletUtils")
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
In addition: Warning message:
In data.class(target) :
closing unused connection 3 (C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpArtVTI\filee1c4328132d/matrix.mtx)
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
== testthat results ===========================================================
OK: 775 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
98.20 1.60 101.12
|
DropletUtils.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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)
> library(DropletUtils)
Loading required package: BiocParallel
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, 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("DropletUtils")
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
In addition: Warning message:
closing unused connection 3 (C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpGwmpqG\file116c6852638f/matrix.mtx)
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, :
Not enough memory to read data! Try to read a subset of data by specifying the index or count parameter.
== testthat results ===========================================================
OK: 775 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
98.56 1.09 101.00
|
|
DropletUtils.Rcheck/examples_i386/DropletUtils-Ex.timings
|
DropletUtils.Rcheck/examples_x64/DropletUtils-Ex.timings
|